Baylands pecies and SCommunity Profiles

Life Histories and Environmental Requirements of Key , Fish and Wildlife Prepared by the Area Ecosystem Goals Project Baylands Ecosystem Species and Community Profiles Life Histories and Environmental Requirements of Key Plants, Fish and Wildlife

Prepared by the San Francisco Bay Area Wetlands Ecosystem Goals Project To order additional copies of this report ($25.00 each), please contact: San Francisco Project c/o S.F. Bay Regional Water Quality Control Board 1515 Clay Street, Suite 1400 Oakland, CA 94612 (510) 622-2465

Please cite this report as: Goals Project. 2000. Baylands Ecosystem Species and Community Profiles: Life histories and environmental requirements of key plants, fish and wildlife. Prepared by the San Francisco Bay Area Wetlands Ecosystem Goals Project. P.R. Olofson, editor. San Francisco Bay Regional Water Quality Control Board, Oakland, Calif.

Also available from the Goals Project: Baylands Ecosystem Goals: A report of habitat recommendations. March 1999. Reprint with minor corrections, June 2000.

Printing of the Species Profiles was made possible, in part, by a grant from the CALFED Bay-Delta Program through the U.S. Bureau of Reclamation to Friends of the Estuary: CALFED Project #99-B10 U.S. Department of the Interior Bureau of Reclamation Grant #00FC200183 n behalf of the Resource Managers Group and all of the other Goals Project O participants, we offer our sincere thanks and appreciation to the authors of these profiles. The authors willingly volunteered their time to construct a good part of the biological foundation of the Habitat Goals. Little did they know when they started that their work eventually would comprise this fine report. We also want to recognize the role of the San Francisco Bay Regional Water Quality Control Board in the preparation of this document. Without the support of the Regional Board’s top managers—Loretta Barsamian, Larry Kolb, and Bruce Wolf—the profiles would likely still be a pile of interesting papers on the flora and fauna of the San Francisco Bay area, rather than a unified compendium. By en- couraging their staff to compile and polish the profiles, they helped provide the public with a scientific document that will lead to the improvement of habitat con- ditions and water quality throughout the Bay and along its tributaries. Above all, we would like to extend a special thanks to Peggy Olofson of the Regional Board. Peggy not only helped to manage the Goals Project through its four-year life, but she spent the better part of the past year preparing this docu- ment for press. Her work far exceeded merely editing the draft profiles. Rather, she collaborated with many of the report authors in acquiring data and expanding sections of text, cajoled authors into clarifying certain points, obtained photographs, hunted down references, created the report design, and laid out each page. And she did all this while attending to her regular duties as a Water Resources Engineer. We all owe Peggy our gratitude for a job well done.

Michael Monroe Carl Wilcox

Resource Managers Group Co-Chairs San Francisco Bay Area Wetlands Ecosystem Goals Project

Credits

Editor Peggy R. Olofson — San Francisco Bay Regional Water Quality Control Board

Authors

David G. Ainley Leora Feeney Robert E. Jones Thomas P. Ryan Joy D. Albertson Steve Foreman Kurt F. Kline Michael K. Saiki Janice M. Alexander Stephen L. Granholm Brita C. Larsson Howard S. Shellhammer Peter R. Baye Brenda J. Grewell Robert A. Leidy Ted R. Sommer Dennis R Becker Janet T. Hanson William Z. Lidicker, Jr. Lynne E. Stenzel William G. Bousman Laura A. Hanson Kevin MacKay John Y. Takekawa Andrée M Breaux Elaine K. Harding Wesley A. Maffei Robert N. Tasto Michael L Casazza Bruce Herbold Lt. Dante B. Maragni Scott Terrill Steven C. Chappell Catherine M. Hickey Carolyn M. Marn Lynne A. Trulio Howard L. Cogswell Kathryn A. Hieb Michael F. McGowan David C. VanBaren Ron Duke Glen Holstein A. Keith Miles Nils Warnock Jules G. Evens Mark R. Jennings Michael R. Miller Sarah E. Warnock Phyllis M. Faber Michael L. Johnson Gary W. Page Frank G. Wernette

Report Production

Report Design &- Text & Copy Editing: Cristina Grosso (lead) Layout: Peggy Olofson Elisa Gill Terra Hendrich Cover Design: Nina Lisowski Harini Madhavan Computer & GIS- Michael Monroe Support: Jeff Kapellas Dewey Schwarzenberg Jill Sunahara

Credits i Additional Assistance In addition to the authors and production staff, we also thank the many people who provided support and assistance to make this publication possible. We thank Marcia Brockbank and her staff at the San Francisco Estuary Project for ongoing help with funding and coordination, and the staff at CALFED and the Bureau of Reclamation for fund- ing assistance. For generous and timely support for preliminary editing and document design, we thank the Coastal Conservancy, and particularly Nadine Hitchcock. Special thanks to Kathy Hieb, who provided extensive organizational and editing assistance with the fish profiles, in addition to authoring several of them herself. Several other authors, includ- ing Peter Baye, Bill Bousman, Howard Cogswell, Jules Evens, and Glen Holstein worked patiently with the editor over many months to provide additional tables and figures for the report. For their guidance in publication planning and preparation, we thank Michelle Yang, Mark Rodgers, and the rest of the staff at Alonzo Environmental. Also, we thank Debbi Nichols for helping to keep things together when it was needed most. Photography and Artwork We would especially like to thank the photographers and artists who so graciously donated the use of their images for this publication:

Peter Baye Dr. J.L. King Berkeley Digital Library Peter LaTourrette www.birdphotography.com Nancy Black, Monterey Bay Whale Watch Denise Loving [email protected] www.gowhales.com Wesley Maffei [email protected] Ted Brown, California Acadamy of Sciences Peter Moyle, from Inland Fishes of California, Mia Bruksman copyright 1976. Permission by the Re- California Dept. of Fish and Game (CDFG) gents of the University of California Les Chibana [email protected] Ruth Pratt Citizens’ Committee to Complete the Refuge T. Douglas Rodda [email protected] Jack Kelly Clark, Statewide IPM Project. Per- M. Roper, Aquatic Research Organisms, mission by the Regents of the University Hampton, NH (1991) of California Tom Rountree Howard L. Cogswell Brad Shaffer Josh Collins Ted Sommer Don DesJardin Rick Stallcup www.camacdonald.com/birding/DesJardin Dr. Daniel Sudia [email protected] Joe DiDonato, bioQuest Wildlife Photogra- U.S. Fish and Wildlife Service (USFWS) phy and Consulting (510)769-9209 U.S. Geological Survey, National Biological Dr. Richard B. Forbes Service (USGS/NBS) Dr. Allan Francis [email protected] Staffan Vilcans Rick A. Fridell [email protected] Jens V. Vindum, California Acadamy of Sciences S.H. Hinshaw Bob Walker Dan Holland Peter S. Weber www.wildbirdphotos.com Jimmy Hu Zoological Society of Milwaukee County, www.silcom.com/~njhua/otter/otter.html Wisconsin www.zoosociety.org Marshall Iliff [email protected]

ii Baylands Ecosystem Species and Communities Contents

Credits ...... i

Contents ...... iii

List of Tables ...... ix

List of Figures ...... xi

1. Communities a. Plants of Shallow and Subtidal Habitat and Tidal Flats (with an emphasis on eelgrass) by Laura A. Hanson...... 1 b. Tidal Marsh Plants of the San Francisco Estuary by Peter R. Baye, Phyllis M. Faber, and Brenda Grewell ...... 9 c. Plants and Environments of Diked Baylands by Peter R. Baye...... 33 d. Plants of San Francisco Bay Salt Ponds by Peter R. Baye...... 43 e. Plant Communities Ecotonal to the Baylands by Glen Holstein ...... 49

2. Estuarine Fish and Associated Invertebrates a. Opossum Shrimp (Neomysis mercedis) by Bruce Herbold ...... 69 b. Dungeness Crab (Cancer magister) by Robert N. Tasto ...... 71 c. Rock Crabs (Cancer antennarius and Cancer productus) by Robert N. Tasto ...... 76 d. Bat Ray (Myliobatus californica) by Kurt F. Kline ...... 79 e. Leopard Shark (Triakis semifasciata) by Michael F. McGowan...... 81 f. Pacific Herring (Clupea pallasi) by Robert N. Tasto ...... 81 g. Northern Anchovy (Engraulis mordax) by Michael F. McGowan...... 85 h. Sacramento Splittail (Pogonichthys macrolepidotus) by Ted R. Sommer ...... 87

Contents iii i. Chinook Salmon (Oncorhynchus tshawytscha) by Lt. Dante B. Maragni ...... 91 j. Steelhead (Oncorhynchus mykiss irideus) by Robert A. Leidy ...... 101 k. (Hypomesus transpacificus) by Ted R. Sommer and Bruce Herbold ...... 104 l. Longfin Smelt (Spirinchus thaleichthys) by Frank G. Wernette ...... 109 m. Jacksmelt (Atherinopsis californiensis) by Michael K. Saiki ...... 113 n. Topsmelt (Atherinops affinis) by Michael K. Saiki ...... 115 o. Threespine Stickleback (Gasterosteus aculeatus) by Robert A. Leidy ...... 118 p. Brown Rockfish (Sebastes auriculatus) by Kurt F. Kline ...... 121 q. Pacific Staghorn Sculpin (Leptocottus armatus armatus) by Robert N. Tasto ...... 123 r. Prickly Sculpin (Cottus asper) by Bruce Herbold ...... 126 s. Striped Bass (Morone saxatilis) by Ted R. Sommer ...... 129 t. White Croaker (Genyonemus lineatus) by Kurt F. Kline ...... 130 u. Shiner Perch (Cymatogaster aggregata) by Michael F. McGowan...... 132 v. Tule Perch (Hysterocarpus traskii) by Robert A. Leidy ...... 134 w. Arrow Goby (Clevelandia ios) by Kathryn A. Hieb ...... 136 x. Bay Goby (Lepidogobius lepidus) by Kathryn A. Hieb ...... 139 y. Longjaw Mudsucker (Gillichthys mirabilis) by Kathryn A. Hieb ...... 142 z. California Halibut (Paralichthys californicus) by Michael K. Saiki ...... 144 aa. Starry Flounder (Platichthys stellatus) by Kurt F. Kline ...... 148 3. Invertebrates a. Franciscan Brine Shrimp (Artemia franciscana Kellogg) by Brita C. Larsson ...... 151 b. California Vernal Pool Tadpole Shrimp (Lepidurus packardi Simon) by Brita C. Larsson ...... 153 c. Reticulate Water Boatman (Trichocorixa reticulata Guerin) by Wesley A. Maffei ...... 154 d. Tiger (Cincindela senilis senilis, C. oregona, and C. haemorrhagica) by Wesley A. Maffei ...... 156 e. Western Tanarthrus (Tanarthrus occidentalis Chandler) by Wesley A. Maffei ...... 161

iv Baylands Ecosystem Species and Community Profiles f. Inchworm Moth (Perizoma custodiata) by Wesley A. Maffei ...... 163 g. Pygmy Blue Butterfly (Brephidium exilis Boisduval) by Wesley A. Maffei ...... 165 h. Summer Salt Marsh Mosquito (Aedes dorsalis (Meigen)) by Wesley A. Maffei ...... 167 i. Winter Salt Marsh Mosquito (Aedes squamiger (Coquillett)) by Wesley A. Maffei ...... 169 j. Washino’s Mosquito (Aedes washinoi Lansaro and Eldridge) by Wesley A. Maffei ...... 172 k. Western Encephalitis Mosquito (Culex tarsalis Coquillett) by Wesley A. Maffei ...... 173 l. Winter Marsh Mosquito (Culiseta inornata (Williston)) by Wesley A. Maffei ...... 177 m. Brine Flies (Diptera: Ephydridae) by Wesley A. Maffei ...... 179 n. Jamieson’s Compsocryptus Wasp (Compsocryptus jamiesoni Nolfo) by Wesley A. Maffei ...... 183 o. A Note on Invertebrate Populations of the San Francisco Estuary by Wesley A. Maffei ...... 184

4. Amphibians and Reptiles a. California Tiger Salamander (Ambystoma californiense) by Mark R. Jennings ...... 193 b. California Toad (Bufo boreas halophilus) by Mark R. Jennings ...... 196 c. Pacific Treefrog (Hyla regilla) by Mark R. Jennings ...... 198 d. California Red-Legged Frog (Rana aurora draytonii) by Mark R. Jennings ...... 201 e. Western Pond Turtle (Clemmys marmorata) by Mark R. Jennings ...... 204 f. California Alligator Lizard (Elgaria multicarinata multicarinata) by Mark R. Jennings ...... 208 g. Central Coast Garter Snake (Thamnophis atratus atratus) by Kevin MacKay and Mark R. Jennings ...... 210 h. Coast Garter Snake (Thamnophis elegans terrestris) by Kevin MacKay and Mark R. Jennings ...... 212 i. San Francisco Garter Snake (Thamnophis sirtalis tetrataenia) by Mark R. Jennings ...... 214

5. Mammals a. (Reithrodontomys raviventris) by Howard S. Shellhammer ...... 219 b. California Vole (Microtus californicus) by William Z. Lidicker, Jr...... 229 c. Salt Marsh Wandering Shrew (Sorex vagrans haliocoetes) by Howard S. Shellhammer ...... 231

Contents v d. Suisun Shrew (Sorex ornatus sinuosis) by Kevin MacKay ...... 233 e. Ornate Shrew (Sorex ornatus californicus) by Elaine K. Harding ...... 236 f. North American River Otter (Lutra canadensis) by Michael L. Johnson ...... 238 g. Southern Sea Otter (Enhydra lutris nereis) by David G. Ainley and Robert E. Jones ...... 241 h. Harbor Seal (Phoca vitulina richardsi) by William Z. Lidicker, Jr. and David G. Ainley ...... 243 i. California Sea Lion (Zalophus californianus) by David G. Ainley and Robert E. Jones ...... 246 j. Non-Native Predators: Norway Rat and Roof Rat (Rattus norvegicus and Rattus rattus) by Andrée M. Breaux ...... 249 k. Non-Native Predator: Red Fox (Vulpes vulpes regalis) by Elaine K. Harding ...... 251 6. Waterfowl and Shorebirds a. Tule Greater White-Fronted Goose (Anser albifrons gambelli) by Dennis R. Becker ...... 253 b. Mallard (Anas platyrhynchos) by Steven C. Chappell and David C. Van Baren...... 259 c. Northern Pintail (Anas acuta) by Michael L. Casazza and Michael R. Miller ...... 263 d. Canvasback (Aythya valisineria) by John Y. Takekawa and Carolyn M. Marn ...... 268 e. Surf Scoter (Melanitta perspicillata) by A. Keith Miles...... 273 f. Ruddy Duck (Oxyura jamaicensis) by A. Keith Miles...... 277 g. Western Snowy Plover (Chardrius alexandrinus) by Gary W. Page, Catherine M. Hickey, and Lynne E. Stenzel...... 281 h. Marbled Godwit (Limosa fedoa) by Gary W. Page, Catherine M. Hickey, and Lynne E. Stenzel...... 284 i. Black Turnstone (Arenaria melanocephala) by Stephen L. Granholm ...... 289 j. Red Knot (Calidris canutus) by Catherine M. Hickey, Gary W. Page, and Lynne E. Stenzel...... 292 k. Western Sandpiper (Calidris mauri) by Nils Warnock and Sarah E. Warnock ...... 296 l. Long-Billed Dowitcher (Limnodromus scolopaceus) by John Y. Takekawa and Sarah E. Warnock...... 301 m. Wilson’s Phalarope (Phalaropus tricolor) by Janet T. Hanson ...... 306 n. Waterfowl and Shorebirds of the San Francisco Estuary by John Y. Takekawa, Gary W. Page, Janice M. Alexander, and Dennis R. Becker ...... 309

vi Baylands Ecosystem Species and Community Profiles 7. Bayland Birds Other than Shorebirds and Waterfowl a. Eared Grebe (Podiceps nigricollis) by Howard L. Cogswell ...... 317 b. Western and Clark’s Grebes (Aechmophorus occidentalis and A. clarkii) by David G. Ainley ...... 320 c. American White Pelican (Pelecanus erythrorhynchus) by David G. Ainley ...... 321 d. Brown Pelican (Pelecanus occidentalis) by David G. Ainley ...... 322 e. Double-Crested Cormorant (Phalacrocorax auritus) by David G. Ainley ...... 323 f. Snowy Egret (Egretta thula) by William G. Bousman ...... 325 g. Black-Crowned Night Heron (Nycticorax nycticorax) by William G. Bousman ...... 328 h. California Clapper Rail (Rallus longirostris obsoletus) by Joy D. Albertson and Jules G. Evens ...... 332 i. California Black Rail (Laterallus jamaicensis coturniculus) by Lynne A. Trulio and Jules G. Evens ...... 341 j. Common Moorhen (Gallinula chloropus) by William G. Bousman ...... 346 k. California Gull (Larus californicus) by Thomas P. Ryan ...... 349 l. Forster’s Tern (Sterna forsteri) by Thomas P. Ryan ...... 351 m. Caspian Tern (Sterna caspia) by Thomas P. Ryan ...... 355 n. California Least Tern (Sterna antillarum browni) by Leora Feeney ...... 359 o. Western Burrowing Owl (Athene (Speotyto) cunicularia hypugaea) by Lynne A. Trulio ...... 362 p. Salt Marsh Common Yellowthroat (Geothlypis trichas sinuosa) by Scott Terrill ...... 366 q. Savannah Sparrow (Passerculus sandwichensis) by Howard L. Cogswell ...... 369 r. Song Sparrow (Melospiza melodia samuelis, M. m. pusillula, and M. m. maxillaris) by Howard L. Cogswell ...... 374 s. Response of Birds to Managed Water Levels at – A Case Study by William G. Bousman ...... 386 t. The Use of Salt Ponds by Some Selected Birds Other than Shorebirds and Waterfowl by Howard L. Cogswell ...... 390

Appendix A: Author Contact Information ...... 403

Contents vii viii Baylands Ecosystem Species and Community Profiles List of Tables

1. Plant Communities

Table 1.1 Acreage of Individual Eelgrass Beds in San Francisco/ in 1989 ...... 3 Table 1.2 Comparison of Three Northern California Relative to Size of Estuary and Total Acres of Eelgrass (Zostera marina) ...... 3 Table 1.3 Historic Changes in the Distribution and Abundance of Selected Native Species Occurring in Tidal Marshes of the San Francisco Estuary ...... 23 Table 1.4 Rare Plant Species Found in the Nine Counties Adjacent to the San Francisco Bay Estuary, by Plant Community or Ecotone ...... 61

2. Estuarine Fish and Associated Invertebrates

Table 2.1 Annual Abundance of Rock Crabs Caught by Otter Trawl (crabs/tow) in the San Francisco Estuary ...... 78 Table 2.2 Annual Abundance of Rock Crabs Caught by Ring Net (crabs/tow) in the San Francisco Estuary...... 78 Table 2.3 Historical and Recent Collections of Splittail ...... 88 Table 2.4 Migration Characteristics of Sacramento-San Joaquin Chinook Salmon Runs ...... 25 Table 2.5 Estimated Number of Sacramento-San Joaquin Chinook Salmon Returning to Spawn: 1967-1991 ...... 95 Table 2.6 Bay Goby Salinity and Statistics: 1980-92 ...... 140

3. Invertebrates Table 3.1 Known Collection Sites For Trichocorixa reticulata ...... 155 Table 3.2 Known Collection Sites For Tiger Beetle Populations ...... 158 Table 3.3 Known Collection Sites For Tanarthrus occidentalis ...... 16 Table 3.4 Known Collection Sites For Perizoma custodiata ...... 164 Table 3.5 Known Collection Sites For Brephidium exilis ...... 166 Table 3.6 Known Collection Sites For Brine Flies ...... 181 Table 3.7 Known Collection Sites For Compsocryptus jamiesoni ...... 183 Table 3.8 Partial Summary of Organisms Associated with Alkali Heath ...... 186 Table 3.9 Food Web Taxa by Major Common Name Category ...... 190 Table 3.10 Known Terrestrial or Semi-aquatic Invertebrate Surveys or Studies of Selected Invertebrate Taxa ...... 191

List of Tables ix 5. Mammals

Appendix 5.1 Important Data Sets for Salt Marsh Harvest Mouse (1971-1991) ...... 222

6. Waterfowl and Shorebirds

Table 6.1 Peak Monthly Population Indices for Tule Greater White-fronted Goose on Migration, Stopover, and Wintering areas in Oregon and California for 1978-79 through 1981-82, 1988-89, and 1989-90 ...... 256 Table 6.2 Regional Recommendations to Support Western Snowy Plover ...... 283 Table 6.3 Recommendations to Support Western Snowy Plover in the South Bay ...... 283 Table 6.4 Regional Recommendations to Support Marbled Godwit ...... 288 Table 6.5 Recommendations to Support Marbled Godwit in the North Bay ...... 288

7. Other Birds of the Baylands Ecosystem Table 7.1 Estimated Breeding Pairs of Snowy Egrets on West Marin Island ...... 327 Table 7.2 Estimated Breeding Pairs of Black- Crowned Night Herons on West Marin Island ...... 331 Table 7.3 California Gull Breeding Sites in the South Bay ...... 350 Table 7.4 Forster’s Tern Breeding Sites in the North Bay ...... 352 Table 7.5 Forster’s Tern Breeding Sites in the South Bay ...... 353 Table 7.6 Caspian Tern Breeding Sites in the San Francisco Bay ...... 357 Table 7.7 Censuses in California Bayside Marsh or Adjacent Grasslands Where Savannah Sparrows Were Reported ...... 371 Table 7.8 Key Usage by Three Salt Marsh Song Sparrow Races...... 379 Table 7.9 Census Data from 1980 and 1981 for Charleston Slough...... 387 Table 7.10 Fifteen Most Common Species Censused at Charleston Slough in 1980 – sorted by 1980 rank order ...... 388 Table 7.11 Eighteen Most Common Species Censused at Charleston Slough in 1981 – sorted by 1981 rank order ...... 388

x Baylands Ecosystem Species and Community Profiles List of Figures

1. Plant Communities

Figure 1.1 Comparison of Percent Eelgrass Coverage in Three West Coast Estuaries ...... 4

2. Estuarine Fish and Associated Invertebrates

Figure 2.1 Seasonal Distribution of Juvenile Dungeness Crab Within San Francisco Bay ...... 73 Figure 2.2 Annual Distribution of Juvenile Dungeness Crab Within the San Francisco Bay – Caught by Otter Trawl, May-December ...... 74 Figure 2.3 Traditional Pacific Herring Spawning Areas in Central San Francisco Bay ...... 84 Figure 2.4 Trends in Age-0 Splittail Abundance for 1975-1995 as Indexed by Eight Independent Surveys ...... 89 Figure 2.5 Trends in Adult Splittail Abundance for 1976-1995 as Indexed by Six Independent Surveys ...... 90 Figure 2.6 Life History of Chinook Salmon ...... 92 Figure 2.5 Spatial and Temporal Distribution of Young-of-the-Year Pacific Staghorn Sculpin ...... 124 Figure 2.6 Spatial and Temporal Distribution of Adult Pacific Staghorn Sculpin...... 124 Figure 2.7 Annual Abundance Indices of White Croaker ...... 131 Figure 2.8 Annual Abundance Indices of Arrow Goby from San Francisco Bay, Beach Seine ...... 137 Figure 2.9 Annual Abundance Indices of All Sizes of Bay Goby, Otter Trawl ...... 141 Figure 2.10 Annual Abundance Indices of Starry Flounder ...... 149

3. Invertebrates Figure 3.1 Reticulate Water Boatman – Trichocorixa reticulata ...... 154 Figure 3.2 Known Trichocorixa reticulata Localities Within San Francisco Bay Tidal and Diked Marshes ...... 155 Figure 3.3 Tiger Beetle – Cicindela senilis senilis ...... 156 Figure 3.4 Known Tiger Beetle Localities Within San Francisco Bay Tidal and Diked Marshes ...... 157 Figure 3.5 Cicindela senilis senilis Larva in Burrow...... 159 Figure 3.6 Western Tanarthrus Beetle – Tanarthrus occidentalis...... 160 Figure 3.7 Known Tanarthrus occidentalis Localities Within San Francisco Bay Tidal and Diked Marshes ...... 161 Figure 3.8 Inchworm Moth – Perizoma custodiata ...... 163 Figure 3.9 Known Perizoma custodiata Localities Within San Francisco Bay Tidal and Diked Marshes ...... 163

List of Figures xi Figure 3.10 Adult Pygmy Blue Butterfly – Brephidium exilis ...... 165 Figure 3.11 Brephidium exilis Egg and larva ...... 165 Figure 3.12 Known Brephidium exilis Localities Within San Francisco Bay Tidal and Diked Marshes ...... 165 Figure 3.13 Adult Winter Salt Marsh Mosquito – Aedes squamiger ...... 169 Figure 3.14 Terminal Abdominal Segment of a Fourth Instar Larva ...... 178 Figure 3.15 Aedes Squamiger Distribution in the San Francisco Bay Area, 1950 ...... 179 Figure 3.16 Terminal Abdominal Segment of C. tarsalis larva...... 173 Figure 3.17 Wing of an Adult Cs. inornata ...... 177 Figure 3.18 Terminal Abdominal Segment of a Fourth Instar Larva ...... 177 Figure 3.19 Adult Ephydra millbrae ...... 179 Figure 3.20 Adult Lipochaeta slossonae ...... 180 Figure 3.21 Ephydra millbrae Larva and Pupa ...... 180 Figure 3.22 Known Brine Fly Localities Within San Francisco Bay Tidal and Diked Marshes ...... 180 Figure 3.23 Jamieson’s Compsocryptus Wasp – Compso+cryptus jamiesoni ...... 183 Figure 3.24 Known Compsocryptus jamiesoni Localities Within San Francisco Bay Tidal and Diked Marshes ...... 183 Figure 3.25 A Partial Web of the Organisms Associated With Alkali Heath (Frankenia salina) in San Francisco Tidal Marshes ...... 185 Figure 3.26 A Partial Web of the Organisms Associated With Common Pickleweed (Salicornia virginica) in San Francisco Bay Lower High Tidal Marshes ...... 187 Figure 3.27 A Partial Web of the Organisms Associated With Willow (Salix lasiolepis) ...... 188 Figure 3.28 Partial Web of Organisms Associated With Mid Tidal Marsh Pans ...... 188 Figure 3.29 A Partial Web of the Organisms in the Baumberg and Oliver Brothers Salt Crystallizer Ponds, Hayward, California ...... 189

4. Anphibians and Reptiles

Figure 4.1 California Tiger Salamander – Some Locations ...... 194 Figure 4.2 California Toad – Presumed Bay Area Distribution ...... 197 Figure 4.3 Pacific Treefrog – Presumed Bay Area Distribution ...... 199 Figure 4.4 California Red-Legged Frog – Some Current Locations ...... 202 Figure 4.5 Western Pond Turtle – Presumed Bay Area Distribution ...... 206 Figure 4.6 California Alligator Lizard – Presumed Bay Area Distribution ...... 209 Figure 4.7 Central Coast Garter Snake – Presumed Bay Area Distribution ...... 211 Figure 4.8 Coast Garter Snake – Presumed Bay Area Distribution ...... 213 Figure 4.9 San Francisco Garter Snake – Current Known Location ...... 215

5. Mammals Figure 5.1 Salt Marsh Harvest Mouse – Some Current Locations and Suitable Habitat...... 210 Figure 5.2 California Vole – Some Current Locations and Suitable Habitat ...... 230 Figure 5.3 Salt Marsh Wandering Shrew – Some Current Locations and Suitable Habitat ...... 232 Figure 5.4 Suisun Shrew – Some Current Locations and Suitable Habitat ...... 235 Figure 5.5 Ornate Shrew – Some Current Locations and Suitable Habitat ...... 237

xii Baylands Ecosystem Species and Community Profiles Figure 5.6 North American River Otter – Some Current Locations and Suitable Habitat ...... 239 Figure 5.7 Southern Sea Otter – Some Current Locations ...... 242 Figure 5.8 Harbor Seal – Some Current Haul-out Locations and Suitable Habitat ...... 244 Figure 5.9 California Sea Lion – Current Locations and Suitable Habitat ...... 247

6. Waterfowl and Shorebirds

Figure 6.1 Distribution of Tule Greater White-Fronted Goose in San Francisco Bay ...... 255 Figure 6.2 Maximum Counts of Mallard ...... 260 Figure 6.3 Mean Mid-Winter Survey Counts of Pintails by Decade in and San Francisco Bay ...... 264 Figure 6.4 Maximum Counts of Northern Pintail ...... 265 Figure 6.5 Radio-Marked Pintail Locations in Suisun Marsh During the Fall and Winter of 1991-92 and 1992-93 ...... 265 Figure 6.6 Common Day and Night Movement Patterns for Pintails Wintering in Suisun Marsh ...... 266 Figure 6.7 Maximum Counts of Canvasback ...... 270 Figure 6.8 Maximum Counts of Surf Scoter ...... 275 Figure 6.9 Maximum Counts of Ruddy Duck ...... 278 Figure 6.10 Relative Use of Different Baylands Areas by Marbled Godwit, Willet, Whimbrel, and Long-billed Curlew Combined...... 286 Figure 6.12 Relative Use of Various Tidal Flat and Adjacent Shoreline Areas by Rocky Substrate Species (Black Turnstone, Ruddy Turnstone, Surfbird, Spotted Sandpiper, Black Oystercatcher, and Wandering Tattler) ...... 290 Figure 6.13 Relative Use of Different Mudflat Areas by Red Knots ...... 293 Figure 6.14 Maximum Counts of Red Knot ...... 294 Figure 6.15 Maximum counts of Western Sandpiper, Least Sandpiper, and Dunlin Combined ...... 297 Figure 6.16 Maximum Counts of Western Sandpiper ...... 298 Figure 6.17 Maximum Counts of Dowitcher Species ...... 302 Figure 6.18 Maximum Counts of Long-billed Dowitcher ...... 303 Figure 6.19 Maximum Counts of Phalarope Species ...... 307 Figure 6.20 Relative Use of Salt Ponds by American Avocet, Snowy Plover, Black-necked Stilt, and Phalaropes...... 308 Figure 6.21 Relative Use (High, Medium, Low) of Different Mudflat Areas by Tidal Flat Specialists, as Indicated from the Proportion of Shorebirds Counted in Different Survey Areas ...... 313 Figure 6.22 Relative Use (High, Medium, Low) of Different South Bay Salt Pond Areas by Salt Pond Specialists as Indicated from the Proportion of Shorebirds Counted in Different Survey Areas ...... 314 Figure 6.23 Waterfowl Use of Salt Ponds in the North Bay ...... 315 Figure 6.24 Waterfowl Use of Salt Ponds in the South Bay ...... 315

7. Other Birds of the Baylands Ecosystem

Figure 7.1 Christmas Bird Count data for Snowy Egret ...... 326 Figure 7.2 Christmas Bird Count data for Black-Crowned Night Heron ...... 330

List of Figures xiii Figure 7.3 Known Distribution of the California Clapper Rail ...... 335 Figure 7.4 Distribution and Relative Abundance of Black Rails (Laterallus jamaicensis coturniculus) in the San Francisco Bay Region ...... 343 Figure 7.5 Christmas Bird Count data for Common Moorhen ...... 347 Figure 7.6 Summary of Data from Six Bird Count Studies Conducted Between Late Fall 1984 and Winter 1985 ...... 372 Figure 7.7 Numbering System for the Salt Ponds of South San Francisco Bay ...... 392

xiv Baylands Ecosystem Species and Community Profiles Introduction

he San Francisco Bay Area Wetlands Ecosystem Goals Project began in T 1995 as a cooperative effort among nine state and federal agencies and nearly 100 Bay Area scientists. The Project’s purpose was to develop a vision of the kinds, amounts, and distribution of habitats needed to sustain healthy populations of fish and wildlife in and around San Francisco Bay (Figure 1). This vision was presented to the public in the Goals Project’s final report, the Baylands Ecosystem Habitat Goals1. Developing the Habitat Goals involved several steps, many of which were carried out by teams of scientists. First, each team selected “key” spe- cies (or plant communities, in the case of the Plants Focus Team). Then they compiled available information regarding each species’ historic and modern dis- tribution, use of habitats, migration, relationship and interaction with other species, conservation and management issues, and research needs. When time and data were available, some team members compiled additional information on life history and other relevant topics. The teams then discussed the habitat needs of their species and developed initial habitat recommendations. Ulti- mately, the habitat recommendations of all the teams were integrated to form the Project’s final recommendations. Compiling the information on key species and plant communities into “profiles” was a crucial step in developing the Habitat Goals. Sharing these profiles enabled team members to better understand the habitat needs of a large proportion of the bayland’s flora and fauna. It also facilitated the development of more balanced and diverse habitat recommendations. When Project participants began sharing the profiles, they realized that much of the information had never before been compiled They also recognized that, although some of the profiles were not comprehensive, other researchers interested in the Bay and its watersheds might find them useful. The intent of this report is to provide useful information to those work- ing to restore the baylands ecosystem. However, because the profiles were com- piled to inform a specific process, this report should not be considered a com- plete treatise. Rather, it should be seen as a reference and a starting point. Contact information for the profile authors is included in Appendix A for the reader who would like additional information or clarification, or who would just like to continue the process of scientific discussion and discovery.

1 Copies of the Baylands Ecosystem Habitat Goals report may be obtained from the San Francisco Estuary Project at the address indicated in the front of this report.

Introduction xv Figure 1. The Project Area of the San Francisco Bay Area Wetlands Ecosystem Goals Project – The baylands and adjacent and associated habitats of the San Francisco Bay-Delta Estuary, down- stream of the Sacramento-San Joaquin Delta

xvi Baylands Ecosystem Species and Communities 1 Plants

Plant Communities

marsh areas. As these tidal waters recede, organic mate- Plants of Shallow Subtidal Habitat rials are transported downslope to tidal flats where they become food sources for millions of detritus-feeding in- and Tidal Flats vertebrates. (with an emphasis on eelgrass) The environmental conditions of shallow subtidal areas and tidal flats are stongly influenced by suspended Laura A. Hanson sediments. In general, the San Francisco Bay Estuary has high of suspended sediments (Hanson Introduction and Walton 1988). This suspended particulate matter There are about 200,000 acres of shallow subtidal habi- is comprised of 70 - 97% non-organic sediment made tat and tidal flats in San Francisco Bay, San Pablo Bay, up of silty clay; the remaining content is comprised of and . Of this area, approximately 171,000 living and other organic matter (Conomos and Peterson acres are subtidal habitat and about 29,000 acres are tidal 1977). Suspended sediment concentrations are influ- flats. While relatively simple in terms of species diver- enced by wind speed, substrate, particle size, wave ac- sity, the plant communities that occur in these areas are tion, current velocity, tidal action, water depth and sea- important components of the estuarine ecosystem. sonal runoff (Cyrus and Blaber 1987). Human activities Although this paper describes the plant commu- such as type of land use (Kemp et al. 1983), channel nities of shallow subtidal habitat and tidal flats, it focuses dredging (LaSalle 1988, Hanson and Walton 1988), on the eelgrass (Zostera marina) community. For more construction and use of marinas and ferry terminals, and detailed information on the other plant communities propeller wash (Walker et al. 1989, Thom and Shreffler (primarily microalgae and macroalgae) that occur in the 1995) can also affect water clarity. shallow subtidal areas and on tidal flats of the San Fran- Total suspended solids (TSS) in Suisun and San cisco Bay Estuary, please refer to Silva (1979), Nichols Pablo bays average between 50 mg/l in the summer to and Pamatmat (1988), Meiorin et al. (1991), and Her- 200 mg/l in the winter (Nichols and Pamatmat 1988). bold et al. (1992). In North Bay and Central Bay, can have a signifi- cant influence on sediment resuspension, particularly Environmental Setting during spring tides and during the ebbs preceding lower low water when the current speeds are highest. Shallow subtidal areas and tidal flats are defined by their Central Bay – characterized by cold, saline, and rela- elevation in relation to tidal height. The shallow subtidal tively clear ocean water – has the lowest TSS concen- range includes the areas between mean lower low water trations, at 10 to 60 mg/l. South San Francisco Bay (MLLW) and the approximate bathymetric contour 18 has slightly higher TSS concentrations than Central feet below MLLW. Tidal flats generally occur between Bay (O’Connor 1991). the mean level (MTL), or the lower elevation limit Salinity levels vary depending on season, weather, of Spartina (cordgrass) flats, to about 2.5 feet below amount of diverted fresh water, and location in the Bay. MLLW. Tidal flat composition can include various com- In general, salinity levels within the water column and binations of clay, silt, sand, shell fragments, and organic within tidal flats increase along a gradient from the Delta debris. Daily tidal cycles submerge and expose tidal flat to the . For example, the salinity in Suisun surfaces twice every 24.8 hours. During each tidal cycle, Bay averages about seven parts per thousand (ppt), and tidal flats are also exposed to fluctuating wave action, in Central Bay it averages about 30 ppt (Fox et al. 1991). current velocities, and nutrient supply. Where tidal During dry years, South Bay averages salinity levels up marshes still exist, incoming tides flood into the upper to 35 ppt.

Chapter 1 — Plant Communities 1 Intertidal and Subtidal Plant Communities

The shallow subtidal areas and tidal flats of the San Fran- cisco Bay Estuary support relatively few plant commu- nities. These communities include diatoms and other

Plants microalgae, macroalgae, and eelgrass. Microalgae form the basis for the estuarine food web. These algae, consisting of diatoms and blue-green algae, often form dense patches on tidal flats, creating a brown hue to the substrate surface during low tide. Mi- croalgae and settled phytoplankton represent a readily available food source for creatures, such as worms and clams, within the mudflats (Nichols and Pamatmat 1988). Shorebirds and waterfowl then consume these creatures. Macroalgae (seaweeds) are also found throughout the Estuary, particularly in the more saline areas. Few

macroalgae can make the necessary adjustments in in- Laura Hanson ternal water and mineral content to survive at low salin- Uprooted Zostera marina from intertidal zone off of ity levels. The exceptions include Gracilaria sjoestedtii, shroreline. Leaves may be 1.5–12 mm wide Enteromorpha spp. and the closely related Ulva spp. G. and up to 15 meters in length. sjoestedtii is usually found from the mid-intertidal to the shallow subtidal zone attached to rocks partially buried system functions to stabilize the soft bottom. Its leaves in coarse sand. It also grows attached to small bits of clam slow currents and dampen wave action, causing sedi- and oyster shell in muddy portions of the Bay. In such ment and organic material to accumulate. Z. marina situations, the plants and associated substrata are easily is found in intertidal areas, becoming exposed during moved by currents and wave action. Enteromorpha and the lower spring tides; it also occurs in subtidal areas Ulva form bright green patches and can occur in great at depths less than one to two meters below MLW abundance throughout the intertidal zone, often grow- (Kitting 1994). ing on any available hard substrate. Enteromorpha can be found occupying higher tidal zones where shade is Historic and Modern Distribution (of available. It is especially prevalent on boat hulls, buoys, Eelgrass) docks, and woodwork. Ulva occupies the lower tidal zones, completing its life cycle in a few weeks and vary- Information on historic distribution of Zostera marina ing its distribution over a short time period. These kinds in the San Francisco Bay Estuary is very limited. San of macroalgae often undergo seasonal cycles of abun- Francisco Bay may have supported extensive Z. marina dance, becoming common in the warmer months and meadows in the past. (Setchell 1929, Wyllie-Echev- virtually disappearing in colder months. Maximum erria and Rutten 1989). Low light availability within abundance occurs in late summer and early fall (Jones the water column has been found to limit the devel- and Stokes Associates, Inc. 1981). Many species of Ulva opment of extensive eelgrass meadows and may be the are often common in heavily polluted areas because they principal cause of eelgrass decline in San Francisco can use ammonia as a nitrogen source and are generally Bay (Alpine and Cloern 1988, Zimmerman et al. tolerant of organic and metal pollution (Dawson and 1991). Foster 1982). In the absence of eelgrass, Ulva can pro- In 1989, Wyllie-Echeverria and Rutten pub- vide a preferred habitat for several invertebrate species lished the first survey on the distribution of Zostera ma- (Sogard and Able 1991). rina in San Francisco Bay (including San Pablo Bay) and Eelgrass (Zostera marina) is currently the only mapped a total of 316 acres (Table 1.1). As Table 1.2 seagrass found in San Francisco Bay. Belying its com- and Figure 1.1 show, the per area abundance of eelgrass mon name, it is not a grass but is a that within San Francisco Bay is much less than that of has adapted to living submerged in the shallow waters Humboldt Bay or Tomales Bay, two other northern Cali- of protected bays and estuaries in temperate regions of fornia estuaries. the world (Den Hartog 1970, Phillips and Menez 1988). The 1989 Wyllie-Echeverria and Rutten survey de- Z. marina reproduces both sexually through pollination scribed the Zostera marina populations as “ patchy” and of seeds, and asexually through a rhizome meristem that some as “ stressed.” Since that time a few of these beds extends through the sediments (Setchell 1929). Where have increased in size, and new patches have been sited abundant, Z. marina’s dense, matted root and rhizome (Kitting 1993 and pers. comm.).

2 Baylands Ecosystem Species and Community Profiles Table 1.1 Acreage of Individual Eelgrass Beds in Macroalgae and eelgrass provide food, shelter, and San Francisco/San Pablo Bay in 1989 spawning grounds for many Bay fish and invertebrates.

The major subtidal spawning areas for Clupea harengus Plants Location Acres (Pacific herring), recently the most valuable fishery in California, are and the large shallow area San Pablo Bay 124 between Richmond and Oakland. In these areas, spawn- Point Orient 3 ing occurs predominantly on Gracilaria ssp. and small Naval Supply Depot 12 patches of Zostera marina (Spratt 1981). When available, Point Molate Beach 26 C. harengus preferentially uses Z. marina habitats for Toll Plaza, East 0.5 spawning (Taylor 1964, Spratt 1981). Toll Plaza, West 0.5 Zostera marina beds support a variety of organisms, Point Richmond, North 7 more than that of non-vegetated areas (van Montfrans Point Richmond, South 4 et al. 1984, Kitting 1993, Hanson 1997). Z. marina Richmond Breakwater, North 18 roots and leaves provide habitat for many plants and Richmond Breakwater, South 7 . For example, the long blade-like shoots provide Emeryville 13 shelter and serve as a nursery ground for many fish spe- Alameda 55 cies. Small plants (epiphytes) and animals (epizoites) at- Bay Farm, North 2 tach to the leaves, motile animals find cover between the Bay Farm, South 4 leaves, and burrowing animals live among the roots. Coyote Point 1 Epiphytes are an important part of the eelgrass commu- nity, contributing up to 22% of the total primary pro- Richardson Bay 13 ductivity (Jones 1968, Marshal 1970, Penhale 1977). Angel Island 3 They, in turn, provide food for resident invertebrate Belvedere Cove 5 grazers (Kitting et al. 1984). Within the rich organic Point Tiburon 1 sediment, anaerobic processes of microorganisms regen- Keil Cove 10 erate and recycle nutrients and carbon (Kenworthy et al. Paradise Cove, North 4 1982). Paradise Cove, South 3 Because Zostera marina contains noxious sulfated TOTAL ACRES 316 phenolic compounds that can inhibit bacterial degrada- Table from NMFS SW Region. Wyllie-Echeverria and Rutten 1989 Administra- tion and animal grazing, few animals consume it (Tenore tive Report SWE-89-05 1977, Harrison and Chan 1980, McMillan et al. 1980). Notable exceptions include several species of waterfowl such as Anas americana (wigeon), Anas strepera (gadwall), Associated Fauna Including Rare and Anas acuta (pintail), Branta canadensis (Canada goose), Sensitive Species and Branta nigricans (black brant) (Phillips 1984). Z. marina has been an obligate food for black brant along Tidal flats include a living system of diatoms, microal- its flyway (Einarsen 1965). Black brant populations are gae, and protozoa that are fed upon by suspension or in great decline along the Pacific Flyway, possibly due surface deposit feeding invertebrates. The bottom inver- to this species’ dependence on dwindling eelgrass re- tebrates are in turn fed upon by larger consumers such sources (Einarsen 1965). as fish, shrimp, and crabs. During low tide, these pri- Some bird species also forage on the fauna associ- mary and secondary consumers are exploited by millions ated with Zostera marina. An example is the Sterna of migratory shorebirds. The extensive intertidal mud- albifrons browni (California least tern) that was listed as flats of San Francisco Bay are considered a key migra- an endangered species in 1970. Least terns are known tory staging and refueling area for over-wintering shore- to forage on juvenile and small fishes (Magenheim and birds of the Pacific Flyway (Harvey et al. 1992). Rubissow 1993) that inhabit Z. marina beds, particu-

Table 1.2 Comparison Extent of Eelgrass of Three Northern Location (km2) (Bottom coverage, acres) Reference California Estuaries Relative to Size of Estuary and Total Humbolt Bay 62.4 3,053 Phillips 1984 Acres of Eelgrass Tomales Bay 30.0 965 Spratt 1985 (Zostera marina) San Francisco Bay 1,140.0 316 Wyllie-Echeverria 1990

Table from NMFS SW Region. Wyllie-Echeverria (1990)

Chapter 1 — Plant Communities 3 0.20 ent life history, morphology, and preferred habitat than Z. marina (Harrison and Bigley 1982). Culture experi- 0.18 ments determined that Z. japonica is not likely to dis- place existing Z. marina beds (Harrison 1982). This may 0.16 not be the case in San Francisco Bay. Z. japonica favors

Plants the intertidal zones, the areas where Z. marina has been 0.14 limited to in San Francisco Bay. Thus far, Z.japonica oc- cupies only a small fraction of its potential habitat in 0.12 North America, threatening significant changes in the ecology of the intertidal sediments as this seagrass spreads 0.10 (Harrison and Bigley 1982). Zostera asiatica is found from Tomales Bay in the 0.08 north, to Santa Monica Bay in the south. Phillips and Wyllie-Echeverria (1990) published the first record of 0.06 this species in the Eastern Pacific. It is a wide bladed Zostera that occurs sub-tidally from five meters below 0.04 MLLW to 17 meters below MLLW. Z. asiatica has not yet been identified in San Francisco Bay. This is prob- 0.02 ably due to its deeper water distribution where photo- synthetic processes could be limited in San Francisco 0 Bay. Humboldt Tomales San Francisco Factors Limiting Eelgrass Distribution – Under Bay Bay Bay suitable conditions, Zostera marina can form dense, con- Figure 1.1 Comparison of Percent Eelgrass tinuous, and extensive carpets as seen in Tomales and Coverage in Three West Coast Estuaries (Based Humboldt bays. Light, temperature, salinity, tidal range on Wyllie-Echeverria (1990)) and water motion all affect growth and productivity of Z. marina (Thayer et al. 1984, Fonseca et al. 1985, larly at a major nesting site near the Oakland Interna- Fonseca and Kenworthy 1987). The amount of time it tional Airport and the Alameda Naval Air Station is exposed to air during low tides determines the upper (Collins and Feeney 1983-6, Feeney 1988 and 1989, limits of Z. marina, and the amount of available light Harvey et al. 1992). determines the lower limits (Backman and Barilotti Invertebrates such as juvenile Cancer magister 1976; Dennison and Alberte 1982, 1985, 1986; Bulthuis (Dungeness crab) appear to grow up most successfully 1983; Bulthuis and Woelkerling 1983; Wetzel and in the nursery-like habitat that Zostera marina provides, Penhale 1983; Lewis et al. 1985; Josselyn et al. 1986; particularly in the northern reaches of the Bay. The iso- Duarte 1991). The primary factor responsible for a pod, Synidotea laticauda is periodically found in high worldwide decline in Z. marina and other submerged numbers (up to 200/m2) among Z. marina beds in Cen- aquatic vegetation is reduced light availability (Giesen tral San Francisco Bay (Hanson 1998). They are an et al. 1990, Dennison et al. 1993). important food item for economically valuable sport In San Francisco Bay, Zostera marina requires

fishes such as young striped bass, starry flounder, steel- somewhere between three and five hours of Hsat (length head trout, king salmon, white sturgeon, plus other of irradiance-saturated photosynthesis) each day (Zim- fishes in San Francisco Bay (Morris et al. 1980) merman et al. 1991). In areas with favorable light con- The transport of Zostera marina fragments acts as ditions, Z. marina plants have adequate carbon reserves a vector for animal dispersal (Highsmith 1985, Worces- to withstand at least 30 days of light limitation (Zim- ter 1994). Kitting (1993) found several fish species and merman et al. 1991); however, due to frequent and per- a variety of invertebrates usually associated with Z. ma- sistent periods of high , it is unlikely that plants rina on dead blades found at depths greater than four at the deeper edge of eelgrass meadows in San Francisco meters below MLW. Bay can accumulate large carbon reserves (Zimmerman et al. 1991). Average turbidity of the Bay and, more criti- Conservation Issues cally, brief periods of high turbidity limit Z. marina dis- tribution in deeper water and limit establishment of seed- Exotic Plants – There is some potential for two lings and vegetative propagules (Zimmerman et al.

exotic Zostera species to invade San Francisco Bay. The 1991). If daily, monthly, and seasonal Hsat requirements Asian seagrass, Zostera japonica, introduced to British are not met, long-term survival of the plants may be lim- Columbia, Washington, and Oregon has not yet been ited (Zimmerman et al. 1991). Any activities that in- reported in San Francisco Bay. Z. japonica has a differ- crease turbidity within Bay waters, whether natural or

4 Baylands Ecosystem Species and Community Profiles There are several actions that should be undertaken when designing potential restoration or enhancement

projects: Plants 1. Conduct a thorough survey to assess physical conditions of the site. Collect and evaluate environmental data and/or pilot test the planting at a particular site before commitment of a full restoration project. The success of any seagrass re- vegetation effort, including long-term plant growth, is strictly dependent upon a physical

Laura Hanson environment suitable for initial establishment Zostera marina plants, discernable as dark blotches in (Zimmerman et al. 1991). the foreground, near Belvedere Cove, Marin County. 2. Carefully evaluate light availability before proceed- ing with any major transplant effort. Water column anthropogenic, have detrimental effects on existing eel- turbidity is sufficiently high throughout much of grass populations and associated food webs. the Central Bay, limiting the euphotic zone (depth Current Restoration Success – The technology where irradiance falls to 1% of surface irradiance) for successfully establishing seagrass beds has been un- to less than 1 m (Alpine and Cloern 1988). reliable (Phillips 1974, 1980; Lewis 1987), although, in 3. Use stocks for planting from a site with conditions 1989 Zimmerman et al. (1995) successfully transplanted as similar as possible to the planting site. There Zostera marina at two locations in San Francisco Bay. should be similar or equal water depths, salinity, According to Fonseca et al. (1988), waning interest in temperature, tidal currents, wave exposure, and Z. marina restoration was due to a net loss of habitat sediment composition (Fonseca 1994). Until we through seagrass mitigation projects. Planting projects learn more about the genetic structure of this have often failed as a result of poor selection of planting species, matching of phenotypes among restoration sites or plant material and incorrect use of planting meth- and donor sites remains the best guide for stock ods. Factors that limited success include a general lack selection. of knowledge of physiological requirements and un- 4. Limit planting to areas with small tidal ranges known local environmental factors controlling Z. marina rather than high tidal ranges to provide greater growth (Lewis 1987, Merkel 1990). For example, in light availability (Koch and Beer 1996), thus 1984, an eelgrass transplant was initiated in San Fran- increasing survival success. cisco Bay. Limited transplant success was attributed to 5. Plant in areas where parameters for deeper vertical a lack of data on local eelgrass autecology coupled with distribution are available make the bed less nearby dredging operations and diminished water qual- vulnerable to adverse conditions (such as storm ity (Fredette et al. 1988). events or desiccation) due to availability of energy from the neighboring deeper shoots (Tomasko and Conclusions and Recommendations Dawes 1989). 6. Plant in late spring and summer. Periods of high Z. There has been considerable interest in protecting and marina growth and production coincide with expanding existing Zostera marina beds in San Francisco warmer and greater light availability and San Pablo bays (Fredette et al. 1988). Since the 1989 (Ewanchuk and Williams 1996). survey, sitings have indicated a marked change in the distribution and abundance of this species. Better con- References serving this species in the Estuary will require more fre- quent monitoring of individual populations. Alpine, A.E. and J.E. Cloern. 1988. Phytoplankton It also is imperative to protect the current eelgrass growth rates in a light limited environment, San beds from further decline. Because of the inherent dif- Francisco Bay. Mar. Ecol. Prog. Ser. 44: 167-173. ficulties in establishing eelgrass, plantings conducted Backman, T.W. and D.C. Barilotti. 1976. Irradiance in exchange for permitted losses (mitigation projects) reduction: effects on standing crops of the eelgrass could result in a greater loss of habitat and should not Zostera marina in a coastal lagoon. Mar. Biol. 34: be allowed. The current Zostera marina populations 33-40. may be the last remnants in San Francisco Bay and Bulthuis, D.A. 1983. Effects of in situ light reduction are extremely vulnerable to local extinction (Kitting on density and growth of the seagrass Heterozostera and Wyllie-Echeverria 1991); therefore, plantings tasmanica (Martens ex Aschers.) den Hartog in should be used to enhance current beds or to create Western Port, Victoria, Australia. J. Exp. Mar. Biol. new beds. Ecol. 67: 91-103.

Chapter 1 — Plant Communities 5 Bulthuis, D.A. and W.J. Woelkerling. 1983. Seasonal Fonseca, M.S., W.J. Kenworthy and G.W. Thayer. 1988. variations in standing crop, density and leaf growth Restoration and management of seagrass systems: of the seagrass Heterozostera tasmanica, in Western a review. Chapter 38 pp 353-368. In: D.D. Hook Port, Victoria, Australia. Aquat. Bot. 16:111-136. et al. (eds). The ecology and management of wet- Collins, L.D. and L.R. Feeney. 1983-6. California least lands, Vol. 2. Management, use and value of wet-

Plants tern nesting season at the Oakland Airport. Port lands. Portland, OR. Timber Press. of Oakland. Fox, J.P., T.R. Mongan and W.J. Miller. 1991. Long- Conomos, T.J. and D.H. Peterson. 1977. Suspended- term annual and seasonal trends in surface salinity particle transport and circulation in San Francisco of San Francisco Bay. Journal of Hydrology. 122: Bay: An Overview. In: M. Wiley (ed). Estuarine 93-117. processes. Vol. 2. Academic Press, New York. pp Fredette, T.J., M.S. Fonseca, W.J. Kenworthy and G.W. 82-97. Thayer. 1985. Seagrass transplanting: 10 years of Cyrus, D.P. and S.J.M. Blaber. 1987. The influence of Army Corps of Engineers Research. P. 121-134 In: turbidity on juvenile marine fishes in estuaries. J F.J. Webb (ed). Proc. of the 12th Ann. Conf. on Exp. Mar. Biol. Ecol. 109(1): 53-70. Wetlands Restoration and Creation. Hillsborough Dawson, E.Y. and M.S. Foster. 1982. Seashore Plants Comm. Coll., Tampa Fl. of California. Univ. of Ca Press. Berkeley, Calif. Fredette, T.J., M.S. Fonseca, W.J. Kenworthy and S. 226 pp. Wyllie-Echeverria. 1988. An investigation of eel- Den Hartog, C. 1970. Seagrasses of the World. North- grass (Zostera marina) transplant feasibility in San Holland, Amsterdam. 275 pp. Francisco Bay, CA COE Report EL-88-2. Army Dennison, W.C. and R.S. Alberte. 1982. Photosynthetic Engineer Waterways Experiment Station, Vicks- response of Zostera marina L. (eelgrass) to in situ burg, MS. 33 pp. manipulations of light intensity. Oecologia. 55: Hanson, C.H. and C.P. Walton. 1988. Potential effects 137-144. of dredging on early life stages of striped bass ______. 1985. Role of daily light period in the depth (Morone sasatilis) in the San Francisco Bay Area: distribution of Zostera marina (eelgrass). Mar. Ecol. An overview. pp 38-56 In: C.A. Simenstad (ed). Prog. Ser. 25: 51-61. Effects of dredging on anadromous Pacific Coast ______. 1986. Photoadaptation and growth of Zostera fishes. Workshop proceedings. Seattle, Wa. marina L. (eelgrass) transplants along a depth gra- Hanson, L.A. 1998. Effects of suspended sediments on dient. J. Exp. Mar. Biol. Ecol. 98: 265-282. animals in a San Francisco Bay eelgrass habitat. Duarte, C.M. 1991. Seagrass depth limits. Aquatic MS Thesis. Calif. State Univ., Hayward. 72 pp. Botany. 40:363-377. Harrison, P.G. 1982. Comparative growth of Zostera Einarsen, A.R. 1965. Black brandt: sea goose of the Pa- japonica Asher. and Graebn. and Z. marina L. un- cific Coast. Seattle, WA. Univ. of Washington Press. der simulated intertidal and subtidal conditions. Ewanchuk, P.J. and S.L. Williams. 1996. Survival and Aquatic Botany. 14: In Press. re-establishment of vegetative fragments of eelgrass Harrison, P.G. and R.E. Bigley. 1982. The recent intro- (Zostera marina). Can. J. Bot. 74:1584-1590. duction of the seagrass Zostera japonica Aschers. Feeney, L.R. 1988. California least tern breeding season and Graebn. To the Pacific Coast of North America. at the Metropolitan Oakland International Airport. Can. J. Fish. Aquatic. Sci. 19: 1642-1648. . Harrison, P.G. and A.T. Chan. 1980. Inhibition of the ______. 1989. California least tern breeding season at growth of microalgae and bacteria by extracts of eel- the Metropolitan Oakland International Airport. grass (Zostera marina) leaves. Mar. Biol. 61: 21-26. Port of Oakland. Harvey, T.E., K.J. Miller, R.L. Hotham, M.J. Rauzon, Fonseca, M.S. 1994. A guide to planting seagrass in the G.W. Page and R.A. Keck. 1992. Status and Trends Gulf of Mexico. Publ no. TAMU-SG-94-601 Sea Report on Wildlife of the San Francisco Estuary. Grant College. 25 pp. Prepard by the U.S. Fish and Wildlife Service for Fonseca, M.S., W.J. Kenworthy, G.W. Thayer, D.Y. the San Francisco Estuary Project, U.S. Environ- Heller and K.M. Cheap. 1985. Transplanting of mental Protection Agency. January. San Francisco, the seagrass Zostera marina and Halodule wrightii Calif. 283 pp and appendices. for sediment stabilization and habitat develop- Herbold, B., A.D. Jassby and P.B. Moyle. (1992) Status ment on the east coast of the United States. U.S. and trends report on aquatic resources in the San Army Corps of Engineers Tech. Rep. EL-85-9, Francisco Estuary. San Francisco Estuary Project, 49 pp. US Env. Prot. Agency. Fonseca, M.S. and W.J. Kenworthy. 1987. Effects of Highsmith, R.C. 1985. Floating and algal rafting as po- current on photosynthesis and distribution of tential dispersal mechanisms in brooding inverte- seagrasses. Aquat. Bot. 27: 59-78. brates. Mar. Ecol. Prog. Ser. 25: 169-179.

6 Baylands Ecosystem Species and Community Profiles Jones and Stokes Associates, Inc. 1981. An ecological In: M.J. Durako, R.C. Phillips and R.R. Lewis III characterization of the central and northern Cali- (Eds). Proceedings of the Symposium on Subtropi-

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Chapter 1 — Plant Communities 7 Setchell, W.A. 1929. Morphological and phenological Van Montfrans, J., R.L. Wetzel and R.J Orth. 1984. notes on Zostera marina. Univ. Calif. Pub. Botany. Epiphyte-grazer relationships in seagrass meadows: 14: 389-452. Consequences for seagrass growth and production. Silva, P.C. 1979. The benthic algal flora of central San Estuaries. 7: 289-309. Francisco Bay. In: T.J.Conomos (ed). San Francisco Walker, D.I., R.J. Lukatelich, G. Bastyan and A.J.

Plants Bay: the urbanized estuary. Pacific Division, Amer. McComb. 1989. Effect of boat moorings on Assoc. for the Advancement of Science, San Fran- seagrass beds near Perth, Western Australia. cisco, Calif. pp 287-311. Aquatic Bot. 36: 69-77. Sogard, S.M. and K.W. Able. 1991. A comparison of Wetzel, R.G. and P. Penhale. 1983. Production ecology eelgrass, sea lettuce macroalgae, and marsh creeks of seagrass communities in the lower Chesapeake as habitats for epibenthic fishes and decapods. Es- Bay. Mar. Technol. Soc. J. 17(2): 22-31. tuarine, Coastal and Shelf Science. 33: 501-519. Worcester, S.E. 1994. Adult rafting versus larval swim- Spratt, J.D. 1981. Status of the Pacific herring, Clupea ming: dispersal and recruitment of a botryliid as- harengus pallasii, resource in California 1972 to cidian on eelgrass. Mar. Biol. (Berlin), 121: 309: 1980. Fish Bulletin 171. Calif. Dept. Fish and 317. Game. Wyllie-Echeverria, S. and P.J. Rutten. 1989. Inventory Taylor, F.H.C. 1964. Life history and present status of of eelgrass (Zostera marina L.) In: San Francisco/ Columbia herring stocks. Fish. Res. Board Can. San Pablo Bay. Administrative Report, Southwest Bull. 81 pp. Regional NOAA, National Marine Fisheries Ser- Tenore, K.R. 1977. Growth of the polychaete, Capitella vice, Terminal Island, CA 18 pp. capitata, cultured on different levels of detritus de- Wyllie-Echeverria, S. 1990. Distribution and geographic rived from various sources. Limnol. Oceanogr. 22: range of Zostera marina, eelgrass in San Francisco 936-941. Bay, California. In: K.W. Merkel and R.S. Hoffman Thayer, G.W., W.J. Kenworthy and M.F. Fonseca. 1984. (eds). Proceedings of the Calif. Eelgrass Sympo- The ecology of eelgrass meadows of the Atlantic sium. Chula Vista Calif. Sweetwater River Press. Coast: A community profile. U.S. Fish Wildl. Serv. National City, Calif. pp 65-69. FWS/OBS 84/02, 147 pp. Zimmerman, R.C., J.L. Reguzzoni, S. Wyllie-Echeverria, Thom, R. and D. Shreffler. 1995. Mitigating impacts M. Josselyn and R.S. Alberte. 1991. Assessment of ferry terminals on eelgrass in Puget Sound. Ab- of environmental suitability for growth of Zostera stract In: Estuaries: Bridges from Watershed to marina L. (eelgrass) in San Francisco Bay. Aquatic Coastal Seas. 1995 Texas A and M Univ. Sea Grant Botany. 39: 353-366. College Program. Zimmerman, R.C., J.R. Reguzzoni and R.S. Alberte. Tomasko, D.A. and C.J. Dawes. 1989. Evidence for 1995. Eelgrass (Zostera marina L.) transplants in physiological integration between shaded and un- San Francisco Bay: Role of light availability on shaded short-shoots of Thalassia testudinum. Mar. , growth and survival. Aquat. Bot. 51: Ecol. Progr. Ser. 54: 299-305. 37-86.

8 Baylands Ecosystem Species and Community Profiles tocene epoch, the site of the modern Estuary consisted Tidal Marsh Plants of the of broad stream valleys far above glacial low sea level.

Pleistocene tidal marsh plant communities were prob- Plants San Francisco Estuary ably associated with either stream mouths or backbar- Peter R. Baye rier lagoons at the edge of an emergent broad coastal Phyllis M. Faber plain, now submerged and eroded or buried offshore Brenda Grewell from the modern Golden Gate. Tidal marsh plant spe- cies probably migrated upstream in valleys and embay- Introduction ments as sea level rose. Ancestral Pleistocene populations of tidal marsh plant species in today’s estuaries may not The general ecology San Francisco Bay has been re- have been as discontinuously distributed as they are to- viewed by Josselyn (1983), who included a brief treat- day: coastal plain shorelines (e.g., East Coast of North ment of its tidal marsh plant community composition America) often provide widespread tidal inlets and tidal and structure. Macdonald (1977, 1988) reviewed the marsh (Davies 1980). Holocene fragmentation of salt vegetation of California salt marshes, including San Fran- marshes from more extensive or continuous Pleistocene cisco Bay, with emphasis on sedimentation, drainage, to- coastal plain salt marsh distributions may account for his- pography, salinity, flooding, community structure, and toric disjunct, relict populations of species in San Francisco summaries of autecology of selected dominant species. Bay which are now found only in south-central or south- Newcombe and Mason (1972) made descriptive ac- ern California tidal marshes (e.g., Solidago confinis (south- counts of the Suisun Marsh area vegetation. Atwater et ern goldenrod), Suaeda californica (California sea-blite)). al. (1979) summarized and interpreted the relationships Tidal marshes of the Estuary fluctuated in vegeta- between tidal marsh vegetation of the San Francisco tion composition during the Holocene epoch, apparently Estuary and its landforms and geomorphic processes. in relation to changes in long-term climate. This is in- Wells and Goman (1994) reviewed and expanded the dicated by stratified deposits of fossil pollen and plant quaternary history of the San Francisco Estuary. The fragments which indicate periods of accumulation of purpose of this plant community profile is to supplement plants associated with near-freshwater marsh conditions previous reviews, and provide additional information on with species associated the more saline (brackish) con- historic changes in the composition, distribution, and ditions (Wells and Goman 1994). These findings are abundance of tidal marsh plants of the Estuary. consistent with independent evidence on climate changes during the last 6,000 years which show prolonged peri- Environmental Setting ods of drought and high rainfall compared with historic conditions (Ingram et al. 1996, Peterson et al. 1989). Prehistoric Tidal Marsh Development – Tidal The tidal marshes in San Francisco Bay were also not marshes of the modern San Francisco Estuary formed static prior to European influence. Some marsh shore- around 10,000 years ago during the Holocene submer- line configurations indicate long-term scarp retreat across gence when the rate of sea-level rise slowed sufficiently marshes with large sinuous tidal creeks and growth of for tidal marsh sediments to accrete near sea-level berms and sand spits (Atwater et al. 1979). Areas of rapid (Atwater et al. 1979). Prior to that time, during the Pleis- marsh growth in some parts of south San Francisco Bay,

Tidal Marsh along shows complex channels and natural salt pans. Josh Collins

Chapter 1 — Plant Communities 9 outside the influence of Sierran gold mining and prior Comparison With Other Estuaries – The tidal to extensive diking, were evident in maps of the Bay pre- marshes of the San Francisco Estuary are the most ex- pared in the 1870s (U.S. Coast Survey maps). tensive on the central coast of California, and their plant Marsh Sediments and Plants – Depositional en- communities are distinct from other central coast tidal vironments of tidal marshes in the San Francisco Estu- marshes in many respects. Most other large central coast

Plants ary are variable and are significant for the distribution tidal marshes are associated with shallow embayments of uncommon plant species. In most of the San Fran- with large open tidal inlets (e.g., Tomales Bay, Drakes cisco Estuary, the sediments of the middle-marsh marsh Estero and Bolinas Lagoon in Marin County; Bodega plain consists of bay mud (fine silt and clay) with sig- Bay in Sonoma County; Elkhorn Slough in Monterey nificant percentage of organic matter in mature marshes. County; Morro Bay in San Luis Obispo County) which Local coarse sediment deposits, often beach ridges impose strong marine influence on the character of their (marsh berms, or marsh-beach ecotones) composed of sediments, salinities, and vegetation. Central coast tidal sand, shell fragments, organic debris, or mixtures, cre- marshes tend to be isolated and few because of the steep ate physically mobile (periodically eroded and redepos- modern shoreline with few valleys or wave-sheltered ited), well-drained high marsh habitats with affinity for bays. These tidal marshes have extensive sandy sub- some common high marsh species (e.g., Grindelia stricta strates, relatively small, local inputs of fine sediment and var. angustifolia, gumplant) and probably also species freshwater discharges and brackish (mesohaline) condi- now locally extinct or rare, such as Suaeda californica, tions, and are inundated by water approaching marine Atriplex californica (California saltbush), and Castilleja salinity (34 ppt) during most of the growing season. ambigua (salt marsh owl’s clover or Johny-nip). Marsh Some tidal marshes associated with stream mouths have berms are associated with relatively high wave energy en- relatively more freshwater influence and brackish marsh vironments in the Estuary, located near coarse sediment vegetation (e.g., pre-historic Elkhorn Slough and Sali- sources such as eroding bluffs, submerged fossil sand and nas River, Monterey County; Russian River estuary, shell deposits, stream mouths, and eroding marsh edges. Sonoma County), but in association with seasonal reduc- Such features were commonly represented on U.S. Coast tion in tidal influence because of partial or complete clo- Survey maps of the mid-1800s, but persist today in very sure of coastal inlets at river mouths (dammed by sand few localities of the Estuary (e.g., Point Pinole, Redwood beach ridges during periods of relatively low river dis- City area, San Leandro area, and northern San Francisco charge). In contrast, the tidal marsh plant communities peninsula). Similar coarse-sediment features probably oc- of the San Francisco Bay Estuary developed under con- curred as natural levees of upstream reaches of large tidal ditions of abundant and predominantly fine sediment sloughs with significant coarse sediment loads, as is ob- (bay mud, clayey silts and silty clays with high nutrient- served today in Morro Bay. Alluvial fans also create holding capacity), relatively large tidal range, and exten- gradually sloping ecotones with uplands, with variably sive brackish marshes associated with relatively large textured sediments and freshwater runoff and seeps. Few freshwater discharges, distributed over broad, fluctuat- small alluvial fans exist at tidal marsh edges of the Estu- ing salinity gradients (Atwater et al. 1979) ary today (e.g., Point Pinole, Whittell Marsh), but were Historically, salt pans (unvegetated, seasonally in- historically abundant in parts of the Estuary, support- undated depressions or flats within the tidal marsh) and ing diverse ecotonal plant communities (Cooper 1926). local salt ponds (perennial deposits of crystalline salt in Analogous alluvial fan-tidal marsh ecotones occur in hypersaline ponds) were well-developed in San Francisco maritime salt marshes of Point Reyes and Tomales Bay Bay tidal marshes (U.S. Coast Survey T-charts, 1850s), areas, where they support distinctive local plant assem- supporting distinctive vegetation (widgeongrass, Ruppia blages, including uncommon to rare species. maritima, in some pans) or microalgal floras (in salt ponds). Pans are relatively infrequent in other central coast tidal marshes compared with the historic condi- tions of the San Francisco Estuary, and natural salt ponds were not known to occur in other central coast tidal marshes. Today, edges of high marsh pans are associated with at least two regionally rare species (Cordylanthus mar- itimus ssp. palustris and Castilleja ambigua ssp. ambigua), and may have been associated with many others in the past (e.g., Lepidium latipes, L. oxycarpum; Table 1.3)

Peter Baye Tidal Marsh Plant Communities Regionall rare salt marsh owl’s clover, or Johnny-nip (Castilleja ambigua ssp. ambigua). (Tidal marsh, The distribution of tidal marsh plants is strongly (but Whittell Marsh, Point Pinole) not exclusively) influenced by tidal elevation and salin-

10 Baylands Ecosystem Species and Community Profiles dance in some maritime salt marshes of the region (e.g., Atriplex californica, Castilleja ambigua, Puccinellia nut-

kanensis). Few species associated with high marsh zones Plants of maritime salt marshes in the region were historically absent from the San Francisco Estuary (e.g., Astragalus pycnostachyus var. pycnostachyus (coastal marsh milk- vetch), Castilleja ambigua ssp. humboldtiensis (Humboldt Bay owl’s clover), Leymus x vancouveriensis (Vancouver’s ryegrass), and Grindelia stricta var. stricta (gumplant)). Differences exist also between the structure of veg- etation found in predominantly marine-influenced salt marshes of the central coast and tidal marshes of the San Francisco Estuary. Although the middle marsh zone of San Francisco Bay salt marshes has been described as

Peter Baye supporting “ prostrate” growth forms of pickleweed Pickleweed (Salicornia virginica), a dominant within (Macdonald 1977), the middle marsh plains of sandy or the salt marsh middle marsh zone, shown enshrouded sandy peat salt marshes of Bolinas Lagoon (Allison 1992), by parasitic dodder (Cuscuta salina). Point Reyes, Tomales Bay, and Morro Bay often support very thin, low (< 10 cm) turf-like vegetation mosaics with ity (Hinde 1954, Atwater and Hedel 1976). Following extremely short, sparse, or prostrate pickleweed as a rela- Peinado et al. (1994), three elevation “ zones” of the tidal tively minor component, or at most co-dominant with marsh can be objectively distinguished (and are visually species such as Triglochin concinna (slender sea arrow- conspicuous): (1) the low marsh zone, occurs from ap- grass; uncommon to rare in San Francisco Estuary). proximately mean sea level to mean high water; (2) the These salt marsh turfs often support high plant species middle marsh zone, occurs from approximately mean diversity compared with San Francisco Bay salt marsh high water to mean higher high water; and (3) the high plains, which tend to be dominated by pickleweed, marsh zone (colloquially also called the “ upland transi- which often grows in dense stands (usually over 20 cm tion” or “ peripheral halophyte” zone; “ upper salt marsh thick; up to 50-60 cm in some fringing marshes of San zone” of Peinado et al. 1994), occurs near and above Pablo Bay). Low, turf-like middle marsh vegetation is mean higher high water up to several meters above ex- very uncommon in San Francisco Bay, both in brackish treme high water line (Peinado et al. 1994). The typical and salt marshes. species composition of these zones is described below for Salt Marsh Plants and Their Associations – Salt tidal salt marsh and tidal brackish marsh. Unlike beach, marsh here refers to tidal marsh plant associations that dune, and bluff communities (Barbour and Johnson approximate the species composition typical of near- 1977, Barbour et al. 1973), there is no empirical evi- marine salinity during the growing season (34 ppt). Few dence of salt marsh zonation attributable to salt spray; if any salt marshes in the San Francisco Estuary are ac- estuaries and embayments are relatively low-energy wave environments (Davies 1980, Carter 1988). Other poten- tially significant influencing factors have not yet been well studied. There are significant floristic differences between the tidal marshes of San Francisco Estuary and other central coast tidal marsh systems. These include: 1. The dominance of Spartina foliosa (Pacific cord- grass), either absent today or historically absent from most or all other central coast tidal marshes (Macdonald 1977); 2. The presence of rare species of disjunct distribu- tion, such as Suaeda californica (native only to Morro Bay and San Francisco Bay); and 3. The presence of local endemic species such as soft bird’s-beak (Cordylanthus mollis ssp. mollis) and Suisun thistle (Cirsium hydrophilum var. hydrophilum). Peter Baye Soft bird’s-beak (Cordylanthus mollis ssp. mollis). The Conversely, some uncommon tidal marsh species hairy of the flowering stems are jeweled with which have either declined severely or become extirpated salt-encrusted glands. (Brackish tidal marsh, South- in the San Francisco Estuary still occur in local abun- hampton Marsh, Benecia)

Chapter 1 — Plant Communities 11 tually regularly exposed to near-marine salinity, but in the upper estuarine salinity range (roughly 20 ppt and above), they are effectively salt marsh in vegetation char- acter. The salt marsh plant community is typical of San Francisco Bay and the outer marshes of most of San

Plants Pablo Bay. The low salt marsh zone in San Francisco Bay is usually dominated by a single species, Spartina foliosa (Pacific cordgrass), but is increasingly becoming domi- nated by the invasive introduced Atlantic species, Spar- tina alterniflora and its highly variable hybrids and novel “ ecotypes” (Callaway and Josselyn 1992; Daehler and

Strong 1994, 1997; Daehler et al. 1999). S. foliosa stands Peter Baye occur as uniform fringes along tidal creek banks or as Annual pickleweed (Salicornia europaea)— Occasion- broad uniform plains on prograding marshes at the edges ally found in conspicuous colonies on higher mudflats of broad tidal mudflats. They extend from approximately between upper cordgrass and lower pickleweed zones, it more commonly grows as a short, dense single mean high water to mean sea level (Hinde 1954, Atwater plant. It turns brilliant crimson in fall, in contrast with the et al. 1979). On gentle elevation gradients, they inter- dominant dull green-brown Salicornia virginica. grade with middle marsh plains in mixed stands of Sali- cornia virginica (pickleweed), as at Dumbarton-Mowry marsh and eastern San Pablo Bay fringe marshes. They native and introduced cordgrasses have not yet been con- may also occur as abrupt zones at the edge between tidal ducted. The only other species of the low marsh is Sali- mudflats and wave-cut peat scarps. Pioneer colonies of cornia europaea (annual pickleweed), which occasionally Pacific and smooth cordgrasses on mudflats are abun- occurs in the upper edge of the zone, often in accreting dant in some years, particularly in years of high or late high mudflats in transition between low and middle rainfall. They apparently establish by seedlings and re- marsh zones. generated rhizome fragments, but the relative propor- The middle salt marsh zone composes the exten- tion of these of propagule types is unknown. Pioneer sive salt marsh plains of San Francisco Bay (Hinde 1954, colonies of S. alterniflora were observed on open mud- Atwater et al. 1979). Younger marshes tend to be char- flats of the delta in 1991, and are vis- acterized by low-diversity vegetation dominated by Sali- ible in aerial photographs of the area cornia virginica (Cuneo 1987), but some older marsh around 1980. Seedlings and pioneer colonies of S. foliosa remnants (e.g., Greenbrae and Heerdt Marsh; upper were common on high mudflats of San Pablo Bay and Newark slough marsh) may comprise complex and an- its tributaries in the late 1990s. The taller S. alterniflora nually variable mosaics of S. virginica, Distichlis spicata appears to be able to spread clonally below mean sea level, (saltgrass), Cuscuta salina (salt marsh dodder), Jaumea but long-term comparisons of colonial spread between carnosa (fleshy jaumea), Frankenia salina (alkali-heath) and Atriplex triangularis (spearscale or fat-hen). Species diversity in the middle salt marsh is not necessarily cor- related with marsh age: old marshes at China Camp and Whittell Marsh (Point Pinole) also support relatively low- diversity vegetation dominated by S. virginica. The para- sitic Cuscuta salina (dodder) can become conspicuously co-dominant or even dominant in the middle marsh zone by mid-summer in some marshes in some years, turn- ing the middle marsh into an orange and green mosaic visible at great distances (Dumbarton-Mowry marsh, San Pablo Bay fringe marshes). Colonization and species re- covery dynamics associated with dodder-induced dieback of marsh vegetation have not been investigated. Relatively uncommon species of the middle marsh zone of San Francisco Bay include Triglochin maritima (sea arrow-grass), Limonium californicum (sea-lavender), Peter Baye and Polygonum prolificum and P. patulum (non-native Locally rare Point Reyes bird’s-beak (Cordylanthus knotweeds). Reports of the rare Point Reyes endemic maritimus ssp. palustris), is abundant in salt marshes of Tomales Bay, Bolinas Lagoon, and Limantour Estero. Polygonum marinense (Marin knotweed) in San Francisco (Salt marsh, Marin City shoreline) Bay require taxonomic verification. Species which sel-

12 Baylands Ecosystem Species and Community Profiles dom occur in the middle salt marsh zone of San Fran- coides or L. x multiflorus (creeping wildrye), or Juncus cisco Bay include Cordylanthus maritimus ssp. palustris lesueurii (salt rush, wire rush), as still occurs commonly

(Pt. Reyes bird’s-beak; Richardson Bay, Heerdt Marsh), in maritime salt marshes of the region. Plants Puccinelia nutkaensis (Pacific alkali grass; Ravenswood Cooper (1926) described a broad high salt marsh fringe marshes and Newark), Plantago maritima (sea- zone along the Palo Alto shoreline dominated by Distich- plantain) and Triglochin concinna (slender arrow-grass). lis spicata and Grindelia stricta var. angustifolia (an asso- These latter species are locally abundant in maritime salt ciation still evident in reduced extent today), and a high marshes of Marin County. Invasive exotic species of the salt marsh - alluvial transition zone which no longer middle salt marsh include Spartina densiflora (Chilean exists. Cooper’s reconstructed high salt marsh ecotone cordgrass; Richardson Bay and Point Pinole), Spartina community was dominated by native composites— patens (saltmeadow cordgrass; near Burlingame and in Hemizonia pungens ssp. maritima, H. congesta (tarweeds), brackish middle marsh at Southhampton Bay) and Helianthus bolanderi (Bolander’s sunflower), Aster subu- Cotula coronopifolia (brass buttons; early introduction, latus (as “ A. exilis” ; slim or salt marsh aster), Aster chilensis widespread but never persistent as a dominant in tidal (Chilean aster; possibly also including the rare A. lentus), marsh). The invasive exotic Salsola soda (Mediterranean Baccharis douglasii (salt marsh baccharis), Euthamia saltwort) also is spreading from high salt marsh to the occidentalis (western goldenrod), and Iva axillaris (pov- middle marsh zone (Dumbarton-Mowry marsh). erty weed). Of these, I. axillaris, A. chilensis, H. pungens, High or upper salt marsh may occur as topographic B. douglasii, and E. occidentalis still occur in high tidal highs within the marsh plain (e.g., channel bank levees, brackish marsh of San Pablo Bay and Suisun Marsh. It wave-deposited ridges or mounds) or along the upland therefore appears likely that historic upper edges of some or alluvial edges of the marsh. This zone today com- salt marshes were at least locally brackish or subsaline monly includes natives such as Grindelia stricta var. an- rather than hypersaline in character, influenced by sur- gustifolia (frequently a dominant in this zone), Distich- face and subsurface freshwater discharges. This is also lis spicata, erect-ascending phenotypes of Salicornia indicated by Cooper’s description of water table-depen- virginica, Cuscuta salina, Frankenia salina, Limonium dent, salt-intolerant tall (to 9 m) thickets of willow, cot- californicum (sea-lavender), and Atriplex triangularis tonwood, box-elder, ash, blackberry, ninebark, and Cali- (spearscale, fat-hen). Where the upper marsh intergrades fornia rose at the high marsh edge (Salix lasiolepis, with low-lying alluvial soils and high groundwater (a con- Populus trichocarpa, Acer negundo, Fraxinus oregona, dition today very rare in San Francisco Bay), the high Rubus ursinus, Physocarpus capitatus, Rosa californica). marsh zone is dominated by dense stands of Leymus triti- Cooper (1926) interpreted this community from isolated remnants of what he assumed was undisturbed vegeta- tion, but the disturbance history of the South Bay marsh edge at the time of his observations, and older reports he collected, is uncertain. The high salt marsh zone also historically included many other native species, which are now uncommon, rare, or extirpated in San Francisco Bay (Table 1.3). Most of these still persist at other California salt marsh localities. Most high salt marsh zones in San Francisco Bay today occur on artificial slopes and substrates at the upper marsh edge, and include many non-native species that sometimes dominate the zone. Common non-na- tive plants of the high salt marsh zone include Lepidium latifolium (broadleaf peppercress, perennial peppergrass), Bassia hyssopifolia (bassia), Salsola soda (saltwort), Beta vulgaris (wild beet), Mesembryanthemum nodiflorum (an- nual iceplant), Carpobrotus edulis and its hybrids (ice- plant), Atriplex semibaccata (Australian saltbush), Bromus diandrus (ripgut brome), Hainardia cylindrica and Parapholis incurva (sicklegrasses), and Polypogon monspe- liensis (rabbit’s-foot grass). Brackish Marsh Plants and Their Associations – Brackish tidal marshes prevail over northern San Pablo

Josh Collins Bay (slough systems of the Petaluma River, , Tiidal salt marsh low marsh zone dominated by Pacific , and ), the Suisun Marsh area, cordgrass (Spartina foliosa). and the Contra Costa marshes (North Bay marshes).

Chapter 1 — Plant Communities 13 They also occur in transition with San Francisco Bay salt marshes where significant freshwater discharges occur (e.g., fringing marshes of Mud Slough, Coyote Creek, Artesian Slough, Alviso Slough, and Guadalupe Slough). The distinction between “ salt marsh” and “ brackish

Plants marsh” is a recent convention in descriptions of San Francisco Bay Area tidal marshes: brackish marshes were indiscriminately described as “ salt marshes” by early Cali- fornia botanists, making it difficult to separate distinct elements of “ salt” and “ brackish” marsh associations. The description and demarcation of brackish marsh plant communities is essentially a matter of convenience and convention: there is no precise, stable salinity thresh- old at which tidal marshes are known to switch from one “ type” to another (Adam 1990). Instead, brackish marsh vegetation in the San Francisco Estuary is typically a dy- namic continuum between salt marshes of San Francisco Bay and freshwater tidal marshes of its major tributary Peter Baye rivers, fluctuating with variable influence of rainfall and Sea-milkwort (Glaux maritima) is found in tidal marshes freshwater discharges which alter marsh salinity and veg- on the northern Pacific Coast, and on the Arctic, etation gradients geographically and over time. Associ- American, and European Atlantic coasts. (Tidal marsh, ated changes in local tidal elevations (related to fresh- Rush Ranch, Suisun Marsh) water discharges) may also possibly interact with salinity variations in altering the character of brackish marsh compared with salt marsh. Grewell (1993 et seq.) com- vegetation. Changes in brackish marsh vegetation be- piled extensive vascular plant species lists of the Suisun tween dry and wet years at the same location may be Marsh (including uplands of dikes and artificial uplands), dramatic: cover can change from that typical of San Fran- and presented the only comprehensive and contempo- cisco Bay salt marsh (dominant pickleweed) to that typi- rary synthesis of Suisun Marsh plant ecology and its his- cal of Suisun Marsh (mosaic of rushes, bulrushes, alkali- tory (Grewell et al. 1999). Mason (Newcombe and bulrush, cattails, saltgrass, and many broad-leaved Mason 1972) described plant community composition herbaceous species) in very few years. The causes of these of brackish tidal marshes extending into the Sacramento- dramatic changes in brackish tidal marsh vegetation are San Joaquin Delta. presumably related to plant interactions (competition, The low brackish marsh zone differs from the cor- facilitation, and parasitism) which are influenced by sea- responding zone in the San Francisco Estuary salt sonal and annual variation in salinity and drainage marshes in several respects: it supports multiple domi- (Pearcy and Ustin 1984), but are poorly understood nant species in variable mixtures or monospecific stands; beyond descriptive observation. it extends to the low end of intertidal zone, and it regu- The most extensive tidal brackish marshes occur larly develops tall, dense vegetation. In San Pablo Bay in the Petaluma Marsh, but relatively large relict tidal and western Suisun Marsh, alkali-bulrush (predomi- brackish marshes also occur along the Napa River (Fagan nantly Scirpus maritimus around San Francisco and San Slough marsh) and in the Hill Slough/Rush Ranch area Pablo bays and western Suisun Marsh, but also includ- in Suisun Marsh. Relatively young but large and well- ing S. robustus, a taxon formerly misapplied to S. mari- developed brackish marshes also occur bayward of dikes timus in floras of the region) occurs in the upper por- constructed after the 1870s, particularly in the Napa- tion of the low marsh, often dominant in the saline end Sonoma marsh complex and Suisun Marsh, including of the brackish marsh gradient. The tallest graminoid marsh islands of Suisun Bay. The Contra Costa marshes species, tules and cattails, dominate where freshwater are predominantly intermediate between fully tidal influence is relatively strong; these include Typha angus- marsh and diked (reduced tidal range) brackish marshes. tifolia, T. latifolia, T. dominguensis and hybrids; Scirpus The extensive wave-influenced, prograded pickleweed- californicus (California tule), S. acutus (hardstem tule) dominated marsh plain and low natural marsh levee and hybrids. These graminoid species can also establish along northern San Pablo Bay are transitional between within poorly drained portions of the middle marsh salt marsh and brackish marsh, exhibiting increases in plain. brackish-associated species (particularly Scirpus mariti- The middle brackish marsh zone was historically mus at the east end of the Bay) in series of wet years. dominated by Distichlis spicata (saltgrass), as it commonly Plant species richness and diversity markedly in- is today (Newcombe and Mason 1972). Other native crease in brackish marshes of the San Francisco Estuary species of the high marsh which occur in variable abun-

14 Baylands Ecosystem Species and Community Profiles dance (common to co-dominant) include Salicornia vir- Ambrosia psilostachya (western ragweed), Euthamia ginica, Atriplex triangularis, the Juncus balticus-lesueurii occidentalis (western goldenrod), Epilobium brachycar-

complex, Jaumea carnosa, Frankenia salina and Cuscuta pum, E. ciliatum (willow-herbs), Polygonum spp. (smart- Plants salina. Locally common natives include Limonium cali- weeds, knotweeds), Triglochin maritima (sea arrow-grass) fornicum (sea-lavender), Glaux maritima (sea-milkwort), and Eryngium articulatum (coyote-thistle). Uncommon and Scirpus koilolepis cernuus and S. cernuus (clubrush; to rare species such as Lathyrus jepsonii var. jepsonii also in high brackish marsh), Eleocharis macrostachya (Delta tule pea), Aster lentus (Suisun aster), A. subulatus (creeping spikerush), Helenium bigelovii (Bigelow’s var. ligulatus (slim aster), Plantago elongata (dwarf sneezeweed), and Deschampsia cespitosa ssp. holciformis plaintain), Rumex occidentalis (western dock), Eleocha- (tufted hairgrass; especially eastern Suisun Marsh). In- ris parvula (spikerush), and endangered Cordylanthus frequent to rare species of this zone include Lilaeopsis mollis ssp. mollis (soft bird’s beak) and Cirsium hydrophi- masonii and L. occidentalis (Mason’s and western lilae- lum var. hydrophilum (Suisun thistle) typically occur lo- opsis; on exposed eroding channel bank edges as far west cally in the lower end of well-drained high marsh gradi- as Tolay Creek), Triglochin maritima (locally common), ent, often on slight topographic relief above the marsh T. concinna, T. striata, Sium suave (water parsnip), plain. Salicornia virginica (common pickleweed) and Oenanthe sarmentosa (ditch-carrot), Cicuta maculata ssp. occasionally S. subterminalis (Parish’s glasswort) can also bolanderi (water hemlock), Eleocharis parvula (slender be abundant elements of high brackish marsh near Sui- spikerush), Pluchea odorata (salt marsh fleabane), and sun. The composition of high brackish marsh vegetation Lythrum californicum (California loosestrife; eastern Sui- appears to vary with slope, drainage, and local surface sun Marsh and Delta). In wet years, depressions in the or subsurface freshwater influence, but no studies have middle marsh plain support increased abundance of Scir- yet analyzed vegetation patterns or related environmen- pus americanus (Olney’s bulrush) or S. maritimus (alkali- tal factors in brackish marshes of the region. bulrush; western Suisun and San Pablo Bay) and Phrag- Invasive non-native species (weeds of mesic and mites australis (common reed; eastern Suisun Marsh, also habitats with slight salt tolerance) of the high in the low-middle marsh zone). The dominant non-na- brackish marsh zone are numerous, particularly in years tive species of the middle brackish marsh is again Lepi- of high rainfall, but the most aggressive and successful dium latifolium, which rapidly forms dense monotypic is again Lepidium latifolium. Lotus corniculatus (bird’s- clonal populations, spreading into the marsh plain. foot trefoil) and Lolium multiflorum (ryegrass) are other Other exotic species which have established in the brack- exotics which are locally abundant along portions of the ish middle marsh zone include Apium graveolens (wild upper brackish marsh edge some years. Elytrigia pontica celery, widespread and abundant in Suisun Marsh), ssp. pontica (tall wheatgrass, currently local around Lythrum hyssopifolium (annual loosestrife), Cotula coro- Alameda Creek and ), Rumex crispus and R. nopifolia (brass-buttons) and Chenopodium chenopodio- pulcher (curly and fiddle docks), Asparagus officinalis (lo- ides (fleshy goosefoot; Napa-Sonoma marshes). cally abundant near Napa-Sonoma marshes) have also The high brackish marsh zone is today typically naturalized along brackish marsh edges, but are seldom altered by artificial dikes and invasive plants (particularly invasive. Lepidium latifolium (perennial or broadleaf peppercress), Conium maculatum (poison hemlock), Foeniculum vulgare (fennel), and Mediterranean grasses. However, many native remnants of the brackish high marsh com- munity have regenerated on old, stable, relatively undis- turbed levees, or have persisted locally along undiked tidal marsh edges. They include Achillea millefolium (yar- row), Baccharis douglasii (salt marsh baccharis), B. pilularis (coyote-brush), Leymus triticoides and L. x multiflorus (creeping wildrye), Scrophularia californica (California bee-plant), Rubus ursinus (blackberry, in the upland ecotone) Rosa californica (California rose, also in the upland ecotone), Iva axillaris (poverty-weed), Atri- plex triangularis (fat-hen or spearscale), Grindelia stricta var. angustifolia (and intermediates with G. camporum), Calystegia sepium ssp. limnophila (morning-glory), Cressa

truxillensis (alkali-weed), Frankenia salina (alkali-heath), Peter Baye Lathyrus jepsonii var. californicus (California tule pea), Ditch-carrot (Oenanthe sarmentosa), a common Juncus balticus - lesueurii complex (salt or wire rush), freshwater marsh plant, also occurs in fresher phases of Juncus mexicanus (Mexican rush), J. bufonius (toad rush), brackish tidal marshes. (Southhampton Marsh, Benicia)

Chapter 1 — Plant Communities 15 Tidal Marsh Pans and Vegetation – Poorly (particularly Enteromorpha and Ulva spp.). According to drained flats, depressions, and barrier-impounded areas Mason (Newcomb and Mason 1972), brackish ponds in of tidal marsh lacking emergent vascular vegetation, Suisun Marsh also support Zannichellia palustris and called pans (alternatively spelled “ pannes” ), range from Potamogeton pectinatus, submerged species typical of nearly planar unvegetated marsh areas subject to shal- freshwater ponds. The halophilic microflora of salt ponds

Plants low periodic ponding, to steep-sided or cliff-edged shal- is discussed in the salt pond profile(this volume). Shal- low ponds which are persistently inundated (Pestrong low, relatively planar and ephemeral pans in San Pablo 1965, Pethick 1974, Atwater et al. 1979). Pans have Bay are either periodically or marginally colonized by various modes of origin and development, which have pickleweed, which dies back during years of frequent not been completely clarified (Adam 1990, Carter 1988, flooding or high rainfall. The steep-sided edges of well- Pethick 1974, Chapman 1960). In San Francisco Bay defined, nearly circular old pans sometimes develop small Area marshes, pan variation includes nearly circular natural levees of locally improved drainage, and some- ponds between drainage channels (Pestrong 1965), his- times support certain species at frequencies more typi- toric long ponds parallel with impounding bayfront cal of high marsh vegetation. In the high marsh, on gen- marsh berms (Atwater et al. 1979), shore-parallel pans tly sloping alluvial fans, “ dry pans” (small playa-like flats historically present along portions of the back edge (up- with very short flooding periods and superficial salt films) land or lowland margin) of tidal marsh (depicted in also develop, often on relatively coarse (sandy, silty, or 1880s U.S. Coast Survey Maps), and natural historic salt even gravel-silt mixtures) sediments. These features are ponds impounded by low estuarine ridges (Atwater et very rare today because of diking, but fine examples al. 1979). Some sloped to planar pans in the high marsh persist at Point Pinole (Whittell Marsh). Here, as at simi- (bare flats, rarely submerged) may be related to wrack lar pans on alluvial fans at tidal marsh edges in maritime deposition and smothering, or local substrate conditions. Marin County, the pan-marsh edges are associated with Little is known of the ecology of pan types that are no local abundance of the regionally rare salt marsh owl’s longer represented in the altered modern Estuary. clover (Castilleja ambigua ssp. ambigua; salt-tolerant Many pans are reported to become seasonally hy- ecotypes). Salt marsh bird’s-beak (Cordylanthus mariti- persaline (Pestrong 1965) or even salt-crystallizing mus ssp. palustris) also exhibits a pan-margin local dis- (Atwater et al. 1979; see also salt pond profile, this vol- tribution pattern in western San Pablo Bay (e.g., ume) and lack vascular plants, but some pans along the JEPS83457). Analogous artificial features (gently slop- landward edge of the tidal marsh develop marginal veg- ing, formerly disturbed silty to sandy high marsh fills etation typical of brackish or fresh marshes (e.g., China with residual vegetation gaps) elsewhere in the Estuary Camp). Ponded pans within the marsh plain have been have also become colonized with rare plants such as described as “ unvegetated” (Pestrong 1965), but they Cordylanthus mollis (Hill Slough near Lawler Ranch; B. often support a dense submerged mixed vascular and Grewell, pers. obs.) and Cordylanthus maritimus (near non-vascular vegetation variously composed of widgeon- Marin City). Natural and artificial high marsh pans of grass (Ruppia maritima) and membranous green algae this type, associated with alluvial or deltaic deposition

High marsh pan in Whittell Marsh (Point Pinole, Contra Costa County), fringed with salt-marsh owl’s clover (Castilleja ambigua). Whittell Marsh is the last known tidal marsh locality of this species in the San Francisco Estuary. Peter Baye

16 Baylands Ecosystem Species and Community Profiles cies typical of vernal pools and wet grassland (R. Gros- singer, pers. comm. 1999). Examples of brackish and

even freshwater vegetation at edges of salt marsh with Plants pans near zones of groundwater discharge can be ob- served today at China Camp (Marin County) and Point Pinole (Contra Costa County), and in maritime Marin County tidal marshes. Diked seasonal wetlands in his- toric tidal marsh (this volume) may also approximate this type of lost habitat, since numerous seasonal wetland species of vernal pools and alkali basins have colonized diked Baylands.

Uncommon, Rare, Declining, and Extir- pated Plant Species Peter Baye Regionally rare smooth goldfields (Lasthenia glabrata). There is a widespread impression, even among ecologists (Whittell Marsh, Point Pinole, Contra Costa County) familiar with the San Francisco Estuary, that native plant species richness of tidal marshes (particularly salt marsh) or erosion, have not been identified in the regional lit- is relatively low, and that rare species in the Estuary are erature on salt marsh ecology, and require study. principally wildlife taxa, not plants. This impression is The number of species from former alkali-subsa- due in part to reviews of species richness in tidal marshes line vernal pools around San Francisco Bay which were based solely on modern surveys: for example, Atwater et historically reported from local salt marshes as well (see al. (1979) reported only 15 vascular plant species for San diked wetlands profile, this volume) suggests that eco- Francisco Bay, based on modern reports. Josselyn (1983) logically equivalent habitat occurred in both . discussed only a small representation of the San Fran- Although there are very few intact remnants of the elon- cisco Estuary flora, and did not address either its historic gate pans which occurred along tidal marsh edges (rep- or modern species richness. In addition, very few plants resented clearly in historic U.S. Coast Survey maps of native to the San Francisco Estuary are federally listed the 1850s), it is possible that some of these seasonally as endangered or threatened, and only two of these (soft ponded depressions in the upper marsh ecotone were bird’s-beak, Cordylanthus mollis ssp. mollis, and Suisun partial ecological equivalents of subsaline vernal pools. thistle, Cirsium hydrophilum var. hydrophilum) currently Strong historic evidence for this conclusion is found in inhabit this Estuary. The modern lack of attention to rare Jepson’s (1911) range and habitat descriptions for the plants in the Estuary is probably due to unfamiliarity typical vernal pool species, Downingia pulchella, which with plant species which were known only to early bota- he described as “ abundant and of rank growth in the salt nists, but are either now entirely extinct (or even extir- marshes near Alvarado” [now Union City]. Other spe- pated) in the Estuary. Plant species that were historically cies indicative of vernal pools and similar seasonally recorded in the tidal marshes of the Estuary, or along ponded/desiccated alkaline/subsaline environments, its edges (high marsh), but have become uncommon, such as Lasthenia conjugens (JEPS25099), L. platycarpha rare, regionally extirpated, or extinct, are summarized in (DS695549, Greene 1894) and L. glabrata (CAS897444, Table 1.3. Most of these species were known from tidal DS73122, DS286573) have been collected from the marsh edges, transitional habitats of high ecological di- edges of San Francisco Bay. versity. This is significant, because original remnants of Although pans are often presumed to be generally this ecotone are almost completely eliminated from the hypersaline, some appear to have occurred historically Estuary, and their modern counterparts are mostly in alluvial lowlands with probable groundwater or sur- weedy, disturbed habitats like dikes. face discharges that could maintain brackish conditions Extinct species of the Estuary include California in pans along tidal marsh edges. A number of charac- sea-blite, Suaeda californica, a federally endangered teristic freshwater marsh species were reported by Jepson shrubby true halophyte (salt-tolerant plant) which today (1911) and others from historic salt marsh habitat (e.g., inhabits relatively well-drained marshy beach ridges Agrostis exarata, Carex aquatilis, C. densa, Lycopus asper), along relatively high-energy shorelines with coarse sedi- suggesting that freshwater sub-habitats occurred margin- ment in Morro Bay. According to Jepson (1911) and ally along tidal salt marshes. Unpublished historic writ- Greene (1894), it was never abundant in San Francisco ings of southeastern San Francisco Bay marsh borders Bay even in the late 19th century. The distribution of by 19th century botanist Joseph Burtt-Davy, archived its sandy marsh habitats was unfortunately in areas of at the Jepson Herbarium, University of California, de- the greatest urbanization: San Francisco, Oakland, scribe extensive colorful wildflower meadows with spe- Alameda, and San Leandro were its core populations,

Chapter 1 — Plant Communities 17 although it was also collected in Palo Alto (where shell when it was misidentified as seaside goldenrod (S. hash beaches today occur) and at the former San Pablo sempervirens). In California tidal marshes today, S. Landing (Richmond, where local sand beaches still per- confinis is known only locally from the high brackish sist). The species today is restricted to sandy salt marsh marsh zone of southern Morro Bay. P. racemosa was for- edges of Morro Bay, San Luis Obispo County, and also merly reported from the edges of salt marshes and sa-

Plants exists in cultivation. It was last collected in San Fran- line soils at Cooley’s Landing and near Alviso (Thomas cisco Bay in 1958 in San Leandro (JEPS25020) More 1961), but has not been reported from salt marsh edges recent local reports are based on misidentification of the in recent decades. Another species, Adobe sanicle similar species, S. moquinii, in diked Baylands. (Sanicula maritima), was found locally in lowlands ad- Many other salt marsh species that have affinity jacent to salt marshes at Alameda (Behr 1888, Greene for high sandy salt marsh were also reported from San 1894, Jepson 1911) and in San Francisco (Brandegee Francisco Bay, but are now extinct or rare in the Bay 1892). It is now extinct in the Bay Area, and is very rare (Jepson 1911, Greene 1894). They include California elsewhere (known from fewer than 10 sites in Monterey saltbush (Atriplex californica), still found in Tomales Bay and San Luis Obispo Counties today; Skinner and and Point Reyes sandy salt marshes, but extinct in the Pavlick 1994). Bay, and Plantago maritima, common in sandy maritime Two popcornflower species (genus Plagiobothrys, salt marshes, uncommon to rare in the Bay. The sea-pink well represented in vernal pools) that were found in sa- (Armeria maritima) a showy pink spring wildflower line soils near the edge of the Estuary are now presumed which still occurs locally along sandy edges of Point to be extinct (although it is possible that buried dormant Reyes salt marshes, was cited by Jepson (1911) to range seed may persist somewhere in diked Baylands, await- within San Francisco Bay. (This may possibly have been ing resurrection). They include Petaluma popcornflower along former sandy beaches, sandy salt marsh, or stabi- (Plagiobothrys mollis var. vestitus), which was probably lized former bayside dunes. There are no historic her- distributed in alkaline or subsaline seasonally wet depres- barium specimens from San Francisco Bay salt marshes sions (vernal pools) in grasslands and lowlands adjacent to corroborate Jepson’s report, however.) Other rare spe- to tidal marsh in the Petaluma Valley, and Hairless cies, such as Cordylanthus maritimus ssp. palustris and popcornflower (P. glaber), a species of seasonally wet al- Castilleja ambigua ssp. ambigua, are less uncommon in kaline/subsaline soils of tidal marshes of the south San sandy maritime salt marshes, but are rare in San Fran- Francisco Bay (reported by Jepson (1911) from Alvarado cisco Bay. The decline or demise of these species in the [now Union City]), as well as some interior valleys. Al- Bay is very likely a result of the near-complete elimina- most nothing is known of the ecology of these species tion of its sandy estuarine barrier beaches. because of their early historic extinction. Two other species which are probably extinct in Other species that are known to occur in subsaline San Francisco Bay, but occur elsewhere, include two to alkaline vernal pools, and which historically occurred members of the Aster family: southern goldenrod (Sol- in salt marshes (presumably along lowland edges), in- idago confinis) and Pyrrocoma racemosa (=Haplopappus clude several species of goldfields (Lasthenia spp.). Fleshy racemosa). Southern goldenrod was formerly reported as goldfields, Lasthenia platycarpha (presumed extinct in the rare only by Henry Bolander in 1863 (Jepson 1911), Estuary) was known from salt marshes near Vallejo (Greene 1894), and smooth goldfields (L. glabrata ssp. glabrata) was reported from edges of salt marshes (Tho- mas 1961, Jepson 1911, Greene 1894). L. glabrata was recently confirmed to occur naturally at Whittell Marsh, Point Pinole, and a population of undetermined origin occured briefly in 1998 on a hydroseeded levee at the Sonoma Baylands tidal marsh restoration project’s pilot unit. Behr (1888) listed L. glabberima as a species oc- curring “ near salt marshes,” but is not otherwise reported from tidal marshes in the region. The federally endan- gered vernal pool goldfields species, Contra Costa gold- fields (L. conjugens) was reported by Jepson (1911) from “ subsaline soils” near Antioch and Newark, and was re- cently discovered in subsaline vernal pools in Fremont near the diked edge of the at the Warm Springs Unit of the National Wildlife Refuge in Fremont and adjacent Peter Baye Federally listed as endangered, California sea-blite derelict fields. L. conjugens was also observed along high (Suaeda Californica) is extinct in San Francisco Bay. tidal marsh edges of Hill Slough in the early 1990s. An- (Morro Bay) other well-known vernal pool species, the showy Down-

18 Baylands Ecosystem Species and Community Profiles ambigua, but typical of ssp. insalutata of Monterey County). Salt-tolerant locally adapted populations of this

subspecies also occur at Rodeo Lagoon and Bolinas La- Plants goon, but are otherwise rare in central coast tidal marshes (very local in Limantour estero and Tomales Bay). A re- lated salt marsh endemic subspecies, C. a. ssp. humbold- tiensis, occurs only in Humboldt Bay and Tomales Bay. Non-halophyte populations of C. a. ssp. ambigua occur somewhat more widely in coastal grasslands, headlands, and bluffs. Still surviving but rare within its historic range in brackish tidal marshes from Petaluma Marsh to Antioch is another annual Snapdragon family herb, soft bird’s-

Peter Baye beak (Cordylanthus mollis ssp. mollis). This white-yellow The southern-most population of Point Reyes bird’s- flowered herb is covered with salt-encrusted secretory beak (Cordylanthus maritimus ssp. palustris), in a small glands. It is listed as federally endangered, and is re- marsh on the Marin City shoreline. stricted mostly to the Suisun Marsh area, especially in old relict tidal brackish marsh. It formerly ranged as far ingia pulchella (producing spring masses of blue, white, west as Petaluma Marsh (Howell 1949). Like the other and yellow flowers resembling lobelias) was described by annual hemiparasitic salt marsh Snapdragon relatives, its Jepson (1911) to occur abundantly in South Bay salt numbers fluctuate tremendously from year to year marshes. It still occurs in the subsaline vernal pools ad- (Rugyt 1994), sometimes disappearing for a year or more jacent to tidal marsh at the Warm Springs Unit of the before regenerating from dormant seed banks. Refuge in Fremont, and in diked agricultural Baylands Numerous other species, particularly grasses and (former tidal marsh) near Fairfield. The rare annual sedge species, were cited by early California botanists as milkvetch (locoweed), Astragalus tener var. tener, was for- commonly occurring in salt marshes, but are scarce or merly collected from “ saline areas along San Francisco absent today in the San Francisco Bay Area. By analogy Bay” as far south as Mayfield (Mountain View area; with relatively intact tidal marshes of Point Reyes to the Thomas 1961). Once found in alkali vernal pools, it was north and Elkhorn Slough to the south, it appears very collected in the Bay Area in 1959 (Skinner and Pavlick likely that these “ missing” salt marsh species occurred 1994) and was recently rediscovered near the historic Bay along upland or lowland (alluvial) margins of tidal edge in Fremont (G. Holstein, pers. comm. 1999). marshes. Some, like Agrostis exarata (= A. asperifolia), Two hemiparasitic annual snapdragon family herbs Juncus xiphioides, J. lesueurii, and J. effusus var. brunneus are extinct in the salt marshes of south San Francisco were described as common in Bay Area salt marshes Bay, but occur elsewhere in the Estuary or region. The (Jepson 1911, Brewer et al. 1880, Howell 1949), al- Point Reyes bird’s-beak (Cordylanthus maritimus ssp. though they occur only very locally in Bay Area tidal palustris), a close relative of the endangered salt marsh marshes today. Other grass species, like Leymus triticoides bird’s beak of (C. m. ssp. maritimus), (including L. x multiflorus), are presumed to be former was formerly found almost throughout San Francisco marsh edge dominants based on relict occurrences at Bay. It is now restricted to very few populations in the intact lowland tidal marsh edges (e.g., Rush Ranch, Central Bay, with small remnant populations probably Point Pinole) and colonizing behavior on levees which persisting in Petaluma Marsh and near Gallinas Creek, have not been maintained (Dutchman Slough and Mare Marin County. The remaining San Francisco Bay popu- Island, San Pablo Bay). The salt marsh grass Puccinelia lations of Marin County are typically showier (usually nutkaensis, in contrast, occurred in periodically inun- more conspicuous, rosy purple flowers and purplish dated middle salt marsh zones in the South Bay as well herbage) than most of the core populations of Point as on levees (Thomas 1961). It is rarely found in San Reyes, which typically have gray-green foliage and white- Francisco Bay today, such as near Ravenswood, Palo Alto and-maroon flowers. Another annual Snapdragon fam- and Newark. Other grasslike plants, such as Plantago ily herb, Johnny-nip or salt marsh owl’s clover (Castilleja elongata, were reported as common in Bay Area tidal salt ambigua ssp. ambigua) was formerly found in the salt marshes (Brewer et al 1880, Greene 1894) but have be- marshes of San Francisco Bay (Berkeley, Oakland, come uncommon or rare here. Other grasslike plants of Alameda, Bay Farm Island, Burlingame), but is nearly uncertain former abundance in tidal marshes, which are extinct there now. The only salt marsh population of this scarce or absent in Bay Area tidal marshes today, include colorful annual herb in the San Francisco Estuary is from Carex aquatilis var. dives, C. densa, and C. praegracilis Point Pinole, which supports a form with purple-tinged (Thomas 1961, Jepson 1911); C. praegracilis occurs in- foliage, bracts, and flowers (atypical of the subspecies frequently in tidal brackish marshes of the Suisun Marsh

Chapter 1 — Plant Communities 19 area. Sedges such as Carex subbracteata, and C. obnupta stature of S. alterniflora enables it to endure high tides would also be expected to have occurred in former salt with relatively little submersion of its foliage, even when marsh edges, as they do in other estuaries of the Cen- rooted below mean sea level. Turf-forming S. patens (salt tral Coast, especially northward. meadow cordgrass) and dwarf strains of S. alterniflora Many broadleaved herbs were also more plentiful (Daehler et al. 1999) present in the Bay may be latent

Plants along tidal marsh edges, but have become localized or invaders of salt marsh plains. The tendency for S. rare today. They include Aster lentus (Greene 1984, alterniflora pollen to swamp the pollen of the native S. Jepson 1911), a species now generally rare in any estua- foliosa and produce hybrids and introgressants threatens rine habitat; Chilean aster (Aster chilensis) (Howell 1949, to genetically assimilate the native Pacific cordgrass over Thomas 1961), a common species of non-saline habi- a significant portion of its geographic range (D. Ayers tats which has nearly disappeared from salt marsh edges and D. Strong, pers. comm. 1999). The higher densi- but persists occasionally in Suisun, Petaluma, and Napa- ties, larger plant size, and greater colonizing ability of Sonoma marshes. Salt marsh baccharis (Baccharis dou- S. alterniflora at lower tidal elevations also suggest that glasii) was formerly abundant in salt marshes (Jepson its spread may have significant geomorphic impacts on 1911) but is now uncommon to rare in brackish the Estuary, particularly on channel stability, sedimen- marshes, mostly in the North Bay (Best et al. 1996, Tho- tation, and mudflat colonization, and their indirect ef- mas 1961). Two species which were inferred by Coo- fect on wildlife habitat (Grossinger et al. 1998). per (1926) to be major elements of his reconstructed Lepidium latifolium invasion is particularly a con- “ willow-composite” community at South Bay salt marsh cern for the conservation and recovery of rare or endan- edges, slim aster (Aster subulatus var. ligulatus), and gered plant species of the San Francisco Estuary, most spikeweed (Hemizonia pungens var. maritima) are now of which occur in the high marsh zone where L. latifo- scarce in tidal marshes, and occur mainly in the North lium is dominant. L. latifolium actively encroaches on Bay (Best et al. 1961; B. Grewell, pers. obs. 1997). Other populations of endangered Cordylanthus mollis ssp. mollis spikeweeds, H. parryi sspp. parryi and congdonii, were and Cirsium hydrophilum var. hydrophilum in Suisun locally common in the South Bay salt marshes (Munz Marsh (B. Grewell, pers. obs. 1998) and Southhampton 1959), but are generally rare today. Species that were Bay (P. Baye, pers. obs. 1998). The impact of exotic plant formerly frequent in North Bay brackish and salt marshes invasions in the high marsh zone is magnified by the trun- (Greene 1894) include morning-glory (Calystegia sepium cation and degradation of this habitat by widespread dik- var. limnophila) and sea-milkwort (Glaux maritima), ing, which compresses the high marsh zone into a relatively which are now uncommon to rare. Other herbs which invariant, steep slope of disturbed Bay mud. have historically declined to a significant extent in fre- Tidal Marsh Restoration Design – Tidal marsh quency, distribution, and abundance in Bay Area tidal restoration in the San Francisco Estuary has convention- marshes and their edges include Hutchinsia procumbens (Greene 1894, Thomas 1961), tidy-tips, Layia chrysanthemoides (Howell 1949, Thomas 1961), native annual peppercress species Lepidium dictyotum, L. latipes, and L. oxycarpum (Thomas 1961, Munz 1959, Howell 1949, Greene 1894), salt marsh fleabane, Pluchea odorata (Jepson 1911), and butterweed, Senecio hydrophilus (Greene 1894, Jepson 1911).

Conservation Issues

Exotic Plants – There are many exotic plants that have become established within, or along the edges of, the San Francisco Estuary, but only a few are aggressive invaders that have become widespread and dominant, or threaten to do so (Grossinger et al. 1998). Of these, Le- pidium latifolium, Spartina alterniflora (and hybrids), and Salsola soda have demonstrated ability for rapid, exten- sive invasion and development of monodominant stands in the San Francisco Estuary. Spartina densiflora, an ex- otic cordgrass from Chile with a bunchgrass growth Peter Baye habit, has become a dominant species in Humboldt Bay, Invasive exotic Lepidium latifolium (background) looms over the endangered Cordylanthus mollis ssp. and is expected to be able to achieve the same dominance mollis at the high marsh edge. (brackish tidal marsh, if its spread is unchecked in San Francisco Bay. The taller Southampton Marsh, Benecia.)

20 Baylands Ecosystem Species and Community Profiles ally been designed for wildlife species, treating plants Many natural resource agencies are cautious about only as habitat for wildlife species rather than as the restoration and reintroduction of rare plants, probably

subject of restoration aims. Restoration designs have because this has conventionally been considered in a Plants generally afforded little or no consideration for soils or mitigation context (Berg 1996). Restrictive generalized slopes of the high marsh zone, variations in sediment policies on geographic specificity of reintroduction to texture, surface or subsurface freshwater flows, and varia- documented historic localities, regardless of natural tem- tion in incident wave energy that influence the microen- poral and spatial scales of plant population dynamics and vironmental variables which are significant for plant di- ecosystem processes, in some cases has narrowed oppor- versity. Highly managed estuarine wetlands (e.g., tunities for re-establishment of rare plants (White 1996). artificial salt ponds, extremely microtidal or non-tidal salt In situations where the range of rare plants is extremly marshes) generally support an artificially low diversity of reduced, historic collection data are sparse and vague native tidal marsh plant species. Plans for rare tidal marsh (which is generally the case), and relatively few poten- plant reintroduction have only recently been proposed tial source populations for founders exist, an experimen- (e.g., Pier 98, ; , tal approach may be most appropriate for reintroduction Presidio/Golden Gate National Recreation Area), and planning. Successful reintroduction will likely require none has yet been implemented. Of the rare plant refu- much replication over years (variable climate conditions) gia in relict tidal marshes of the Estuary (e.g., Hill and at many localities. Caution is appropriate, however, Slough, Fagan Marsh, Rush Ranch, Peytonia Slough, when the taxonomic interpretation or population vari- and Whittell Marsh), none has site-specific rare plant ability is at issue when determining suitable populations management plans or programs, despite imminent for reintroduction. threats by invasive species. There is no Estuary-wide Artificial Salinity Manipulation – In Suisun program to survey and map rare plant species popula- Marsh, salinity control gates on Montezuma Slough were tions; plant inventories are biased towards species with installed to enforce standards for salinity based on the special legal status, and are typically driven by environ- perceived needs of waterfowl marsh management in mental impact assessment for projects rather than re- diked wetlands, aimed at maintaining low channel wa- gional conservation. Other surveys consist of voluntary ter salinity. The impacts of sustained low marsh salinity and opportunistic reports. Conservation of plant diver- on the progression of exotic plant invasions and the natu- sity in the Estuary will require both active protection ral dynamics of brackish tidal marsh vegetation (particu- of remnant rare plant refugia, active management of larly rare and endangered species) were not considered conserved areas, systematic inventory of the Estuary’s in the design and operation of the salinity control gates, botanical resources, and large-scale, scientifically and no long-term monitoring of rare plant populations sound tidal marsh restoration and reintroduction during gate operation was authorized. The reduction of projects. periodic high salinity events during drought cycles, and

Pioneer plants (1st year seedling) of native Spartina foliosa and Salicornia virginica colonize the well-consoli- dated upper mudflats bayward of the marsh edge at Mare Island, eastern San Pablo Bay. The erosional scour pools and drainages adjacent to the plants indicate the relatively hight wave energy estuarine environ- ment in which they are able to establish, given stable microhabitats. Peter Baye

Chapter 1 — Plant Communities 21 the subtle changes in tide elevations caused by gate op- sion threatens to encroach into restorable former tidal eration, could potentially have significant adverse long- marsh sites. Single-purpose management of other diked term impacts on rare plant persistence. Scientific inves- wetland types at large scales (salt production, waterfowl tigations of the effects of gate operation on plant production) also restricts opportunities for tidal marsh communities and rare plant populations of Suisun tidal plant community restoration. Large-scale tidal marsh

Plants marshes are urgently needed, as recommended by the restoration near centers of relict tidal marsh plant popu- Brackish Marsh Subcommittee of the Suisun Ecologi- lations (e.g., Cullinan Ranch, Hamilton Airfield, Red- cal Workshop (CWRCB 1999). wood Landfill, and Skaggs Island) offer some hope for In the South Bay, perennial urban wastewater dis- long-term recovery of tidal marsh plant species in decline. charges in confined, diked tidal sloughs have caused con- version of salt marsh to brackish marsh (Harvey and As- Conclusions and Recommendations sociates 1997). The Alviso and Milpitas area marshes were the sites of historic rare plant populations (Table The San Francisco Estuary tidal marshes are poorly un- 1.3) which could not be re-establish naturally or be re- derstood in terms of modern and historic plant species introduced in marsh vegetation dominated by perennial composition, the dynamics of the vegetation, and the pepperweed, bulrushes and tules which are stimulated interaction between vegetation and geomorphic and hy- by augmented and confined freshwater flows and el- drologic processes. Many plant species have become ex- evated nutrient concentrations throughout the growing tirpated or nearly so with little or no attention from season. botanists or ecologists, and many more species have de- Loss of Restorable Habitat – Economic clined significantly. The Estuary’s historic and modern to convert diked Baylands to land uses that are incom- flora is considerably richer than has been generally rec- patible with potential tidal marsh restoration over large ognized. Further attrition of native plant diversity in the contiguous tracts (particularly in connection with up- Estuary is likely because of the uncontrolled spread of lands and alluvial areas) remains high today. Develop- invasive exotic plants, and insufficient planning, man- ments in diked Baylands for extensive housing (Redwood agement, and restoration of the Estuary’s plant commu- Shores, San Mateo County), golf courses (Black Point, nity. Carefully designed tidal marsh restoration Marin County), business parks (old Fremont Airport, projects that promote native plant species diversity Alameda County) have proceeded into the 1990s, and and recovery are needed to conserve the Estuary’s other large scale land use conversions for dredged mate- flora. Recommendations for the conservation of the rial disposal and rehandling (Napa salt crystallizers) have Estuary’s plant communities are presented in the been considered. The largest tracts of undeveloped diked Baylands Ecosystem Habitat Goals Report (Goals Baylands are in San Pablo Bay, where vineyard expan- Project 1999, Appendix A). Peter Baye An example of marsh progradation — Seedling plants of Salicornia virginica and Spartina foliosa are frequently comingled without clear zonation, as in these exceptionally firm upper mudflats in eastern San Pablo Bay. (Mare Island, north of the jetty)

22 Baylands Ecosystem Species and Community Profiles Table 1.3 Historic Changes in the Distribution and Abundance of Selected Native Vascular Plant Species Occurring in Tidal Marshes of the San Francisco Estuary

Taxon Historic References Contemporary Distribution

Agrostis exarata Trin. Jepson 1911: Common in the San Not currently reported from tidal Francisco Bay region in salt marshes marsh ecotone in San Francisco Bay [A. asperifolia Trin.] and other wet places: Berkeley… San Estuary, but common and wide- Francisco; Martinez.” spread in non-tidal moist habitats [Hickman et al. 1993].

Armeria maritima (Miller) Willd. Greene 1894: “ Along sandy beaches Apparently extirpated in San Fran- in wet ground…” cisco Bay Estuary; otherwise restricted ssp. californica (Boiss. ) Pors. Jepson 1911: “ common on the sandy to maritime coastal salt marshes, [Armeria vulgaris Willd.] beaches or fields near the sea… or dunes, bluffs. [Statice armeria L.] about San Francisco Bay.”

Aster chilensis Nees. Cooper 1926: [presumed species of Few current reports known from reconstructed “ willow-composite” edges of San Francisco Bay or San community at salt marsh edges, Palo Pablo Bay tidal marshes; local in Alto vicinity] Suisun Marsh edges. Presumed rare Howell 1949: [Marin Co.] Common from tidal marshes. and widespread from salt marshes and coastal swales to low valleys…” Thomas 1961: “… edges of salt marshes…”

Aster lentus E. Greene Greene 1894: [A.c. var. lentus] “ Plen- Rare; restricted primarily to Suisun tiful along tidal streams in the west- Marsh. Some herbarium collections [A. chilensis Nees. var. lentus Jepson] ern part of the Suisun Marsh…” known from San Francisco Estuary [A. chilensis var. sonomensis (E. Greene) [A. c. var. sonomensis ]“ In open prior to 1960 (Berkeley, Alviso, Napa). Jepson] plains of the , in low Recent status uncertain in San Pablo subsaline ground.” Bay area tidal marshes. Jepson 1911: [A.c. var. lentus]“ very common and conspicuous in the Suisun Marshes.” [A. c. var. sono- mensis] “ subsaline lands: Petaluma, Napa” Munz 1959: [A.c. var. sonomensis]: Coastal Salt Marsh; saline ground around San Francisco Bay. Sonoma, Napa…”

Aster subulatus Michaux Behr 1888: [A. divaricatus] “ Salt No current reports known from edges marshes.” of San Francisco Bay . Uncommon var. ligulatus Shinn. Greene 1894: “ Borders of Suisun Marshes to rare in San Pablo Bay and Suisun [Aster exilis Ell.] and elsewhere on subsaline land” tidal marshes. [Aster divaricatus Nutt.] Jepson 1911: “ Saline soil, not com- mon … .Alvarado.” Cooper 1926: [presumed species of reconstructed “ willow-composite” community at salt marsh edges, Palo Alto vicinity] Thomas 1961: “ Salt marshes along San Francisco Bay and occasionally elsewhere. San Francisco, Palo Alto, Alviso…”

Astragalus tener Gray Jepson 1911: “ Alkaline fields, mostly Recently rediscovered near historic in moist places.” Bay edge in Fremont, Alameda var. tener Thomas 1961: Known locally only County. Known in region from alkali from saline areas along San Francisco vernal pools, Solano County. Bay. San Francisco and Mayfield.”

Chapter 1 — Plant Communities 23 Table 1.3 (continued) Historic Changes in the Distribution and Abundance of Selected Native Vascular Plant Species Occurring in Tidal Marshes of the San Francisco Estuary

Taxon Historic References Contemporary Distribution

Atriplex californica Moq. Greene 1894: “… along the edges of Extirpated in San Francisco Bay Estu- salt marshes, from near San Fran- ary margins. Small relict populations cisco and Alameda, southward.” occur on bluffs of Golden Gate in Jepson 1911: “ Sandy beaches along San Francisco. Maritime salt marsh the ocean and about San Francisco populations occur at Limantour Bay.” Estero and Tomales Bay (Marin Co.).

Baccharis douglasii DC. Jepson 1911: “… abundant in the salt Now uncommon to rare in alluvial marshes about San Francisco Bay.” high marsh and upland ecotone, Thomas 1961: [SW San Francisco Bay] San Pablo Bay area and and Suisun “… occasionally along the edges of Marsh; one colony occurs along salt salt marshes… Alviso…” pond edge at a seep in Coyote Hills, Alameda Co., possibly rare else- Best et al. 1996: “ Uncommon. Damp where in San Francisco Bay. thickets, salt marshes.”

Carex aquatilis Wahlenb. Brewer et al. 1880: “ In salt marshes, No current reports known from edges about San Francisco Bay of San Francisco Bay or San Pablo var. dives (Holm) (Bolander)…” Bay tidal marshes. Presumed rare or [C. sitchensis Prescott] Jepson 1911: “ Salt-marshes about extirpated from tidal marshes. San Francisco Bay and northward along the coast” . Munz 1959: “ Rare, swampy places, usually near the coast…”

Carex densa Bailey Jepson 1911: [C. b. var. densa] “ Salt No current reports known from edges marshes near San Francisco…” of San Francisco Bay or San Pablo [C. brogniartii Kunth. var. densa Bay tidal marshes. Presumed rare or Bailey] extirpated from tidal marshes.

Carex praegracilis W. Boott Thomas 1961: “ Boggy areas along Rare in Suisun area tidal marshes, the edges of salt marshes; San Fran- west to Southampton Bay. Common [Carex Douglasii var. brunnea Olney] cisco, Woodside, Mayfield…” in alkaline, moist places in California [C. usta Bailey] floristic province.

Castilleja ambigua Hook and Behr 1888: “ Marsh near Tamalpais.” Currently reported only from Point Arn. Greene 1894: “ Common along the Pinole salt marsh and pan edges; other historic records at Greenbrae, [Orthocarpus castillejoides Benth.] borders of salt marshes.” Tamalpais (Mill Valley), Hamilton Jepson 1911: “ Marshy ground near Field, Burlingame, Oakland. Halo- the coast. Alameda; W. Berkeley; phytic populations rarely occur in Napa Valley; Sonoma Co.” brackish marsh and salt marsh at Howell 1949: “ low ground along the Rodeo Lagoon, Tomales Bay, upper reaches of the salt marshes, Drakes Estero, Limantour Estero occasional:..Mount Tamalpais; Green- (maritime Marin Co. marshes) brae Marshes; Hamilton Field…”

Centaurium trichanthum Howell 1949: “ in typical form… known No current reports known from edges (Griseb.) Robinson in Marin only from low ground bor- of estuarine tidal marshes. Similar dering the salt marsh near Burdell species C. muehlenbergii occurs in [Erythrea trichantha (Griseb.)] Station” . subsaline diked wetlands, Napa- Munz 1959: “ Moist often saline Sonoma marsh, and tidal marsh places… edge of Coastal Salt Marsh… edge at China Camp. San Mateo Co. to Siskyo Co.”

24 Baylands Ecosystem Species and Community Profiles Table 1.3 (continued) Historic Changes in the Distribution and Abundance of Selected Native Vascular Plant Species Occurring in Tidal Marshes of the San Francisco Estuary

Taxon Historic References Contemporary Distribution

Calystegia sepium (L.) R.Br. Greene 1894: “ Plentiful in brackish Occasional in Suisun Marsh area marshes toward the mouth of the west to Southhampton Bay; rare in ssp. limnophila (E. Greene) Napa River and about Suisun Bay; its San Pablo Bay edges. Brummit roots within reach of tide water; its [Convolvulus sepium L.] stems twining upon rushes and sedges. Munz 1959: “ Occasional in swampy saline places; Coastal Salt Marsh; Marin, Solano and Contra Costa Cos.”

Cicuta maculata L. Jepson 1911: “ Suisun marshes, abun- Uncommon to rare in Suisun Marsh; dant and conspicuous.” not currently reported elsewhere in var. bolanderi (S. Watson) the Estuary. Mulligan Munz 1959: “ Salt marshes, Marin to Solano and Contra Costa cos.” [Cicuta bolanderi Watson]

Cirsium hydrophilum (E. Greene) Jepson 1911: “ Suisun marshes” Extremely rare (federally endan- gered) in Suisun Marsh. Jepson var. hydrophilum Munz 1959: “ Brackish marshes about Suisun Bay” . [Carduus hydrophilus Greene]

Cordylanthus maritimus Benth. Brewer et al. 1880: “ Sandy salt- Currently reported only from Rich- marshes along the coast, from San ardson Bay, Greenbrae, and Pet- ssp. palustris (Behr) Chuang and Francisco Bay to .” aluma marsh (Marin Co.). Recently Heckard Behr 1888: “ Salt marshes, San Fran- reported from Gallinas Creek area [Cordylanthus maritimus Nutt.] cisco.” marsh. Extirpated in central and [Adenostegia maritima (Nutt.) southern San Francisco Bay. Major Greene] Greene 1894: “ Sandy salt marshes populations occur in maritime tidal from near San Francisco southward.” salt marshes of Tomales Bay, Bolinas Jepson 1911: ‘Salt marshes near the Lagoon, and Limantour Estero (Marin coast from San Francisco Bay south…” Co.). San Francisco Estuary popula- Howell 1949: “ Salicornia flats in salt tions have purplish foliage, and rosy, marshes along the bay..:.Almonte, well-exerted inflated flowers. Greenbrae…” Thomas 1961: “ Salt marshes along the borders of San Francisco Bay; San Francisco, Redwood City, Palo Alto, and near Alviso.”

Cordylanthus mollis Gray Brewer et al. 1880. “ Salt-marshes of Rare (federally endangered): local San Francisco Bay, at Mare Island in tidal brackish marsh around Napa ssp. mollis and Vallejo, C. Wright, E.L. Greene.” River, Carquinez Straits tidal marsh, Behr 1888: “ Salt marshes. Vallejo.” Suisun Marsh area. Presumed extir- pated in Petaluma River marshes. Greene 1894: “ Brackish marshes Putative San Francisco (city) record about Vallejo and Suisun.” is erroneous interpretation of early Howell 1949: [Marin Co.] “… San San Francisco Bay Area collection Rafael, acc. Ferris; Burdell Station, acc. L. Heckard. San Antonio Creek… .” Best et al. 1996: [Sonoma Co.]: Rare, estuarine… Petaluma Marsh be- tween San Antonio and Mudhen Slough… (1978)…”

Downingia pulchella (Lindley) Jepson 1901: “… Abundant and of Extirpated in Union City. Occurs in Torrey rank growth in salt marshes near alkaline/saline vernal pools at Warm Alvarado [Union City]” . Springs, Fremont, Alameda Co., and [Bolelia pulchella E. Greene] Munz 1959: “… Coastal Salt Marsh.” in some diked baylands near Fairfield, Solano Co.

Chapter 1 — Plant Communities 25 Table 1.3 (continued) Historic Changes in the Distribution and Abundance of Selected Native Vascular Plant Species Occurring in Tidal Marshes of the San Francisco Estuary

Taxon Historic References Contemporary Distribution

Eleocharis parvula (Roemer [not reported in early floras; Munz Rare in brackish tidal marshes of San and Shultes) Link 1959 reported only from coastal salt Pablo and Suisun Bay area. Local in marshes of San Luis Obispo and diked baylands, lower Napa River. Humboldt Cos.]

Festuca rubra L. [reported only from generalized Not currently reported from San Fran- habitats in early floras; halophytic cisco Bay estuarine tidal marsh edges; populations not distinguished. Specu- halophytic populations presumed lative likely component of historic extirpated. Halophytic populations sandy salt marsh edges of Central occur along edges of maritime salt Bay.] marsh and brackish marsh at Rodeo Lagoon, Limantour Estero, Tomales Bay (Marin Co).]

Glaux maritima L. Behr 1888: “ Salt marshes.” Few recent reports known from San Greene 1894: “ Frequent both along Francisco Bay or San Pablo Bay salt the seabord and in subsaline soils in marshes; reported as infrequent in the interior” Petaluma Marsh; local in tidal marsh near mouth of Tolay Creek, Sonoma Jepson 1911: “ Marshy shores of … Co.; occasional to locally frequent in San Francisco and Suisun bays.” Suisun Marsh area and Fagan Slough Howell 1949: [Marin Co.] “ salt (Napa River). marshes… Burdell…” Thomas 1961: “… Palo Alto, but ex- pected elsewhere in salt marshes” Atwater et al. 1979: [recorded as present in San Pablo Bay] Best et al. 1996: [Sonoma Co.] “ Rare, salt marshes: Petaluma, Davy (1893 UC).”

Heliotropium curassavicum L. Howell et al. 1958: “ salt marsh near No current reports known from San Visitacion Valley [southeastern San Francisco Bay. Recently reported Francisco].” from Suisun Marsh area.

Hemizonia pungens (Hook Greene 1894: “ Borders of salt Local, infrequent species along tidal and Arn.) Torrey and A. Gray marshes about San Francisco Bay.” marsh edge around the San Fran- cisco Estuary. ssp. maritima (E. Greene) Cooper 1926: [dominant species of reconstructed “ willow-composite” [Centromadia maritima Greene] community at salt marsh edges, Palo Alto vicinity.]

Hemizonia parryi E. Greene Munz 1959: [ ssp. congdonii] “ Locally No current reports known from San common… s. end of San Francisco Francisco Bay Estuary tidal marsh ssp. parryi, ssp. congdonii Bay, mostly Alameda Co.” [ssp. edges. Rare. (Robinson and Greenman) Keck parryi] “ Coastal Salt Marsh… to N. San Mateo Co…” [not reported from salt marsh in Jepson 1901, Greene 1894)

Hutchinsia procumbens (L.) Greene 1894: “ Borders of salt No current reports known from San Desv. marshes.” Francisco Bay Estuary tidal marsh edges. Occurs in high marsh eco- [Bursa divaricata (O. Ktze) Nutt.] Jepson 1911: Alkaline soil from tone of central CA coast salt marsh, [Capsella divaricata Walp.] Vallejo (acc. Bot. Cal.), Alameda…” and in other alkaline or subsaline [Capsella procumbens Fries.] Thomas 1961: Known locally from habitats in California floristic prov- [Capsella elliptica C.A. Mey.] saline areas along San Francisco ince. [Lepidium procumbens L.] Bay; Palo Alto and Mayfield.” [Hutchinsia californica, H. desertorum A. Davids]

26 Baylands Ecosystem Species and Community Profiles Table 1.3 (continued) Historic Changes in the Distribution and Abundance of Selected Native Vascular Plant Species Occurring in Tidal Marshes of the San Francisco Estuary

Taxon Historic References Contemporary Distribution

Juncus effusus L. var. Brewer et al. 1880: “… common in the Rare, local at edges of salt marsh salt-marshes about San Francisco and brackish marsh ecotones in San brunneus Engelm. Bay…” Pablo Bay (China Camp). No known Brandegee 1892: “ Salt marshes about reports from San Francisco Bay tidal the bay shore.” marshes. Jepson 1911: “ Common in marshy ground: Monterey to San Francisco and Bolinas Bays and northward.” Howell 1949: “ Swamps and swales generally near the ocean… Tiburon; Sausalito…” Thomas 1961: “ Usually along or near the coast… Palo Alto, near Alviso…”

Juncus lesueurii Boland. Brandegee 1892: “ Salt marshes at Apparently associated with sandy Visitacion Bay. South San Francisco.” salt marsh edges of maritime coast. Howell 1949. “ Common along the Intermediates with J. balticus not upper reaches of salt marshes… uncommon in San Francisco Bay Tiburon; Tamalpais Valley… . In Marin Area tidal marshes; difficult to sepa- County,… [J. balticus] is not readily rate. Rare in south San Francisco Bay distinguished from J. Leseurii… ]” tidal marshes; one colony in seep at salt pond edge, Coyote Hills.

Juncus xiphioides E. Meyer Jepson 1901: “ A common species of Not recently reported; presumed salt marshes… Berkeley; Belmont… rare or possibly extirpated in most Suisun Marshes…” tidal salt marshes of San Francisco Thomas 1961: “ Occasional in sloughs Estuary. … Palo Alto, nr. Alviso…”

Lasthenia glaberrima D.C. Behr 1888: “ Near salt marshes.” No other reports, historic or current, are known from San Francisco Bay estuarine marshes.

Lasthenia conjugens E. Greene Greene 1894: “ Subsaline soil near Occurs in alkaline/saline vernal pools Antioch…” bordering salt pond 22 in Fremont, [Baeria fremontii (Torr.) A. Gray in Alameda Co., and in diked bay- part] Jepson 1911: “ Subsaline fields in the Bay region; Antioch; Newark, etc.” lands at upper end of Hill Slough (Potrero Hills), Solano Co. Historic localities near Mt. Eden along bay shore and near Newark. Rare; feder- ally endangered.

Lasthenia platycarpha (A. Greene 1894: “ Border of salt marsh Historic locality at Redwood City Gray) E. Greene north of Vallejo: rare or local.” shoreline. Apparently extirpated from San Francisco Bay estuarine [Baeria carnosa E. Greene] Jepson 1911: “ Salt marshes at Vallejo marshes. Occurs infrequently in [B. platycarpha A. Gray] (Greene).” alkaline vernal pools, Solano Co.

Lasthenia glabrata Lindley ssp. Behr 1888: “ Common.” Currently reported within San Fran- glabrata Greene 1894: “ Borders of salt marshes cisco Bay Estuary only from Point only; not common.” Pinole (Whittell marsh) salt marsh and new seeded levee slope at Jepson 1911: “ Borders of salt marshes.” Sonoma Baylands. Many historic salt Thomas 1961: Edges of salt marshes marsh collections known from Bur- along San Francisco Bay… Millbrae… dell, Alvarado, Mt. Eden, Alameda, Belmont, Redwood City, Mayfield.” Mowry’s Landing, Denverton. Mari- time salt marsh population occurs in Limantour Estero, Marin Co.

Chapter 1 — Plant Communities 27 Table 1.3 (continued) Historic Changes in the Distribution and Abundance of Selected Native Vascular Plant Species Occurring in Tidal Marshes of the San Francisco Estuary

Taxon Historic References Contemporary Distribution

Lasthenia minor (DC.) Ornd. Brandegee 1891: “ About the borders Apparently extirpated from San of marshes, Islais Creek, Visitacion Francisco Bay estuarine marshes. [Baeria minor (DC.) Ferris Valley, Presidio, South San Fran- [Baeria uliginosa Nutt.] cisco.” [Lasthenia uliginosa (Nutt.) E. Greene]

Lathyrus jepsonii E. Greene var. Greene 1894: “ Suisun marshes.” Occasional to rare in Suisun Marsh. Also occurs locally in tidal brackish jepsonii Jepson Jepson 1911: “ Suisun marshes.” marshes along Napa River (Dutch- man Slough). May be under-reported in drought years.

Layia chrysanthemoides (DC.) Howell 1949: “ Locally common on No current reports known from San A. Gray flats bordering the salt marshes: Francisco Estuary tidal marsh edges. Ignacio;… Chileno Valley.” [Blepharipappus chrysanthemoides Greene] Thomas 1961: “ occasionally in low alkaline soils of San FranciscoBay… Millbrae, Redwood City.”

Leymus triticoides (Buckley) [general grassland habitats reported Occurs locally (abundant) at salt Pilger historically. Presumed abundant or marsh edges at Newark, Alameda dominant species of historic tidal Co.; Rush Ranch, Solano Co; Peta- [incl. Leymus X multiflorus (Gould) marsh edges.] luma Marsh, Marin Co.; China Camp, Barkworth and D.R. Dewey Marin Co.; Dutchman Slough, Solano [Elymus triticoides Buckley] Co.

Lepidium dictyotum A. Gray Greene 1894: “ Along the borders of No current reports known from San marshes at Alameda.” Francisco Bay tidal marsh edges. Presumed extirpated or rare in Estu- ary.

Lepidium latipes Hook. Greene 1894: “ in saline soil at No current reports known from San Martinez, Alameda, etc.” Jepson Francisco Bay tidal marsh edges. 1901: “… alkali flats… Martinez…” Reported rarely in diked baylands and tidal marsh edges, Solano Co. (Suisun Marsh area).

Lepidium oxycarpum Torrey Greene 1894: “ Borders of salt marshes No current reports known from San and A. Gray at Vallejo… also in subsaline soils… Francisco Bay tidal marsh edges. near Alameda.” Rare, Suisun Marsh edges. Howell 1949: “ A rare peppercress of alkaline valley floors and of saline flats adjacent to coastal salt marshes, in Marin Co. known only from low pas- tures bordering San Francisco Bay near Novato.” Munz 1959: “ V. Grassland and edge of Coastal Salt Marsh; largely about San Francisco Bay…” Thomas 1961: “ Saline and alkaline flats along San Francisco Bay and Santa Clara Valley: Redwood City, Cooley’s Landing, Palo Alto, May- field…”

Lilaeopsis masonii Mathias and Jepson 1911: [ as L. lineata, in part] Rare in tidal brackish tidal marshes, Constance “ Salt marshes or brackish mud flats:… Napa Marsh, Suisun Marsh area, to Port Costa to Antioch; Robert’s Is- Tolay Creek, San Pablo Bay. Uncom- [Lilaeopsis lineata (Michx.) Greene, land” . mon in western in part delta fresh-brackish marshes.

28 Baylands Ecosystem Species and Community Profiles Table 1.3 (continued) Historic Changes in the Distribution and Abundance of Selected Native Vascular Plant Species Occurring in Tidal Marshes of the San Francisco Estuary

Taxon Historic References Contemporary Distribution

Lycopus asper E. Greene Jepson 1911: “ Salt marshes: Suisun; No current reports known from San Benicia; San Francisco.” Francisco tidal marsh edges; pre- [Lycopus lucidus Turcz. ] sumed rare or extirpated in Estuary [L. lucidus Benth. misapplied] Hickman et al. 1993: Uncommon. Moist areas, marsehs, streambanks… there. Deltaic GV, SnFrB, GB; to w Can, Great Plains.

Plagiobothrys glaber (A. Gray) Jepson 1911: “ Alvarado [Union City], Hickman 1993: “ PRESUMED EXTINCT. I.M. Johnston margin of salt marshes.” Wet, alkaline soils in valleys, coastal marshes… CCo, s SnFrB… Perhaps a [Allocarya salina Jepson] Munz 1959: “ Coastal Salt Marsh; s. var. of P. stipitatus.” [Allocarya glabra Macbr.] shore of San Francisco Bay…”

Plagiobothrys mollis (A. Gray) Jepson 1911: Petaluma, Congdon, Hickman 1993: “ PRESUMED EXTINCT. 1880; not since collected. Wet sites in grassland, possibly I.M. Johnston var. vestitus coastal marsh margins…” (E. Greene) I.M. Johnston [Allocarya mollis A. Gray var. vestita E. Greene [A. vestita E. Greene]

Plagiobothrys stipitatus (E. Best et al. 1996: “ salt marsh near Reported at Sonoma Baylands, high Sears Point, Keck 1935” tide line, 1996. Otherwise no current Greene) var. stipitatus reports known from San Francisco Estuary tidal marsh edges

Plantago elongata Pursh Brewer et al. 1880: “ Salt-marshes, San Rarely reported from San Francisco [Plantago bigelovii Gray] Pablo Bay, at Benicia and Vallejo, Bay Area high tidal marshes (Suisun Bigelow, E.L. Greene.” Marsh). No recent localities in tidal Greene 1894: “ Borders of saline or marsh edges confirmed. brackish marshes; quite common about the Bay…” Howell 1949: [Marin Co.; not reported from estuarine stations] Thomas 1961: [SW San Francisco Bay] “… edges of salt marshes… Mayfield, Alviso… ] Best et al. 1996: [Sonoma Co.] “ un- common, salt marshes… Petaluma, Congdon (1880); 5 mi. n. of Sear’s Point, Rubzoff (1970).

Plantago maritima L. Greene 1894: “… sandy salt marshes” Infrequent to rare in San Francisco Bay tidal marshes, mostly Richardson [P. maritima L. ssp. juncoides (Lamk.) Jepson 1911: “… West Berkeley…” Bay. Relatively common in maritime Hulten, P. juncoides Lamk. Howell 1949: [Marin Co.] “ occasional salt marshes, and occaisional in var. juncoides] in salt marshes bordering the bay or Suisun Marsh (Hill Slough). ocean: Almonte…” Thomas 1961: “ occasional in salt marshes and on coastal bluffs as far south as San Mateo County: San Francisco, Redwood City, and Mayfield.” Best et al. 1996: [Not reported from estuarine Sonoma Co. stations.]

Chapter 1 — Plant Communities 29 Table 1.3 (continued) Historic Changes in the Distribution and Abundance of Selected Native Vascular Plant Species Occurring in Tidal Marshes of the San Francisco Estuary

Taxon Historic References Contemporary Distribution

Pluchea odorata (L.) Cass. Behr 1888: Salt marshes. No current reports known from San Francisco or San Pablo Bays; uncom- [P. camphorata (L.) DC. and Greene 1894: “ Borders of brackish mon in Suisun marshes. P. purpurascens (Sw.) DC. misap- marshes about Suisun Bay, etc.” plied ] Jepson 1911: “ Common in the salt marshes about Suisun and San Fran- cisco Bays…” Howell 1949: [Marin Co.; not cited] Thomas 1961: [SW San Francisco Bay; not cited]

Puccinelia nutkaensis (J.S. Thomas 1961: “ levees and salt marsh Rare, local, south San Francisco Bay. Presl.) Fern. and Weath. along San Francisco Bay” . No records of San Pablo Bay collec- tions in Howell 1949, Best et al. 1996. [P. grandis Swallen]

Pyrrocoma racemosa (Nutt.) Greene 1894: “ A somewhat rare No current reports known from San plant of subsaline soils at Calistoga Francisco Bay high tidal marsh. Pre- Torrey and A. Gray var. racemosa and near San Jose.” sumed extirpated in San Francisco [Haplopappus racemosa (Nutt.) Thomas 1961: “ edges of salt marshes, Bay. Torr.; P. elata E. Greene] saline soils, and occasionaly dis- turbed areas. Cooley’s Landing, Near Alviso, Agnews, and San Jose.”

Rumex occidentalis S. Watson Greene 1894: “ Frequent in marshy Infrequent to rare in North Bay, Suisun places.” Marsh area brackish tidal marshes. [R. fenestratus E. Greene] Jepson 1911: “ Marshes bordering San Francisco Bay.” Munz 1959: “ Coastal, often brackish marshes, San Francisco Bay…” Hickman et al. 1993: “ Uncommon. wet +/- salty places.”

Salicornia subterminalis Parish [Not reported from estuarine stations Local, rare in South Bay, south Fre- in early floras.] mont, Milpitas (in diked wetlands, [Arthrocnemum subterminale (Par- former Fremont Airport), and at Hill ish) Standley] Slough, Suisun Marsh.

Sanicula maritima Wats. (S. Behr 1888: “ Alameda marshes.” Extinct in San Francisco Bay; known maritima Kellogg) Greene 1894: “ In lowlands adjacent from fewer than 10 stations in 1988, to salt marshes near Alameda, San Monterey and San Luis Obispo Francisco, etc.” Counties. Jepson 1911: “ Local species of low and wet adobe lands in the vicinity of salt marshes bordering San Fran- cisco Bay; near Alameda… and Potrero Hills, San Francisco, the only recorded localities.”

Senecio hydrophilus Nutt. Brewer et al. 1880: “… salt marsh at Apparently extirpated in San Fran- Vallejo (Greene)…” cisco, San Pablo Bay (incl. Peta- Greene 1894: “ Brackish marshes; luma R.); infrequent but locally formerly plentiful at West Berkeley, common in Suisun Marsh area and and on the lower Napa River; still tidal marshes; possi- abundant in the Suisun marshes.” bly Napa R..” Jepson 1911: Abundant in the Suisun Hickman 1993: “ Reduced from wet- Marshes and found in other marshes land development.” about San Francisco Bay”

30 Baylands Ecosystem Species and Community Profiles Table 1.3 (continued) Historic Changes in the Distribution and Abundance of Selected Native Vascular Plant Species Occurring in Tidal Marshes of the San Francisco Estuary

Taxon Historic References Contemporary Distribution

Sium suave Walter Jepson 1911: “ Suisun marshes; Stock- Rare in Suisun Marsh, primarily in wet ton” years. Recently observed near Rush [Sium cicutaefolium Gmel. Ranch, Hill Slough, and Brown’s Is- var. heterophyllum Jepson] land.

Suaeda californica Wats. Brewer et al. 1880: “ In salt-marshes Extinct in San Francisco Bay Estuary, on the coast, about San Francisco.” probably since ca. 1950. Restricted Behr 1888: “ Salt marshes on an island to one large population at Morro near Alameda.” Bay, where it occurs primarily along sandy high marsh edges. Planned for Greene 1894: “ Vicinity of sand reintroduction. Misreported occur- beaches about San Francisco Bay, rences often due to confusion with but seldom seen.” Suaeda calceoliformis, S. moquinii, Jepson 1911: “ Sandy beaches bor- Salsola soda, and Bassia hyssopifo- dering San Francisco Bay, the known lia. stations few: San Pablo Landing; Bay Farm Island.” Thomas 1961: “ Occasional in salt marshes along San Francisco Bay; San Francisco and Palo Alto.”

Solidago confinis Nutt. Jepson 1911: “ Salt marshes, San Apparently long extirpated in San Francisco Bay, Bolander [1863]. Francisco Bay Area. Occurs in brack- [S. sempervirens L. misapplied] Rarely collected. ish tidal marsh edges of Morro bay, [S. confinis var. luxurians Jepson] San Luis Obispo co.

References Behr, H.H. 1888. Flora of the Vicinity of San Fran- cisco. San Francisco, Calif. Adam, P. 1990. Salt marsh ecology. Cambridge Univ. ______. 1892. Botanical Reminiscences. Zoe 2: 2-6. Press. 461 pp. Berg, K.S. 1996. Rare plant mitigation: a policy Allison, S.K. 1992. The influence of rainfall variability on perspective.pp. 279-292. In: D. Falk, C. I. Millar, the species composition of a northern California salt and M. Olwell (eds). Restoring diversity: strate- marsh plant assemblage. Vegetation 101: 145-160. gies for reintroduction of endangered plants. Is- Atwater B.F. and C.H. Hedel. 1976. Distribution of land Press. 505 pp. seed plants with respect to tide levels and water Best, C., J.T. Howell, W.I. Knight and M. Wells. 1994. salinity in the natural tidal marshes of the north- A flora of Sonoma County. 347 pp. Calif. Native ern San Francisco Bay Estuary, California. US Geo- Plant Society. log. Survey, Menlo Park, Calif. Open File Report Brandegee, K. 1892. Catalogue of the flowering plants 76-389. 41 pp. and ferns growing spontaneously in the city of San Atwater, B.F., S.G. Conard, J.N. Dowden, C.H. Hedel, Francisco. Zoe 2: 334-383. R.L. MacDonald and W. Savage. 1979. History, Brewer, W.H., S. Watson and A. Gray. 1880. Geologi- landforms and vegetation of the estuary’s tidal cal survey of California. Botany. John Wilson and marshes. In: T.J. (ed). San Francisco Bay: the ur- Son, Cambridge, Mass. Second Edition. banized estuary. Proc. 58th Ann. Mtg. Pacific Di- Callaway, J. and M. Josselyn. 1992. The introduction v. of the American Association of the Advancement and spread of smooth cordgrass (Spartina of Science. Calif. Academy of Sciences. alterniflora) in South San Francisco Bay. Estuaries Barbour, M.G., R.B. Craig, F.R. Drysdale and M.T. 15: 218-226. Ghiselin. 1973. Coastal Ecology: Bodega Head. California Water Resources Control Board (CWRCB). Univ. of Calif. Publications. 338 pp. 1999. Suisun Ecological Workgroup Report to the Barbour, M.G. and A.F. Johnson. 1977. Beach and dune. Calif. State Water Resources Control Board. Sac- In: M.G. Barbour and J. Major (eds). 1988. Ter- ramento, Calif. restrial Vegetation of California. Calif. Native Plant Carter, R.W.G. 1988. Coastal environments. New York: Society Publication No. 9, 1030 pp. Academic Press. 617 pp.

Chapter 1 — Plant Communities 31 Chapman, V.J. 1960. Salt marshes and salt deserts of Howell, J.T., P.H. Raven and P.R. Rubtzoff. 1958. A the world. Leonard Hill - Interscience Publishers. flora of San Francisco, California. Wasmann J. of 392 pp. Biol. 16: 1-157. Cooper, W.S. 1926. Vegetational development of allu- Ingram, B.L., J.C. Ingle and M.E. Conrad. 1996. A 2000 vial fans in the vicinity of Palo Alto, California. year record of Sacramento- in-

Plants Ecology 7: 1-30. flow to San Francisco Bay Estuary, California. Cuneo, K. 1987. San Francisco Bay salt marsh vegeta- Geology 24: 331-334. tion, geography, and ecology: A baseline for use in Jepson, W.L. 1911. A Flora of middle western Califor- impact assessment and restoration planning. Ph.D. nia. Cunningham, Curtiss and Welch, San Fran- dissertation, Univ. of Calif., Berkeley. cisco. (Revised edition of 1901). 515 pp. Daehler, K. and D. R. Strong. 1994. Variable reproduc- ______. 1925. Manual of the flowering plants of Cali- tive output among clones of Spartina alterniflora fornia. Univ. of Calif. Press. 1238 pp. () invading San Francisco Bay, California: Josselyn, M. 1983. The ecology of San Francisco Bay the influence of herbivory, pollination, and estab- tidal marshes: A Community Profile. US Fish lishment site. Amer. J. Bot. 81: 307-313. Wildl. Serv. OBS-83/23, Oct. 1983. 102 pp. Daehler, K., C.K Antilla, D. R. Ayres, D.R. Strong and Macdonald K.B. 1977. Coastal salt marsh. In: M.G. J.P. Bailey. 1999. Evolution of a new ecotype of Barbour and J. Major (eds). 1988. Terrestrial veg- Spartina alterniflora (Poaceae) in San Francisco Bay, etation of California. Calif. Native Plant Society California, USA. Amer. J. Bot. 86: 543-546. Publ. No. 9, 1030 pp. Davies, J.L. 1980. Geographical variation in coastal de- ______. 1988. Supplement: coastal salt marsh. In: M.G. velopment, 2nd edition. Longman, New York. 212 Barbour and J. Major (eds). 1988. Terrestrial veg- pp. etation of California. Calif. Native Plant Society Goals Project. 1999. Baylands Ecosystem Habitat Goals. Publ. No. 9, 1030 pp. A report of habitat recommendations prepared by Munz, P.A. 1959. A California flora. Univ. of Calif. Press. the San Francisco Bay Area Wetlands Ecosystems 1681 pp. Goals Project. Joint publication of the U.S. Envi- ______. 1968. Supplement to a California flora. Univ. ronmental Protection Agency, San Francisco, Cali- of Calif. Press. 224 pp. fornia and San Francisco Bay Regional Water Qual- Newcombe, C.L. and H. Mason. 1972. An environmental ity Control Board, Oakland, Calif. 210 pp. inventory of the North Bay-Stockton ship channel Grossinger, R., J. Alexander, A. Cohen and J. Collins. area. San Francisco Bay Marine Research Center. 2 vols. 1998. Introduced tidal marsh plants in the San Pearcy R. W. and S. L. Ustin. 1984. Effects of salinity Francisco estuary: regional distribution and pri- on growth and photosynthesis of three California orities for control. San Francisco Estuary Institute, tidal marsh species. Oecologia 62: 68-73. Richmond, Calif. 52 pp. Peinado, M., F. Alcaraz, J. Delgadillo, M. De La Cruz, Greene, E.L. 1894. Manual of the botany of the region J. Alvarez and J.L. Aguirre. 1994. The coastal salt of San Francisco Bay. Cubery and Company, San marshes of California and Baja California: phytoso- Francisco. ciological typology and zonation. Vegetatio 110: 55- Grewell, B. 1993 (et seq.). Unpublished vascular plant 66. species list, Suisun Marsh. Pestrong, R. 1965. The development of drainage pat- [References continued on page 29] terns of tidal marshes. Stanford Univ. Publications Grewell, B., D. Hickson and P. Baye. 1999. SEW (Sui- in Geolog. Sciences 10: 1-87. sun Ecological Workgroup) Brackish marsh veg- Pethick, J.S. 1974. The distribution of salt pans on tidal etation subcommittee report. Report to the Cali- salt marshes. J. Biogeog. 1: 57-62. fornia State Water Resources Control Board. Sac- Peterson, D.H., D.R. Cayan, J.F. Festa, F.H. Nichols, ramento, Calif. R. A. Walters, J.V. Slack, S.E. Hager and L.E. Harvey and Associates. 1997. Marsh plant associations Shemel. 1989. Climate variability in an estuary: of south San Francisco Bay: 1997 comparative effects of riverflow on San Francisco Bay. In: D.H. study. Unpublished report to the City of San Jose. Peterson (ed). Aspects of climate variability in the H.T. Harvey and Associates, Alviso, Calif. Pacific and the western Americas. Geophys. Union. Hinde, H. 1954 . The vertical distribution of salt marsh Geophys. Monogr. 55: 41-442. phanerogams inrelation to tide levels. Ecol. Rugyt, J. 1994. Ecological studies and demographic Monogr. 24: 209-225. monitoring of soft bird’s-beak (Cordylanthus mollis Howell, J.T. 1949. Marin Flora. Univ. of Calif. Press. ssp. mollis), a California listed rare plant species 319 pp. (and habitat recommendations). Report to Calif. ______. 1969. Marin Flora Supplement. Univ. of Ca- Dept. Fish and Game, Natural Heritage Div., Sac- lif. Press. ramento, Calif. 173 pp.

32 Baylands Ecosystem Species and Community Profiles Skinner, M.W. and B.M. Pavlick. 1994. California Na- tive Plant Society’s inventory of rare and endan- Plants and Environments of

gered vascular plants of California, 5th edition. Plants CNPS Publications, Sacramento, Calif. 338 pp. Diked Baylands Thomas, J.H. 1961. Flora of the Santa Cruz Moun- Peter R. Baye tains of California. Stanford Univ. Press. 434 pp. Wells, L.E. and M. Goman. 1994. Late Holocene envi- Introduction ronmental variability in the upper San Francisco Estuary as reconstructed from tidal marsh sedi- This report focuses on wetland areas within historic tidal ments. In: C.M. Isaacs and V.L. Tharp (eds). Proc. marshes that have been isolated from tidal action by dikes 11th Ann. Pacific Climate Workshop, Technical (levees) and converted to non-tidal salt marsh, non-tidal Report 40, Calif. Dept. Water Resources, Sacra- brackish marsh, or subsaline to freshwater seasonal wet- mento, Calif. lands. These areas are referred to herein interchangebly White, P. S. 1996. Spatial and biological scales in rein- as “ diked wetlands” or “ diked Baylands.” Because instan- troduction. pp. 49-86 In: D. Falk, C. I. Millar, taneous salinity (or even average annual salinity) of diked and M. Olwell (eds). 1996. Restoring diversity: wetland soils does not consistently correspond with plant strategies for reintroduction of endangered plants. community composition, and varies over time, these sa- Island Press. 505 pp. linity categories are intended to be broadly descriptive of plant associations rather than quantitative threshold values of soil salinity. Accordingly, the marsh types de- scribed are not discrete, but intergrade continuously and may vary over time at any site. Diked wetlands as treated below do not include artificial salt ponds (treated sepa- rately) or “ muted tidal” managed marshes (marshes with reduced tidal range controlled by tidegates), and cover only wetlands with non-tidal hydrologic inputs (rainfall, groundwater, surface runoff, streamflow, engineered water control structures, or very infrequent overtopping of dikes by extreme tides). Published and unpublished sources of useful, pre- cise data and other information on the vegetation and flora of diked Baylands are very scarce. Most usually are limited to short-term observations and coarse descrip- tive accounts (such as lists of dominant species) at a par- ticular time of year, or generalized accounts of resource management plans (e.g., Eicher 1988, Hudson 1980). Vegetation was usually described for wildlife habitat evaluation, rather than for floristic analysis or quantative plant community description. Relatively more detailed information about some individual diked Bayland sites is sometimes available for sites which are proposed for major development projects, and become the subject of detailed wetland delineations and field studies for envi- ronmental evaluations (e.g., Rugyt 1991, Kaufman and Harvey 1987). The level of detail in vegetation analysis of diked Baylands even for site-specific studies was still low until the mid 1980s when technical vegetation cri- teria for wetland jurisdictional delineations were promul- gated (WES 1997). There are no long-term studies of changes in vegetation in diked Baylands. Some coarse information about vegetation change in diked wetlands is available through inspection of historic aerial photo- graphs, particularly color infrared photos from the 1980s to the present. Based on recent information from some of the more intensively surveyed diked wetlands (e.g., Montezuma Wetlands, Solano County; Cullinan Ranch,

Chapter 1 — Plant Communities 33 Solano County; Renaissance Faire site, Marin County), Environmental Changes From Diking – Follow- it appears that the diversity and dynamics of diked wet- ing the initial phase of dike construction, several changes land vegetation have been substantially underestimated occurred. Mature tidal marsh soils accumulated peaty or- in past assessments. ganic matter under anaerobic conditions, which mini- Historic information on the diking of San Fran- mizes decomposition. Drained marsh soils high in peaty

Plants cisco Bay tidal marshes is based on numerous sources, organic material underwent aerobic decomposition and particularly U.S. Coast Survey maps (multiple series); dewatering, causing land elevations to subside. Dikes also historic accounts of salt pond levee development (Ver caused compression of underlying plastic clayey silts and Planck 1958); and field observations of modern levee peats, and subsided (Madrone Associates et al. 1983). maintenance and repair methods and agricultural drain Differential subsidence of the marsh surface tended to systems. exaggerate relict marsh topographic relief, causing natu- ral levees (containing coarser silts) to stand out against Environmental Setting isolated depressions where peat content was relatively great, and the effects of aerobic peat decomposition were The physical origins of diked wetlands are similar greatest. Tidal creek topography typically persisted as de- throughout the San Francisco Estuary. Most of the tidal pressional sinuous swales. Early-succession diked marsh marshes were reclaimed for agricultural use in the late plant communities, typically dominated by perennial 19th century when the use of mechanical dredges be- pickleweed (Salicornia virginica; drier, more saline con- came commercially available to landowners (after ca. ditions) or alkali bulrush (Scirpus maritimus), bulrush 1870), although many dikes were constructed manually (Scirpus californicus; less often S. acutus) or cattails (Madrone Associates 1977). Tidal marshes were diked (mostly Typha angustifolia; wetter brackish to subsaline for reclamation either as pasture, hayfields, salt ponds, ditches) tend to be best developed in relict swales and or (rarely) cropland. Reclamation involved construction depressions. As salts were drained from the diked basins of dikes (earthen levees made of locally excavated Bay and lands were managed for agriculture, these pioneer mud) along the margins of marsh plains (middle marsh diked salt marsh communities were reduced or elimi- between approximately MWH and MHHW) where they nated (Madrone Associates et al. 1983, Harvey 1987). bordered mudflats or major tidal creeks. The borrow Marsh Progradation and “Second Generation” ditches for dike construction were typically located in- Diked Wetlands – The strong reduction in tidal flows side of the dike, creating narrow canals about 20 ft from caused by diking all but the largest tidal creeks in the the foot of the dikes. Enclosure of tidal marshes by marsh system caused significant increases in sedimen- dikes, and resulting fluctuation between winter flood- tation outside of diked marshes, causing rapid marsh ing and summer desiccation of saline basins, would progradation on sloping mudflats. In addition, slow mi- have rapidly killed most standing tidal marsh vegeta- gration of the pulse of hydraulic mining outwash from tion. When levees were stabilized after several lifts (se- the Sacramento River contributed to marsh progradation quential layers of dewatered dredged Bay muds) tide- in San Pablo and Suisun Bays (Doane 1999, Jaffe et al. gates were installed to enable the enclosed basins to 1998). In some areas (e.g., south of ), drain on low tides. After stabilization, dikes typically marsh progradation was so extensive that a second phase stood about 3 (to 4) ft above the marsh plain (Ver- of diking occurred in the newly accreted marshes. These Planck 1958). progradational marshes are typically broad pickleweed-

Agricultural areas within the diked historic Baylands can pond water and exhibit seasonal wetland plant associations. (North San Pablo Bay diked Baylands after a storm event) Ruth Pratt

34 Baylands Ecosystem Species and Community Profiles dominated plains with fringes of cordgrass, cordgrass/ brush (Baccharis pilularis; South Bay) or mixed coyote alkali bulrush mixtures, or erosional scarps in pickleweed brush and bee-plant (Scrophularia californica; North

peats. Like early-succession diked salt marsh, they sup- Bay), often with sub-dominant mustard, poison-hem- Plants port relatively low salt marsh species diversity, and low lock, and radish. High marsh halophytes (pickleweed, densities of narrow, sparsely branched shore-perpendicu- alkali-heath, gumplant, spearscale) tend to dominate the lar tidal creeks. Because of the influence of wave depo- lower portion of the outboard dike slopes adjacent to salt sition of sediment and coarse organic debris, the tidal marshes, although weedy species can persist for many elevations of these dike-fringing salt marshes is often years after a levee has been disturbed by maintenance and above MHHW in some areas, particularly where incipi- repair activities. ent natural levees form at the edge of mudflats. These The ecological significance of the dike disturbance secondary prograded high marshes with little anteced- cycle for wetland plants is that it has provided corridors ent topography were readily converted to diked agricul- through tidal marshes and diked marshes for a weedy tural land, as in the Baylands of Novato (Hamilton, Bel flora (both exotic halophytes and glycophytes) to dis- Marin Keys). perse, and places weed seed sources along a topographi- Dike Disturbance Cycle and Vegetation – Sub- cally superior location for dispersal into adjacent diked sidence of dikes themselves caused a need to maintain and tidal wetlands. The rapid local spread of weedy halo- dike crest elevations by dredging borrow ditches to re- phytes on dredge spoils along recently maintained/re- supply material. This established a periodic disturbance paired dikes (especially Salsola soda, Lepidium latifolium, regime to dike vegetation and adjacent ditches. In areas Mesembryanthemum nodiflorum) can be observed of high wave energy (long fetch distance, narrow mud- throughout the Bay. Similar halophyte weed dispersal flats), maintenance by topping dikes with dredged muds occurs along side-cast spoils in diked marshes where and repairing erosional slopes may occur in cycles as drainage ditches are created or maintained. Dike distur- short as five years or less. Many bayfront dikes unshel- bance corridors may accelerate the spread of exotic halo- tered by fringing marsh require armoring by placement phyte population outposts into uninvaded wetland habi- of rock or concrete fragments. Well-protected dikes be- tats. In particular, Lepidium latifolium’s invasion of hind extensive salt marsh on firmer peats may have main- brackish marshes appears to have tracked patterns of dike tenance cycles longer than a decade or two. Repaired dike disturbance, invading first along dredge spoil at levee slopes provide bare mineral substrate which is gradually edges, subsequently spreading into diked and tidal wet- leached of salts and open to colonization by upland lands. weeds. Hydrologic Changes in Diked Wetlands – Pat- The dike disturbance cycle has favored a ruderal terns of soil waterlogging and inundation in diked con- flora along the upper slopes and crests of dikes (includ- ditions differ fundamentally from tidal marsh. They de- ing many native and exotic halophytic weeds as well as pend principally on the efficiency of artificial drainage, glycophytes; e.g., mustard (Hirschfeldia incana, Brassica the permeability of substrate (related to soil clay content), spp.), radish (Raphanus sativus), fennel (Foeniculum and the amount and seasonal distribution of rainfall. The vulgare), plantain (Plantago coronopus, P. major, P. efficiency of the early drainage systems in diked marshes lanceolata), annual ice-plant (Mesembryanthemum nodi- was based on the amount of ditching and the pattern of florum; mostly South Bay), sea-fig (Carpobrotus chilense), ditching in relation to subsided marsh topography. Be- hottentot fig (Carpobrotus edulis and hybrids with C. cause of the great extent of the areas diked, density of chilense), poison hemlock (Conium maculatum), Medi- drainage ditches was relatively low. Ditches were mostly terranean brome species (Bromus spp.), wild barley (Hor- confined to the borders of farmed parcels, but sometimes deum murinum ssp. gussonianum,), ryegrass (Lolium multiflorum, L. perenne). Lower portions of disturbed outboard (bayward) dike slopes are typically more saline and wetter, and support brackish marsh or salt marsh species, often with an exaggerated proportion of weedy halophytes (e.g., spearscale, Atriplex triangularis; peren- nial peppercress, Lepidium latifolium, sicklegrasses Parapholis incurva, Hainardia cylindrica; bassia, Bassia hyssopifolia; saltwort, Salsola soda; wild beet, Beta vul- garis). Interior slopes of dikes which face salt ponds, and contiguous fringing nontidal saltmarsh, are either bare or vegetated with saltgrass (Distichlis spicata), Salicornia

virginica, dodder (Cuscuta salina), and alkali-heath (Fran- Josh Collins kenia salina). Dikes with very infrequent maintenance Diked wetlands in Suisun are managed primarily tend to become dominated by dense stands of coyote for waterfowl production.

Chapter 1 — Plant Communities 35 reached across extensive marsh depressions. The drains very close to the groundwater surface. Accordingly, the were originally driven by gravity, drawing drainage wa- proportion of wetland and upland in contemporary con- ter downslope to one-way flapgates which discharged to ditions depends on the intensity of pumping and ditch adjacent tidal marshes at low tide. This original gravity- maintenance. These conditions vary significantly among driven drainage system had limited efficiency. Topo- diked parcels under different ownership and manage-

Plants graphic lows in the diked basins (swales of relict tidal ment. Therefore, the mosaic of wetland and upland in creeks, relict marsh pans) remained poorly drained into diked agricultural lands is relatively variable and unpre- the crop growing season, while relict creek levees and dictable among years and between parcels. higher relict tidal marsh became better drained. Relictual Variability of Artificial Hydrologic Conditions – tidal marsh patterns of wetland and upland are evident The patchiness and instability of diked wetlands is evi- in black and white photographs of diked hayfields in the dent, for example, in recent land-use changes in San mid-20th century. Even with modern pump-driven Pablo Bay. Cullinan Ranch, actively drained and farmed drainage systems, persistent soil waterlogging and inun- oat hayfield until the early 1990s, supported a matrix of dation in depressions occurs following rainstorms (Gran- upland cropland and many seasonally wet depressions holm 1986, Madrone Associates et al. 1983). with wetland weeds. After cessation of pumping by the The proportions of poorly drained (waterlogged or mid-1990s (a period of above average rainfall), the Ranch inundated in spring) and well-drained (aerobic soils in rapidly (within 2 years) and spontaneously converted to spring) soils in diked Baylands vary with precipitation a seasonal freshwater marsh dominated by cattails and amounts and patterns. Years of normal or above normal flats of Eleocharis parvula (Takekawa et al. 1999). rainfall, particularly those with large storms late in the Nearby, between Tolay Creek and the Petaluma River, precipitation season, cause expansion of wetland areas adjacent hayfields with differing schedules of ditch main- in diked conditions. These contract during years of be- tenance changed from very similar extensive winter- low-normal precipitation, especially with a lack of spring ponded swale patterns to striking contrasts of ponded storms. The proportions of effective wetland and upland and drained fields. At another location near Sears Point, also vary with drainage efficiency and the degree of sub- San Pablo Bay, cessation of pumping in relict hayfields sidence. caused conversion to seasonal wetlands dominated by Long-term Drainage of Diked Wetlands – As annual plant species typical of vernal pool communities subsidence increased, wetland areas increased behind (many of which are present in the ephemeral weed flo- dikes, particularly in peaty soils. In the early 20th cen- ras of depressions within hayfields; Downingia pulchella, tury, many diked farmlands failed because the costs of Plagiobothrys bracteatus, Eryngium aristulatum, Callitriche compensating for increased subsidence and dike degen- spp., Eleocharis macrostachya). Thus, the extent of diked eration at times exceeded the return on agricultural ben- wetlands and their character today are very much arti- efits. Many derelict agricultural parcels with degenerated facts of drainage pump activity. dikes are evident in aerial photographs of San Pablo Bay Similar artificial drainage controls wetland plant in the 1940s. After abandonment of diked farmlands, communities in the diked basins of the Suisun Marsh, partial levee and drain failures increased, causing rever- which is managed mostly for waterfowl production. sion of agricultural lands to brackish or salt marsh con- There, relatively low-salinity tidewaters are admitted to ditions. For example, prior to conversion to salt ponds, the basins selectively to sustain fresh-brackish perennial many of the Napa Marsh area’s derelict hayfields in the and seasonal marshes (Jones and Stokes 1976, Mall 1969, 1940s had partially reverted to wetland (Madrone Asso- Meiorin et al. 1991). The proportion of ponded to veg- ciates 1977). etated marsh may be controlled by modifying managed Contemporary Drainage of Diked Wetlands – hydroperiods, so that prolonged flooding causes dieback Today, subsidence of diked active agricultural lands has of vegetation in areas of relatively lower substrate eleva- increased to the point at which it cannot be compensated tion. The seasonal variations in tidewater salinity enable by passive gravity drainage through flapgates alone; the timing of flooding to control substrate salinity, also. drainage sufficient for oat hay farming depends prima- Managed marsh hydroperiods are usually designed to rily on active pumping of water in ditches for discharge favor mixtures of shallow submerged mud, bulrushes to the Bay. It is common for elevations in diked Baylands (Scirpus maritimus, S. americanus, S. pungens), tules (S. of San Pablo Bay to average as low as 0 - 1.0 ft N.G.V.D, californica, S. acutus), cattail (Typha spp.) and brass-but- and some average below -3.0 ft or more over extensive tons (Cotula coronopifolia), and some non-native annual areas, as at Bel Marin Keys and Hamilton Field (USACE grasses (Echinochloa crus-gallii, Polypogon monspeliensis). 1988). In south San Francisco Bay, which was affected Also common in diked brackish marshes are baltic rush by past subsidence due to long-term groundwater extrac- (Juncus balticus), saltgrass (Distichlis spicata) and pickle- tion, diked wetland elevations may be even lower weed (Salicornia virginica). Other species have colonized (Moffett and Nichols and Phil Williams Associates these brackish managed wetlands, including goosefoot 1988). These subsided diked marsh surfaces are often (Chenopodium chenopodioides), docks (Rumex crispus, R.

36 Baylands Ecosystem Species and Community Profiles pulcher), purslane (Sesuvium verrucosum, a recent invader Soil acidity is normally not highly variable in tidal salt native to the Great Basin), celery, (Apium graveolens), marshes, which are buffered by cations of estuarine wa-

Lepidium latifolium, and Conium maculatum. Some ter and relatively stable reduction-oxidation conditions Plants diked brackish marsh communities are essentially arti- established by groundwater surface position in the marsh ficial, in contrast with the incidental nature of wetland soil profile (Adam 1990). In diked conditions, extreme communities in diked Baylands which are either derelict seasonal fluctuations in the soil saturation levels may or managed for hay production, pasture, or salt produc- occur, causing release of sulfides and free metals in marsh tion. soils with high sulfur contents. Some depressions in Salinity in Diked Wetlands – The substrate sa- diked wetlands develop very low pH (pH 4 and occasion- linity conditions in the diked, drained marshes were ally lower) and high concentrations of iron oxide precipi- modified by leaching the silty clay Bay muds with pre- tates (Madrone Associates et al. 1983, Madrone Associ- cipitation, eliminating leached salts through drainage ates 1977). These areas are often barren of vegetation, ditches and tidegates, and excluding tidal inundation by or develop sparse, low diversity vegetation. Less extreme dikes. This caused rapid desalinization of the substrate, but low pH in diked wetlands may inhibit plant produc- enabling glycophytes with relatively low salt tolerance tion, but the abundant phytomass of many diked wet- (compared with the salt marsh flora), such as oats and lands (e.g., rank growth of pickleweed, cattails, pepper- agricultural weeds, to dominate the converted tidal cress) suggests that the seasonal drainage and aeration marsh soils (Harvey 1987, Madrone Associates et al. of diked wetland soils commonly has a stronger overall 1983, Meiorin et al. 1991). The desalinized conditions effect on vegetation production than low pH. Extremely of the substrate were maintained by drainage through low redox potential and sulfite toxicity, which often ac- ditches and tidegates. Subsidence caused (and contin- company low pH, are highly significant inhibitors of ues to cause today) decreased efficiency of drainage, and plant growth (Russell 1973). Soil acidity is highly vari- therefore also decreased flushing of residual or reintro- able in diked wetlands and depends on local soil condi- duced salts. tions and prevailing hydroperiods. Diked wetlands which have been effectively de- Disturbance in Diked Wetlands – The distur- salinized for agricultural production do not remain so bance regimes of diked wetlands are influenced prima- unless substantial maintenance efforts are applied to rily by discing and flooding. Discing is performed for ag- drainage and dikes. Diked wetlands become resalinized riculture, suppression of weed biomass, and suppression by partial failure of tidegates and levees (Madrone Asso- of mosquito production. Episodes of discing have main- ciates et al. 1983). Leaking or ruptured tidegates allow tained a significant ruderal (weedy) element to the diked influx of saline tidal waters in drainage ditches. Saline wetland flora of San Francisco Bay, creating large veg- or brackish ditch water can recharge salts locally in etation gaps suitable for invasion by non-native plants, groundwater, and move into the soil through evapotrans- particularly annuals. Extreme flooding events which are piration and capillary movement. In derelict cattail-lined possible in non-tidal diked marshes also cause distur- ditches of abandoned diked hayfields, late summer ditch bances: deep, prolonged flooding causes mass dieback of water salinity can reach 15 ppt, due to salt leaching and most standing perennial vegetation. Following dieback evaporation. In addition, seepage through dikes (particu- events, similar or very dissimilar plant associations may larly where Bay mud is silty) introduces salts locally. establish. Overtopping (cresting) of dikes during storm surges floods reclaimed salt marsh soils with brackish or saline Diked Bayland Plant Communities water. All these processes recharge soil salinity in diked wetlands. Overtopping typically occurs in winter, and The plant communities present in the diked Baylands is not a rare event, particularly in south San Francisco can resemble those of local tidal salt marshes, tidal brack- Bay (USACE 1988). If poor drainage conditions prevail ish marshes, non-tidal perennial freshwater marshes, or following a substantial tidal flooding event in a diked seasonally wet grasslands. Some also have characteristics basin, wetlands rapidly become recolonized by salt-tol- similar to components of tidal marshes which are now erant vegetation. High salinity in diked Baylands is of- regionally scarce or extirpated, such as high marsh pans ten maintained by episodic tidal flooding events which and alluvial high marsh ecotones. Diked wetlands usu- are not often observed. Residual salinity tends to decline ally have lower native species richness than their analo- very rapidly except where drainage is very poor. gous natural plant communities, and often a larger com- Acidification of Diked Wetlands – Soil acidity ponent of exotic plant species. The typical “ weediness” affects plant growth primarily by altering the availabil- of many diked wetlands is probably more a result of past ity of soil nutrients, or liberating excessive amounts of land uses rather than an intrinsic susceptibility to inva- otherwise low- ions into the soil , cre- sion by exotic vegetation. Some diked wetlands are man- ating toxicity problems for roots. Acid-related toxicity aged actively to maintain community dominance by occurs only at very low pH (Reuss and Johnson 1986). marsh plant species favored by wildlife or game manag-

Chapter 1 — Plant Communities 37 ers (Mall 1969). Most are either managed for purposes curs in distinct salinity horizons, caused by near-surface other than wildlife conservation (hayfields, grazed pas- leaching of salts and accumulation in deeper portions of ture, flood detention basins, salt evaporation ponds) or the soil profile. are derelict (i.e., pending conversion to urban develop- Thus, apparent salt marsh vegetation in diked Bay- ment), but may still support significant marsh plant com- lands may indicate either current high salinity or former

Plants munities. high salinity, and does not necessarily indicate sustained Plant community composition in diked wetlands high residual salinity. It often represents inertia in plant is strongly influenced by the degree of residual soil sa- community structure after relaxation of salinity stress. linity or salt recharge of soils, the efficacy of artificial The term “ non-tidal salt marsh” in the context of the drainage, and the relictual factors of land use history. San Francisco Bay Estuary should be interpreted nar- These factors vary extremely in diked Baylands: some rowly in floristic rather than physiological terms, because exhibit insignificant salinity, maximal drainage and dis- dominance of halophytes in the unstable substrate sa- turbance in some intensively cropped oat hayfields in San linity conditions in diked wetlands is an unreliable in- Pablo Bay; others exhibit high salinity, poor drainage and dicator of current substrate salinity. Some diked salt little disturbance in diked pickleweed marshes in south marshes are truly saline and tend to remain so because San Francisco Bay. Other modifications persisting from of chronically poor drainage or frequent partial dike fail- past land uses which affect plant community composi- ures. Others are in gradual succession to other vegeta- tion include importation of soils or fill (e.g., former air- tion types. Some diked salt marshes with low residual port landing strips, derelict building pads), abandoned substrate salinity are subject to rapid conversion to other berms and ponds of gun clubs, residual effects of past vegetation types following disturbances (e.g., discing or fertilizer applications; industrial waste disposal, and soil flooding). contamination. Species Richness and Composition – The species Relict Halophytic Vegetation – The majority of richness and composition of diked marshes is highly vari- derelict diked wetlands in central and southern San Fran- able among sites, and among different marsh types. High cisco Bay are dominated by species native to local tidal salinity and hypersalinity in diked marshes tend to pro- salt marshes and brackish marshes, such as Distichlis mote low species diversity, selecting for a few tolerant spicata and Salicornia virginica (BCDC and Harvey species. Other extreme soil conditions, such as strong 1983, Madrone Associates et al. 1983). Salt-tolerant acid production and mass release of free iron (often as- glycophyte species have very low physiological nutritional sociated with prolonged inundation followed by summer requirements for salt, and flourish in non-saline and drought) minimize plant species diversity. Truly hyper- subsaline soils (Waisel 1972). They often co-exist with saline seasonal wetlands in the Bay usually support only species with little affinity for saline soil, such as Polypogon sparse Salicornia virginica, Distichlis spicata, and Salsola monspeliensis and Lolium multiflorum (Harvey 1987, soda, with a minor component of Frankenia salina. Hy- Kaufman and Harvey 1987). S. virginica and D. spicata persaline seasonal wetlands are now scarce in the Bay have a significant competitive advantage over salt-intol- Area, mostly scattered around South Bay salt ponds and erant plant species when substrate salinities are in the adjacent lands. A few occur in the North Bay (e.g., parts range of halophytes (over 5 ppt soil salinity), and rap- of Gallinas Creek diked salt marshes, peripheral portions idly establish dominance during episodes of high salin- of the Napa salt ponds). Many former hypersaline diked ity conditions. Some halophytes like S. virginica are ef- wetlands have been altered by water management for ficient colonizers of bare wet mud even when salinity is mosquito abatement and wildlife habitat enhancement, low if seed rain intensity is high. Pioneer halophytes do and are now muted tidal marshes (e.g., New Chicago not necessarily decline in abundance, however, when Marsh in Alviso, Oro Loma Marsh in Hayward). substrate salinities decline as a result of progressive leach- Species diversity in nontidal diked brackish and salt ing and drainage of salts. Many apparent diked “ salt marshes is generally much higher than in hypersaline marshes” are composed of relict vegetation halophyte basins, but this does not reflect relatively greater overall vegetation which persists in relatively low salinity con- diversity of native plant species. Diked brackish to sa- ditions. This condition is indicated by the presence of a line nontidal wetlands support a number of common minor to subdominant component of species with rela- native tidal brackish and salt marsh species (Salicornia tively low salt-tolerance (e.g., ruderal composites, bed- virginica, Distichlis spicata, Frankenia salina, Cuscuta straws, mustards), growing vigorously among halophytes salina, Atriplex triangularis) and sometimes support rela- without indications of salt stress (stunted growth, leaf tively infrequent native species typical of the natural high tip burn, pale leaves) in diked “ salt marshes.” Examples tidal marsh and upland ecotone (Iva axillaris, Leymus are sometimes found in abandoned dredge disposal sites triticoides, Baccharis douglasii). The native perennial grass (Zentner and Zentner 1995, Huffman and Associates Leymus triticoides, historically a dominant species of the 1996). Some mixed halophyte-glycophyte associations upper transition zone of tidal salt and brackish marshes, may also occur where stratification of rooting zones oc- is infrequently found in some diked brackish marshes,

38 Baylands Ecosystem Species and Community Profiles particularly where disturbance has been infrequent. A back after prolonged deep flooding. Other common her- relatively rare historic component of subsaline tidal baceous non-native plant species of diked brackish and

marsh ecotones, Centaurium muehlenbergii is found in saline marshes include Lepidium latifolium, Bassia hys- Plants diked subsaline wetlands at Cullinan Ranch. It is cur- sopifolia, Beta vulgaris, Salsola kali, and Salsola soda. Le- rently reported known from only one tidal marsh/upland pidium latifolium is especially invasive in brackish diked ecotone (China Camp). The sedge Scirpus maritimus, a marshes, particularly where the soil has been disturbed, dominant native component of tidal brackish marshes, but also in areas of marsh with thin or discontinuous is often abundant or dominant in brackish to saline vegetative cover. ditches or deep, wet depressions in diked marshes ((Mad- Diked subsaline and nonsaline Baylands are very rone Associates et. al. 1983, Mall 1969). seldom the subject of careful floristic surveys (e.g., Rugt Conversely, diked salt and brackish marshes gen- 1991, Madrone Associates 1977); vegetation descriptions erally fail to support some important species of corre- usually focus on visually dominant ruderal species, of- sponding tidal marsh communities; Spartina foliosa is ex- ten based on summer survey dates when native annual cluded from nontidal conditions, and Jaumea carnosa, species are not identifiable (Jones and Stokes 1977, Plantago maritima, Triglochin spp. and Limonium cali- Hudson 1980, Werminski 1973). Consequently, the flo- fornicum are absent or very infrequent in nontidal salt ristic diversity and affinities of diked subsaline to fresh marsh; Grindelia stricta is generally less abundant in non- seasonal wetlands has probably in many (perhaps most) tidal salt marsh than tidal marsh. Diked salt marshes cases been underestimated. Diked subsaline and nonsa- typically lack rare tidal marsh species (e.g., Cordylanthus line wetlands are mixtures of exotic species of ruderal spp., Castilleja ambigua, Lasthenia glabrata, Lilaeopsis seasonal wetlands and native species typical of vernal masonii, Cirsium hydrophilum, Aster lentus), and also pools and swales. Diked wetlands which are mostly sub- usually lack most infrequent tidal marsh species (e.g., saline to nonsaline after years of agricultural drainage Pluchea odorata, Senecio hydrophilus, Glaux maritima). support a range of marsh plant associations. These are The failure of these tidal marsh species in diked condi- most common around San Pablo Bay and Suisun Bay, tions is probably due to the relatively greater competi- where grazing pasture and oat hayfields have been main- tion by robust “ generalist” species with broad ecologi- tained for many decades in diked former tidal brackish cal amplitude, and physiological intolerance of extremes marshes. They may have inclusions of relatively brack- of inundation and dryness in diked wetlands. Diked salt ish indicator species where soil salinity and acidity are and brackish marshes in some cases, however, provide locally elevated (e.g., mixtures of Atriplex triangularis, refugia for tidal marsh plants of the high tidal marsh Polypogon monspeliensis, Distichlis spicata) but are domi- which have become (or in some cases have always been) nated by glycophytic wetland plant species, both native regionally rare or infrequent in the modern tidal marsh and non-native. Composition of the fresh/subsaline ecosystem, such as Suaeda moquinii, Hemizonia diked wetland flora is influenced by disturbance. Annu- pungens ssp. maritima, Salicornia subterminalis, Down- ally disked hayfields support wetland “ weeds” which are ingia pulchella, Juncus mexicanus). As such, they may a mixture of native annuals (e.g., Plagiobothrys spp., esp. serve to maintain genetically differentiated salt-toler- P. stipitatus, P. leptocladus), Juncus bufonius, Lilaea ant populations of species displaced from modern tidal scilloides, Callitriche marginata, C. spp. Cicendia quadran- marshes. gularis, Elatine brachysperma, Eryngium spp., Cressa Diked brackish and salt marshes are subject to in- truxillensis; locally, Downingia spp.; non-native annuals vasion by many non-native species and species which are (Lythrum hyssopifolium, Cotula coronopifolia, Polygonum not typical of tidal marshes, or are typically restricted to aviculare, Hordeum marinum ssp. gussoneanum, Polypogon marginal conditions in tidal marshes. Non-native pas- monspeliensis, ) and non-native perennials (Lotus cornicu- ture grasses with moderate salinity tolerance, such as latus, Agrostis avenacea) Grazed pasture land in diked Lolium multiflorum (and hybrids), Polypogon monspelien- Baylands in San Pablo Bay may also support native an- sis, Lotus corniculatus and Hordeum marinum ssp. nuals found in diked disked hayfields, as well as native gussoneanum, and even Rumex crispus are also major com- perennials (Eleocharis machrostachya, Glyceria spp. Juncus ponents of diked salt and brackish marshes, often locally effusus, J. patens) and naturalized non-native perennials dominating either depressions (Polypogon, Hordeum) or (Rumex crispus, R. pulcher, Cirsium arvense, Lolium mul- mounds (Lolium). Exotic halophytic grasses Parapholis tiflorum). The relative abundance of these species in incurva and Hainardia cylindrica are also locally common diked pasture and hayfield wetlands is variable and un- in diked salt or brackish marsh. Cotula coronopifolia is stable. Some diked wetlands, after relaxation of inten- usually only a minor component of tidal salt and brack- sive agricultural manipulation, develop seasonal wetlands ish marsh, colonizing depressions and marsh pan edges, with plant species composition highly similar to that of but is often a major component of diked brackish regional vernal pools and swales (locally dominated by marshes, particularly in disturbed or winter-ponded Downingia spp., Eryngium spp. Eleocharis macrostachya, brackish depressions where other vegetation has died Callitriche spp. Lilaea scilloides, Plagiobothrys spp., etc.)

Chapter 1 — Plant Communities 39 Reference Sites Francisco Peninsula, where sand beach ridges oc- curred. Reference sites for different types of diked wetlands Seasonal freshwater wetlands (vernal pools and would generally not be long-lived because of the preva- swales, springs) occurred within grasslands peripheral to lence of unstable vegetation conditions in diked Bay- the Bay, particularly in the Petaluma River valley, on al-

Plants lands. Droughts, wet years, changes in drainage and luvial terraces near Fremont, portions of Richmond and pumping, disturbances from agricultural practices, and Berkeley, and along much of the Suisun Marsh area. succession can cause profound changes in vegetation in Their distribution and abundance, as suggested by soil short periods of time. The following reference sites re- surveys, were probably not limited to areas mapped as flect conditions observed in the mid-late 1990s. poorly drained; seasonal freshwater wetlands often oc- 1. Diked non-tidal salt marsh (dominant Salicornia cur as local inclusions within soil series in which wet- virginica) lands are not indicated as prevalent. This is indicated by • Fremont Airport (King and Lyons site; proposed records of vernal pool endemics in locations like San for phased tidal restoration), Alameda Co. Francisco, where “ vernal pool” soil types are not mapped, • Gallinas Creek diked wetlands, Marin Co. but winter pools with typical endemic annuals were • Western Marsh and Central Lowlands, Bahia found. Site, Novato, Marin Co. The historical abundance and distribution of these • Dredge pond 3E, Mare Island, Solano Co. wetland types is extremely difficult to quantify in terms • Area H, Redwood Shores, San Mateo Co. of area. Quantitative estimates of historic abundance of 2. Diked non-tidal brackish marsh seasonal wetlands displaced by urbanization depends • Cullinan Ranch, Solano Co. heavily on interpretation and assumptions about early • Suisun Marsh managed marshes, Solano Co. soil surveys (which were not intended to function as • Huichica Unit, CDFG Napa-Sonoma Marsh, maps of actual or potential native vegetation), historical Sonoma Co. accounts, and fragmentary information on species occur- 3. Diked subsaline to nonsaline seasonal wetlands rences in old floras. The qualitative differences in natu- • Black Point/Renaissance Faire site, Novato, ral non-tidal wetland types and their diked Bayland ana- Marin Co. (extirpated 1999) logues further obscures the relevance of quantitative • Twin House Ranch Site, Lower Petaluma River, comparisons between historic losses of natural seasonal Sonoma Co. wetland plant communities and their partial replacement • Leonard Ranch, North Point, Dixon parcels, with wetlands of diked Baylands. Sonoma Co., along Hwy 37 Conservation Issues Historic and Modern Distribution Plant conservation needs for diked wetlands are depen- Wetlands of diked Baylands are relatively recent historic dent on larger-scale wetland management and restora- artifacts. The plant associations they support are analo- tion plans. Diked wetlands usually support less native gous to, but distinct from, wetlands along the margins plant species diversity than mature tidal marshes at of historic tidal marshes. Brackish non-tidal marshes equivalent locations, but may in some cases still provide somewhat similar to diked brackish marshes probably oc- important plant conservation functions. For example, in curred within alluvial deposits at mouths of small streams San Pablo Bay, agriculture and development have elimi- which discharged into tidal marshes with locally poor nated most historic natural seasonal wetlands in supra- drainage, such as near Ignacio (Novato), where riparian tidal grasslands peripheral to the Bay. The original ver- areas converged with dense marsh ponds and few or no nal pool flora which occurred in subsaline to alkaline tidal creeks. Analogous examples of brackish or subsa- depressions around the historic edge of the Bay (as in line marshes with marginal tidal flooding are found to- parts of northeastern Suisun Marsh today) has been day along Drakes Estero and Tomales Bay, particularly largely extirpated in its original location, but persists in near shallow backbarrier lagoons. Salt marsh with re- artificial equivalent topography and edaphic conditions stricted tidal influence probably occurred along portions in some diked seasonal wetlands. These populations of the Bay where local sand beach ridges were likely to maintained in subsaline conditions may provide impor- obstruct tidal flows. One modern example exists at Pinole tant founder populations for opportunities to restore Point (Whittell Marsh), where the proximal end of a vernal pool and swale systems in the original soil types sand spit episodically dams small tidal channels, caus- and topography along the margins of the Bay, in coor- ing seasonal ponding in a small salt marsh cut off from dination with tidal restoration. Similarly, one diked salt regular tidal flows. Prehistoric examples of “ pocket” marsh in the South Bay (former Fremont Airport) pro- nontidal salt marsh probably occurred in the vicinity of vides refugia for Suaeda moquinii, otherwise found Richardson Bay, Alameda, Oakland, and the San around the Bay only in remnant alkali vernal pools ad-

40 Baylands Ecosystem Species and Community Profiles jacent to the Bay at one site (Zentner and Zentner 1996). systems (e.g., vernal pools, alkali basins, alluvial Juncus/ Partial vernal pool floras have also been generated spon- Scirpus marsh, etc.) is precluded by development, some

taneously after cessation or relaxation of agricultural diked wetlands should be considered for modification Plants manipulation at Montezuma Wetlands (Solano County), and management to maintain regionally scarce plant Sears Point (Sonoma County), and a construction site communities. Generally, however, priority should be in Alviso (Santa Clara County). Most diked wetlands are assigned to restore peripheral estuarine plant communi- poorly surveyed, and may act as refugia for many popu- ties in their proper original soils and topographic posi- lations of plants of conservation significance. tion. Where diked wetlands support regionally rare plant Diked wetlands are also conservation threats to populations, they should be given interim conservation plant species diversity when they provide outposts, res- priority until suitable population restoration sites are es- ervoirs, or dispersal corridors for invasive wetland weeds, tablished in more natural or restored habitats. Existing such as Lepidium latifolium and Salsola soda. By increas- diked marshes should be managed to minimize impacts ing seed rain on adjacent tidal marshes, or ad- of exotic invasive plants on adjacent managed or natu- jacent marsh restoration sites, diked wetlands may also ral tidal marshes. Dike maintenance should include best cause degradation of tidal marshes. management practices which favor recolonization of dis- Sea level rise makes long-term conservation of turbed dike surfaces by native vegetation and suppress diked wetlands problematic. In addition to inherent ten- re-invasion by exotic species. dencies of diked systems to suffer levee subsidence and erosion, sea level rise imposes increasing risks of levee References failure and tidal flooding. Breached diked wetlands spon- taneously revert to tidal wetlands, but usually only as low Adam, P. 1990. Saltmarsh ecology. Cambridge Univ. mudflat or marsh to lower middle marsh after even two Press. decades (e.g., White Slough, Vallejo, Solano County) In BCDC (San Francisco Bay Conservation and Develop- addition, some high-sulfur diked marsh soils undergo ment Commission) and H.T. Harvey. 1983. long-term changes in soil chemistry which make them Aquatic and wildlife resources of Richardson Bay. unsustainable for any valuable natural or artificial veg- Unpublished report prepared for the Richardson etation. Bay Special Area Plan Study. Dike maintenance and repair may cause degrada- Doane, S. N. 1999. Shoreline changes in San Pablo Bay, tion to diked and tidal marsh plant communities by fa- California. M.Sc. thesis, Vanderbilt Univ. 116 pp. voring spread and dominance of exotic invasive marsh Eicher, A. L. 1988. Soil-vegetation correlations in wet- plant species. Dike maintenance practices currently lack lands and adjacent uplands of the San Francisco any elements which facilitate recolonization by native Bay estuary, California. U.S. Fish and Wildlife Ser- species. vice Biological Report 88 (21), contract no. 14- Restoration of diked marshes is somewhat self-con- 16-0009-85-001. August 1988 tradictory, since true restoration would entail conversion Granholm, S.L. 1989. Endangered habitat: a report on to the original tidal marsh condition. However, diked the status of seasonal wetlands in San Francisco wetlands can be significantly enhanced as non-tidal Bay. Report sponsored by National Audubon So- marshes by reducing or eliminating adverse land use ciety, San Francisco Bay Area Audubon Society practices. Reduction of intensive drainage efforts and chapters, Save San Francisco Bay Association, Si- elimination of high-frequency disking can enable diked erra Club Bay Chapter. fresh/subsaline wetland plant communities to mature Harvey, T.E. 1987. Fish, wildlife, and habitat manage- and accumulate greater native species. Pasture manage- ment plan for Naval Security Group Activity - ment that tolerates some winter inundation in depres- Skaggs Island, California. U.S. Fish and Wildlife sions, for example, is more compatible with native wet- Service, San Francisco Bay National Wildlife Ref- land plant species diversity than oat crop management. uge, Newark, Calif. Hudson, J. 1980. Bird census of diked-marshland habi- Conclusions and Recommendations tat. In: D.S. Sloan (ed). San Pablo Bay: an envi- ronmental perspective. Environmental Studies Diked wetlands considered for conversion to other marsh Group, Univ. of Calif., Berkeley. types, such as tidal wetlands, should be studied individu- Huffman and Associates 1996. Proposed Section 404 ally for site-specific floristic values, particularly for po- wetland delineation for the Bahia Master Plan, tential functions as refugia for species displaced from his- Novato, California. U.S. Army Corps of Engineers, toric seasonal wetlands and tidal marsh ecotones. Diked San Francisco District, file no. 148831. wetlands should not be assumed to have uniformly low Jaffee, B., R.E. Smith and L.Z. Torressan. Sedimenta- native wetland plant species diversity or “ ruderal” sta- tion changes in San Pablo Bay. U.S. Geological tus. In areas where restoration of seasonal fresh wetland Survey open-file report 98-759.

Chapter 1 — Plant Communities 41 Jones and Stokes. 1976. Suisun Marsh Protection Plan. Reuss J.O. and D.W. Johnson. 1986. Acid Deposition Calif. Dept. Fish and Game, Sacramento, Calif. and Acidification of Soils and Waters. Springer- Kaufman, S. and H.T. Harvey. 1987. Plant list: Army Verlag, New York. Corps of Engineers; Site. File no. 309- Rugyt, J. 1991. of vascular plant species at 01. Harvey and Associates, Alviso, Calif. the Montezuma Wetlands Project site. Appendix to

Plants Madrone Associates. 1977. The natural resources of Montezuma Wetlands Project Technical Report, Napa Marsh. Report prepared for the Calif. Dept. Levine-Fricke Restoration Corp., Emeryville, Calif. Fish and Game, Coastal Wetland Series # 19. Sac- Russell, E.W. 1973. Soil conditions and plant growth. ramento, Calif. 10th ed., Longman, London and New York. Madrone Associates, Philip William and Associates, J.R. Takekawa, J., M. Eagan and R. Laird. 1999. Monitor- Cherniss and N. Wakeman. 1983. Ecological val- ing tidal wetland restoration projects in the San ues of diked historic baylands. A technical report Pablo Bay National Wildlife Refuge. Progress Re- prepared for the San Francisco Bay Conservation port, May 1999. U.S. Geological Survey Biologi- and Development Commission, April 1992 (re- cal Resources Division, Mare Island Field Office, vised 1983). Calif. Mall, R.E. 1969. Soil-water-salt relationships of water- U.S. Army Corps of Engineers (USACE). 1988. San Fran- fowl food plants in Suisun Marsh of California. cisco Bay Shoreline Study: Southern Alameda and State of Calif. Dept. Fish and Game Wildlife Bul- Santa Clara Counties, Interim Office Report. U.S. letin No. 1. Sacramento, Calif. Army Corps of Engineers, San Francisco District. Meiorin, E.C., M.N. Josselyn, R. Crawford, J. Calloway, Ver Planck, W.E. 1958. Salt in California. State of Ca- K. Miller, R. Pratt, T. Richardson and R. Leidy lif. Dept. Natural Resources, Division of Mines, 1991. San Francisco Estuary Project status and Bulletin 175. 168 pp. trends report on wetlands and related habitats Wermunski, J. 1973. Ecological attributes of the Hay- in the San Francisco Estuary. Public Report pre- ward Area Shoreline: a habitat survey with recom- pared under cooperative agreement #815406-01- mendations. Unpublished background technical 0 with the U.S. Environmental Protection report prepared for the Hayward Area Shoreline Agency by the Association of Bay Area Govern- Planning Agency, Hayward, Calif. ments, Oakland California; Romberg Tiburon Waisel, Y. 1972. The biology of halophytes. New York: Centers of San Francisco State Univ., and the Academic Press. U.S. Fish and Wildlife Service, Sacramento Ca- Waterways Experimental Station, U.S. Army Corps of lif. Engineers (WES). 1987. Corps of Engineers Wet- Moffatt and Nichol and Wetland Research Associates lands Delineation Manual. U.S. Army Corps of 1988. Future sea level rise: predictions and impli- Engineers Wetlands Research Program Technical cations for San Francisco Bay. Report prepared for Report Y-87-1, January 1987. the San Francisco Bay Conservation and Develop- Zentner and Zentner. 1995. Section 404 wetland delin- ment Commission, San Francisco, Calif. Revised eation for the Bayside Business Park Phase II, Fre- edition. mont, California. U.S. Army Corps of Engineers, San Francisco District.

42 Baylands Ecosystem Species and Community Profiles along the Alameda shoreline in the vicinity of San Plants of San Francisco Bay Lorenzo Creek and Mount Eden Slough. This reach of

salt marsh was distinguished by a relatively straight-edge Plants Salt Ponds erosional marsh shoreline, little tidal drainage at the edge Peter R. Baye of the mudflats, and evidence of drowned marsh topog- raphy (mapped as emergent sinuous tidal creek levees). Introduction The upland edge was an extensive alluvial lowland, pre- sumably with significant subsurface groundwater dis- The term “ salt pond,” as treated in this discussion, in- charge. No major freshwater creeks were directly asso- cludes both natural and artificial large-scale persistent hy- ciated with the salt ponds. Atwater et al. (1979) suggested persaline ponds that are intermittently flooded with Bay that natural estuarine beach ridges along outer marsh water, and which occur within tidal salt marsh systems edge were responsible for the impoundments of salt of San Francisco Bay and San Pablo Bay. Historic natu- marsh that created salt ponds near San Lorenzo. Some ral salt ponds were characterized by persistent thick ac- salt ponds at the northern end of the local San Lorenzo cumulation of salt inundated with concentrated seawa- distribution were certainly associated with well-defined ter brines. They were restricted to a relatively narrow barrier sand spits (U.S. Coast Survey T-charts, 1850s), reach of San Francisco Bay near San Lorenzo Creek. which were probably nourished by sand eroded from They are distinguished here from related salt marsh fea- submerged Merritt sand deposits (Pleistocene marine tures such as pans and which occur at smaller spatial beach and dune). Less well-defined transgressive berms scales, have distinctive physiographic traits, and lack of sand and coarse organic detritus may have been de- strong persistent (perennial) brines and precipitated posited on top of the erosional marsh edge south of the crystaline salt deposits. Artificial salt ponds (solar sand spits themselves. Similar transgressive beach-marsh salterns) are diked salt marshes which are managed for berms today act as dams enclosing freshwater to brack- the production of concentrated brine and fractional crys- ish ponds and marshes in Drake’s Estero, Point Reyes tallization of sea salts. Natural and artificial salt ponds and at one location in San Francisco Bay (Whittell are presumed to share the same narrowly adapted hyper- Marsh, Point Pinole, Contra Costa County). U.S. Coast saline biota. Survey T-charts also indicate numerous sandy barrier Information on modern artificially engineered salt beaches which dammed (either permanently or intermit- pond systems is derived principally from the biological tently) lagoons. The impoundment of Crystal Salt Pond literature on solar salterns and hypersaline environments by a wave-constructed swash bar or beach ridge would (Javor 1989, and references within), historic documen- distinguish it morphologically, hydrologically, and topo- tation on the salt industry in California from the State graphically from more common salt marsh ponds (pans) Division of Mines (Ver Planck 1958, 1951; Dobkin and which occurred as depressions, sometimes extensive, Anderson 1994) and regional documentation produced between tidal creeks. These were widely distributed in by the local salt industry and government regulatory salt marshes in the South Bay. Extensive, elongate pans agencies (Corps of Engineers, San Francisco District, also occurred near and below the upland borders of salt Regulatory Branch permit and compliance files; Office marshes; these have been termed “ transitional” pans, al- of Counsel files, and references within). Information on though their position and form do not necessarily indi- historic salt pond systems is limited to descriptive his- cate a gradual ecotonal relationship with alluvial or up- toric accounts and descriptions, detailed topographic land habitats. maps of natural salt ponds prior to extensive dike con- Salt ponds today (solar salterns) are artificially man- struction (U.S. Coast Survey T-charts, 1956), and field aged and engineered diked Baylands converted from tidal investigations by the author comparing modern salt pans, salt marsh. The first artificial salt ponds began as exten- marsh ponds, and artificial salt ponds. sions and improvements of natural salt ponds which oc- curred near Hayward (Crystal Salt Pond), but most of Environmental Setting the contemporary man-made salt pond system is estab- lished in former tidal marsh that included few or no Salt ponds are large, shallow, hypersaline impoundments perennial hypersaline ponds. Artificial salt ponds have or depressions in tidal salt marsh systems which undergo entirely displaced their natural forerunners; no natural a sequence of infrequent flooding with saline or brackish true salt-crystallizing ponds remain in San Francisco Bay Bay water, evaporative , and formation of today, although related smaller salt pans and marsh strong hypersaline brines and deposits of gypsum, calcium ponds containing weak brines in summer and fall do carbonate, and crystalline salt (halite; sodium chloride). occur. Historic salt ponds were mapped with a high de- Classification of Salt Ponds – Javor (1989) placed gree of resolution in the 1856 U.S. Coast Survey. They marine-derived hypersaline aquatic environments in four were nested within particular portions of the salt marshes ecological salinity classes:

Chapter 1 — Plant Communities 43 The first salinity class (ca. 60 - 100 ppt) contains cipitation is evident in them. These and similar pans may a highly diverse, productive biota dominated by marine appear white with sun-bleached dried algal mats, which species. This class would correspond to “ low salinity” resemble salt flats. High densities of true natural marsh ponds (a misnomer, since salinity exceeds seawater con- ponds, also termed “ drainage divide ponds” (owing to centration), from intake ponds to the next one or two their position in poorly drained marsh areas between

Plants stages that support abundant macroalgae and fish. tidal creeks), also occur in the Petaluma Marsh. Marsh The second class (ca. 100 - 140 ppt) is dominated ponds are a variation of salt pans which are topographic by specially adapted halophilic species which are related depressions flooded by spring tides, and support to freshwater taxa, not marine taxa. The organisms in- submergent vegetation, typically macroalgae (such as clude abundant cyanobacteria, unicellular green algae, Enteromorpha spp.) and beds of widgeon-grass (Ruppia brine shrimp, and various halobacteria. maritima), indicating brackish to near-marine salinity. The third class (ca. 140 - 300 ppt) is distinguished The beds of marsh ponds are usually a soft organic oil- by marked reduction of species diversity (loss of cyano- like black muck composed of decayed, waterlogged or- bacteria, most invertebrates other than brine shrimp), ganic matter. and dominance of Dunaliella and brine shrimp. In contrast with salt ponds in estuaries with strong The fourth class (300 ppt to salt saturation, near marine influence, such as , San Francisco 360 ppt) contains only Dunaliella and bacteria at low Bay salt ponds are relatively nutrient-rich and sustain productivity. high primary productivity (Javor 1989). Nutrient-poor The first class predominates in modern marsh salt pond conditions promote microbial mats, while ponds. The historic natural salt pond complex probably planktonic microalgae tend to dominate nutrient-rich varied seasonally between Javor’s second to fourth hy- salt pond systems (Javor 1989). Most salt ponds in San persaline classes. Other natural marsh pans were most Francisco Bay support richly pigmented and somewhat likely predominantly in the first class only, becoming sea- turbid organic “ soups” of Dunaliella, halobacteria, cyan- sonally hypersaline, and supporting relatively weak brines obacteria, dissolved organics and organic particulates and macroalgal cover. Natural historic salt ponds were and, often in ponds between approximately 120 - distinguished from other types of inundated depressions 200 ppt salinity, large “ blooms” of brine shrimp which in salt marshes by the persistent thick halite deposits, in- graze primarily on Dunaliella. dicating perennial hypersaline conditions, and their large Historic natural salt ponds were unlike modern lake-like size. In these aspects, they differ from shallow artificial salt ponds in that they were not differentiated marsh ponds and marsh pans, which are regularly geographically into stable hypersaline classes, but varied flooded during higher spring tides, and either remain only seasonally in salinity. Natural salt ponds went persistently ponded or develop thick algal mats which through a seasonal “ intake” phase during extreme high desiccate in summer (bleaching white in the sun, resem- spring tides (December-January and June-July), when bling salt deposits in aerial photographs), or only develop Bay water flooded them and diluted them with brack- thin, temporary salt films on unvegetated mud and peat. ish to saline Bay water, seldom exceeding 20 ppt, and Various marsh pan features are represented in U.S. typically between 2 - 10 ppt in winter. During summer- Coast Survey maps of the mid-19th century, but only a fall evaporation periods, brines formed in situ, ranging few have persisted in modern rare remnant tidal marshes, in salinity over time up to crystallization (saturation) near such as Petaluma Marsh, Rush Ranch and Hill Slough 360 ppt. In contrast, the modern engineered salt pond (Solano County). Elongate marsh ponds are evident system is based on timed transfers of brines between along the upland edge of historic marshes, particularly ponds, resulting in spatial separation of brines at differ- in eastern and southern parts of San Francisco Bay. Some ent stages of concentration, and fractional crystallization of these may have been influenced by surface runoff and of various seawater salts (other than sodium chloride, groundwater seepage from adjacent alluvial uplands, and halite), such as magnesium and potassium salts (bit- could have been less saline than other marsh depressions terns), gypsum (calcium sulfate) and lime (calcium chlo- most of the year. Some historic elongate marsh edge pans ride) in different ponds. In this system, crystallization may also have been the unvegetated upper intertidal sur- is restricted to relatively few ponds engineered to facili- face of alluvial fans and terraces, consistent with small tate harvest of halite deposits, and relatively stable hy- modern “ transitional pans” observed at Hill Slough, persalinity regimes are established for individual evapo- Solano County. These also lack brine and halite devel- rator ponds in the system (Ver Planck 1958). opment. Modern elongate marsh pans have formed in The sequential and spatial separation of brines in recently (100 year) prograded marshes adjacent to Mare artificial salt pond systems also produces salt pond Island dredge ponds. These ponds are about 0.3 m deep “ types” which are not fully analogous to natural systems. in winter and spring, and range from brackish (nearly The late stages of brine production near sodium chlo- fresh) in winter to hypersaline when ponded areas are ride crystallization produce strong non-sodium brines highly reduced in summer, but no significant halite pre- called “ bittern.” Bittern brines (or bittern) are a concen-

44 Baylands Ecosystem Species and Community Profiles trated solution of sodium chloride, magnesium chloride and sulfate, and potassium chloride and sulfate. The

ionic balance of highly concentrated bittern is toxic even Plants to bacteria, and saturated bittern is considered sterile (Javor 1989). During winter rains, dilute bittern strati- fies on top of the concentrated bittern, and brine shrimp may appear seasonally, indicating algal production (Jim Swanson, Rick Coleman, pers. comm.). Natural salt pond brines did include bittern salts; in fact, the “ low quality” of early California solar salt was due to bittern, and the modern solar saltern system is principally devised as a method to fractionate sodium and bittern salts. Crys- Bob Walker tallizer ponds, which are used to precipitate halite, are Modern salt ponds are artificially managed and engineered diked baylands converted from tidal salt also maintained near the limits of halotolerance of Dun- marsh. (South San Francisco Bay) aliella (which can nonetheless fix carbon up to salt satu- ration; Javor 1989), but undergo seasonal dilution dur- ing winter rains. plankton (principally Dunaliella salina), which charact- erize moderate to high hypersaline conditions. Macro- Salt Pond Plant Community algal salt pond communities also correspond with fish- dominated animal communities, while phytoplankton- Salt ponds support a distinctive and highly specialized dominated brines are associated with brine shrimp abun- halotolerant to halophilic biota consisting of microalgae, dance. photosynthetic bacteria, and invertebrates, but no vas- Dunaliella spp. is ubiquitous in salt ponds in San cular plants (except along the edges of artificial salt pond Francisco Bay. It is reported to survive, and can be pho- levees). The dominant photosynthetic organisms of most tosynthetically active, in brines which are close to satu- hypersaline San Francisco Bay salt ponds are a single- rated (near 350 ppt), but may be absent in some ex- celled green algal species, Dunaliella salina (Chlorophy- tremely concentrated brines and bittern (potash-phase, cophyta) and numerous species of blue-green bacteria or potassium-magnesium) brines (Javor 1989, Brock (Cyanobacteria), halobacteria, and purple sulfur-reduc- 1975). Its optimum salinity for growth is near 120 ppt, ing bacteria. The proportions of these organisms vary about four times the concentration of seawater. Dunal- with salinity. Artificial eutrophic salt ponds with salini- iella salina concentrates carotenoid and other pigments ties closer to marine concentrations (near 35 ppt; “ in- in response to various forms of physiological stress, in- take ponds” ) are dominated by marine macroalgae such cluding salinity. It can be used as a crude color-indica- as sea-lettuce (Ulva spp.), Enteromorpha spp., Cladophora tor of brine salinity: cells growing in 50-100 ppt are spp., and also sometimes support Fucus spp. and Codium greenish, and turn yellowish-green in 150 ppt brine. spp. where substrate is stable and firm. They also include Reddish hues occur in brines 200-250 ppt (Javor 1989). marine diatoms, dinoflagellates, and cryptomonads. Purplish-red hues in brines over 200 ppt may be con- There are no detailed studies of the species diversity, dis- tributed by halophilic bacteria. A conspicuous mosaic of tribution or geographic variation of the halophilic mi- salt pond hues are readily visible from aerial views of San croflora communities of San Francisco Bay. Francisco Bay, particularly in summer and fall. Dunal- Managed and engineered contemporary salt iella osmoregulates in hypersaline brines by concentrat- ponds are ecologically similar in many respects to their ing glycerol as a compatible osmotic solute in its cyto- natural precursor salt ponds, and presumably share the plasm (Javor 1989). same algal and bacterial microflora. Indicator Species – There are no detailed classifi- Reference sites cations or analytic studies of salt pond algal communi- ties. Following Javor’s (1989) classification of hypersa- There are currently no reference sites in the San Fran- line environments (see Classification of Salt Ponds, cisco Bay Estuary for true natural salt ponds (ponds above), two broad hypersaline algal communities may be which periodically or chronically produce crystalline salt identified: communities dominated by free-floating ma- deposits). The historic salt pond system near San rine macroalgae typical of upper tidepools near marine Lorenzo Creek in Alameda was eliminated by diking in salinities to low-hypersaline conditions, corresponding the 1850s and 1860s. All modern salt pans and marsh to intake ponds and young brines in a saltern series (e.g., ponds in the Bay Area differ from these historic salt Ulva spp., Enteromorpha spp., Cladophora spp.; also bot- ponds. Most existing marsh ponds are only slightly hy- tom-mat forming cyanobacterial colonies); and commu- persaline, or briefly hypersaline in late summer, and sup- nities dominated by motile unicellular halophilic phyto- port algal mats rather than brines and halite beds. Most

Chapter 1 — Plant Communities 45 existing salt pans within small modern Bay Area salt acres, based on the precise pond outline represented on marshes are comparatively small and produce sparse and the 1856 T-chart (R. Grossinger, personal communica- thin (few mm) salt crusts in summer and fall. In con- tion). If, however, the pond size fluctuated seasonally (as trast, reference sites for artificial salt ponds are abundant. expected from winter rainfall and tidal flooding), the Examples of (relatively) low salinity intake ponds, which ponded area may have been several thousand acres from

Plants are saline or slightly hypersaline, are found at Pond B1/ late fall to spring. Two smaller ponds with similar con- B2 in Mountain View, Pond 1 near , and figuration occurred north of San Lorenzo Creek, and Pond A9 in Alviso. Examples of intermediate hypersa- were clearly associated with sandy barrier beach depos- line ponds (known as concentrators or evaporators) are its at the bayward edge of the marsh. (It is not clear found in ponds A10-14 in Alviso, ponds 2-8 near Coy- whether these northern satellite ponds produced high ote Hills, and ponds 2-6 between Mowry Slough and concentration brine and halite, or were merely intermit- Coyote Creek. High hypersaline ponds (strong brines ap- tently hypersaline lagoons). Crystal salt pond was used proaching or reaching salt saturation, “ pickle” ) are found as a salt source by aboriginal inhabitants of the Alameda in extensive crystallizer beds near Newark and Redwood shoreline, and was exploited by early Mexican, Spanish City, ponds 10 and 26 near Newark, and periodically in and U.S. settlers (Ver Planck 1951, 1958). Early de- drained evaporators before they are re-filled. scriptions of Crystal Salt Pond indicate that it con- Modern salt marsh (and brackish marsh) pans may tained a persistent crust of crystalline salt up to eight be found in few remnant pre-historic tidal marshes at inches thick, and the brines and salt contained “ im- Petaluma Marsh (abundant), China Camp (scarce) and purities” of concentrated non-sodium salts (“ bittern” Point Pinole (Whittell Marsh; scarce). Pans vary in to- salts, principally magnesium chloride and sulfate; Ver pography. Some upper marsh pans are similar to patches Planck 1958). of salt flats, while pans in middle marsh zone depressions The natural halite deposits of Crystal Salt Pond are normally shallow ponds 10-20 cm deep. Pans which were exhausted rapidly by the infant salt collecting in- become ponded, either because of depressional topog- dustry; by 1860 they were largely depleted. Artificial en- raphy or marsh surface drainage barriers, develop algae hancement of solar evaporation of brines was initiated or widgeon-grass. Salt marsh pans also occur in histori- around 1853, when salt harvesters (farmers who used salt cally accreted marshes at Mowry Marsh. Elongate marsh for tanning leather and curing meats, and expanded into pans fringing uplands (“ transitional” pans) have also the salt industry) began manual construction of low formed in the relatively young (20th century) salt marsh berms around natural salt ponds to enhance their capac- at Emeryville Crescent and adjacent to Mare Island ity to retain saline floodwaters and capture and precipi- dredge ponds. Elongate but diffuse shore-parallel marsh tate their salt loads. These artificially enhanced natural pans, perhaps best regarded as incipient pans, are found salt ponds became the nucleus of the solar salt industry. along the east end of the fringing salt marsh at High- By the end of the 19th century, the salt ponds of way 37. Small but well-differentiated semi-circular to San Francisco Bay were still confined to the northern semi-linear salt marsh pans occur in peaty coastal salt portion of the Alameda shoreline, from San Leandro marshes at Limatour Spit, Point Reyes; Bolinas Lagoon; Creek to Alvarado (Union City). They did not comprise Morro Bay; Elkhorn Slough; and along Tomales Bay. a salt pond “ system,” but were an aggregation of many Morro Bay, Bodega Bay, and Bolinas Lagoon also have independently owned and operated enterprises. Exten- elongate shallow salt marsh pans fringing alluvial depos- sive conversion of salt marsh to salt ponds in south San its. Most of these salt marsh pans are brackish in winter Francisco Bay did not occur until the 20th century. This and spring, but become moderately hypersaline (usually was facilitated by the consolidation of almost all the in- 40-60 ppt, rarely > 90 ppt) in summer (Baye, unpub. dependent salt operations to a few (dominated by Leslie data) when inundated. Salt Company) in the 1930s. Permit requests to the Corps of Engineers to dam numerous sloughs and Historic and Modern Distribution marshes in the South Bay were not filed until the early 1920s. Actual levee construction would have taken at The historic (pre-1860) location of natural salt ponds least several years, and new ponds take about 5 - 7 years within San Francisco Bay was probably restricted to the to “ seal” (become impermeable after gypsum and carbon- Alameda shoreline in the vicinity of San Lorenzo Creek ate precipitation; Ver Planck 1958, Dobkin and Ander- (between the historic Thompsons’s Landing and Union son 1994); therefore, the 1920s ponds were probably not City Creek). This area included an extensive complex of fully functional salterns until around 1930. The last both connected and isolated large ponds in a matrix of extensive marshes in the Alviso and Sunnyvale areas were salt marsh. The complex was labelled as “ Crystal Salt not diked for conversion to salt ponds until the early Pond” on the 1856 U.S. Coast Survey T-chart of the 1950s (Pacific Aerial Photo archives). was not area. The San Francisco Estuary Institute estimates the converted to salt pond until the 1950s, although it had acreage of Crystal Salt Pond to be approximately 1660 previously been diked for agricultural use. The modern

46 Baylands Ecosystem Species and Community Profiles extent of salt ponds in the southern reaches of South Bay, to be less “ productive” of salt, and more biologically “ pro- therefore, is relatively recent compared with the north- ductive,” by reducing the efficiency of brine and salt pro-

ern Alameda salt ponds. The Napa salt ponds are even duction. This could be achieved by increasing the flux Plants more recent: the diked Baylands of the Napa marshes in intake ponds, and reducing the residence time of were converted from derelict agriculture (seasonal sub- brines in each pond transfer. In winter, when brines are saline to brackish wetlands) to salt ponds between 1953 diluted by rainwater, they could also be re-mixed with and 1959. Salt production ceased there in the mid- intake Bay water and redischarged to the Bay at near- 1990s, but most of the system remains hypersaline. marine salinities. Relative change – The minimum acreage of true There have been recent tidal marsh restoration de- natural salt pond in San Francisco Bay was less than signs for artificial but naturalistic ponds and pans, but 2,000 acres (SFEI 1998); the maximum acreage (assum- no marsh restoration designs have included equivalents ing seasonal expansion of Crystal Salt Pond by flooding, of salt ponds. In principle, naturalistic salt ponds could and assuming that northern satellite ponds were brine/ be artificially created and naturally maintained by repli- halite ponds) could have been on the order of 3,000 - cating the hypothetical historic conditions of Crystal Salt 4,000 acres. Other marsh pan habitats were not likely Pond (as inferred by Atwater 1979). This would entail to support persistent hypersaline algal communities and deposition of coarse sediments (sand or shell hash) at the were presumably dominated by marine-related macro- edge of a high-energy marsh shoreline, to be reworked algae or Ruppia, as are most salt marsh pans today. How- as beach ridges which restrict marsh drainage. In theory, ever, if a significant proportion of the historic extensive beach ridges would maintain form and size as they re- elongate lake-size marsh ponds fringing uplands (Red- treat with the eroding marsh edge, given ample sediment wood City to Palo Alto, and in the Newark vicinity) were supply and overwash processes. Under less natural geo- seasonally or perennially hypersaline, the total acre- morphic settings for salt ponds, artificial naturalistic salt age of salt pond habitat could have been on the order ponds could be created by constructing low, broad berms of 5,000 - 10,000 acres. There is very weak indica- made of bay mud or sand that would be set at elevations tion that elongate upland-fringing salt marsh pans ever enabling highest spring tides to overtop them. Low, wide contained persistent strong brines supporting the nar- berms would be less prone to gullying and breaching row hypersaline algal/bacterial community, however. than steep levees, but would require some degree of Today, approximately 9,500 acres of derelict salt maintenance. Maintenance would be minimized by set- ponds remain in San Pablo Bay, and over 29,000 acres ting salt pond levees within restored marshes which of artificial salt pond are actively maintained in San would shelter them from wave erosion of the open Bay. Francisco Bay. Restored naturalistic salt ponds would undergo extreme variation of salinity within and between years, depend- Conservation Issues ing on rainfall variation, evaporation conditions, and storm surges. Exotic Species – Salt pond microbial taxa are wide- Sea Level Change and Levee Maintenance – The spread geographically, but narrowly distributed ecologi- modern salt pond levee system requires periodic main- cally. They are probably subject to dispersal by water- tenance, and levees bordering the open Bay (not shel- fowl and marine transport. There are no currently tered by fringing salt marsh) require frequent mainte- recognized exotic species “ threats” to salt ponds as there nance, armoring, or both. The need for levee maintenance are with vascular plants in salt marshes. (topping with fresh dredged sediment) is likely to become Restoration – The crude technology for creating more frequent if storm frequency increases or sea level artificial salt ponds (levee construction, wind-driven rises, as would be expected with global warming (Moffatt pumps, tidegates) has been well developed for over a cen- and Nichol and WRA 1988). Borrow pits along the in- tury. There is little doubt that complete artificial salt terior side of salt pond levees become depleted over time, pond systems can be created and maintained at a wide and some old borrow ditches have been widened so range of sizes, from as little as 20 - 50 acre historic “ fam- much that dredges need to re-handle material to bring ily size” or one-man operations (Ver Planck 1958), to it within reach of levees. Dredging tidal marshes as an the modern systems in the tens of thousands of acres. alternative source of sediment is unlikely, since it Low-salinity “ intake” ponds can also be maintained in- causes conflicts with endangered species habitat. dependently, in the absence of a salt-producing system, Therefore, sea level rise is likely to cause long-term by balancing influx of Bay water, residence time and re- increases in costs and risk of levee failure of the ex- discharge at near-marine salinity. No new salt ponds have isting salt pond system. Sea level rise could also make been constructed since the 1950s, although ponds have naturalistic salt pond restoration more difficult, since been interconverted from one type to another since then beach ridges or low levees are more likely to breach (evaporator ponds to bittern disposal/“ storage” ). Small and allow excessive (though restricted) tidal exchange and autonomous salt pond systems could be modified to impounded areas.

Chapter 1 — Plant Communities 47 Conclusions and Recommendations bay, preferably nested in the landward reaches of restored salt marsh areas, and managed to maintain The commercial salt pond operations of San Francisco intermediate strength brines rather than salt Bay are unlikely to continue indefinitely because of eco- production; nomic changes in the Bay region and in the salt indus- 3. Salt pond restoration and alternative management

Plants try, and due to physical changes in the levee and bor- should aim for temporally variable as well as row ditch system. Salt ponds are not likely to regenerate spatially variable salinity and brine depths; spontaneously as a result of natural geomorphic processes 4. Both artificial and naturalistic salt pond restoration when salt marshes are restored. Other more common should aim for designs which minimize mainte- types of pans and ponds are unlikely to establish in young nance requirements; and salt marshes; they are mature marsh features, associated 5. An initial target acreage for salt ponds should with well-differentiated marsh topography. The environ- reflect the uncertainty of restoring sustainable salt mental setting associated with salt ponds has been radi- pond environments after commercial salt produc- cally altered; the combination of steep and relatively tion ceases. We suggest that an initial target of high-energy Bay shorelines, coarse sediment supply, and approximately 10,000 acres (equivalent to late 19th extensive high salt marsh with impeded tidal drainage century acreage) be stipulated and modified based no longer exists. It is also likely that the feasibility of on the results of salt pond restoration and alterna- maintaining the erosion-prone levee system of the arti- tive pond management. ficial salt ponds will decrease over time, as borrow ditches (sources of mud for levee repair) are depleted. Therefore, References new and artificial measures will be required to conserve at least historic amounts of salt pond habitats within the Atwater, B., S.G. Conard, J.N. Dowden, C.W. Hedel, Estuary in the long term. The highest priority setting R. L. MacDonald and W. Savage. 1979. History, for salt pond restoration of some type would be on the landforms, and vegetation of the Estuary’s tidal Alameda County shoreline, from approximately San marshes. In: T.J. Conomos (ed). San Francisco Bay: Leandro to the Dumbarton Bridge, where the Bay shore- The Urbanized Estuary. American Association for line profile and wave fetch may be conducive for forma- the Advancement of Science, Pacific Division, Proc. tion of beach ridges (marsh berms), given appropriate of the 58th Annual Meeting. sediment size and supply. Brock, T.D. 1975. Salinity and ecology of Dunaliella from There is no minimal ecosystem size for salt ponds. Great Salt Lake. J. General Microbiol. 89:285-282. The basic grazer food chain between Dunaliella and Dobkin, M. and R.B. Anderson 1994. Oliver Bros. Salt Artemia can be maintained in extremely small systems. Co. Alameda County, California: Historic Resource However, the full microbial diversity of San Francisco Evaluation Report. Contract 04F828-EP, Task Or- Bay salt ponds, which has not been analyzed in detail, der #1, ALA-2, P.M. R0.0/R6.4, EA # 003050, would probably not persist in small ponds. Also, since prepared for Calif. Dept. Transportation, District the stability of natural salt ponds is inherently low (sub- 4 (Oakland). ject to ordinary natural fluctuations as well as cata- Javor, B. 1989. Hypersaline Environments. Springer- strophic changes), microbial diversity would be better Verlag. conserved with a large system of semi-independent salt Moffatt and Nichol and Wetlands Research Associates. ponds. Pre-historic salt pond acreage was probably on 1988. Future sea level rise: predictions and impli- the order of 2,000 acres. Aiming at this minimal acre- cations for San Francisco Bay. Report prepared for age, in the absence of any experience at restoration of BCDC (San Francisco Bay Conservation and De- naturalistic salt ponds or “ alternative” management of velopment Commission). solar salterns, would probably be insufficient to conserve San Francisco Estuary Institute (SFEI). 1998. Draft spa- a diverse halophilic microflora. tial analysis of the Baylands ecosystem. San Fran- We therefore recommend that long-term conser- cisco Estuary Institute, Richmond, Calif. vation of salt ponds entail the following actions: Ver Planck, W.E. 1951. Salines in the Bay Area. In: Geo- 1. Pilot projects should be undertaken that incorpo- logic Guidebook of the San Francisco Bay Coun- rate naturalistic salt pond designs as integral ties, Bulletin 154, State of Calif. Dept. Natural components of large-scale tidal marsh restoration Resources, Division of Mines. on the northern Alameda shoreline; ______. 1958. Salt In California. Bulletin 175, State of 2. Some existing salt ponds should be divided into Calif. Dept. Natural Resources, Division of Mines. smaller, autonomous units away from the open 168 pp.

48 Baylands Ecosystem Species and Community Profiles tation that are protected from summer marine air flow Plant Communities Ecotonal and fog. By leaching mineral nutrients from surface soils,

high rainfall also retards growth of herbaceous vegeta- Plants to the Baylands tion that could otherwise compete with forest tree seed- Glen Holstein lings (Holstein 1984a). Bay Area mean annual precipitation varies from 13 Introduction inches at San Jose and Antioch to 47 inches at Kentfield in Marin County (Felton 1965). Not surprisingly, rela- The San Francisco Bay estuary wetlands ecosystem his- tively undisturbed upland vegetation consists of redwood torically included vegetated and non-vegetated areas. and mixed evergreen forests near Kentfield (Shuford Dominant among physical factors influencing estuarine 1993) and of grassland near Antioch and San Jose vegetation was the semi-diurnal tidal cycle. As a conse- (Critchfield 1971). The Bay Area receives its precipita- quence, vegetation exposed to tides differed dramatically tion from cyclonic storms with predominantly southwest from plant communities that existed above the tides. For winds arriving from the Pacific Ocean. Consequently non-estuarine vegetation diurnal factors were relatively stations with large mountains to the southwest lie in rain insignificant; annual climate cycles and non-cyclic geo- shadows with reduced precipitation. Antioch, for ex- logical factors were the dominant influences. Substrates ample, is in the lee of Mount Diablo, and San Jose is in in vegetated parts of the Estuary consisted almost entirely the lee of the Santa Cruz Mountains. Kentfield, para- of Bay mud (Louderback 1951, Wahrhaftig et al. 1993). doxically, is also in the lee of a mountain, Mt. Tamalpais, Beyond it they were much more heterogenous. but is close enough to receive an increase in rainfall caused by its orographic lifting. In most of the bay area, Environmental Setting however, mean annual rainfall is between 15 and 25 inches (Gilliam 1962). Within this range, vegetation is Vegetation increases in structural diversity and species controlled more by geologic substrate and slope exposure richness beyond the estuarine ecosystem boundary in a than relatively minor local differences in mean annual complex pattern caused by interactions between the rainfall (Critchfield 1971). physical factors of climate, geology, and hydrology. In the San Francisco Bay Area, fog and associated Climate – The San Francisco Bay Area, like all the marine air chilled by offshore reduce summer California Floristic Province (Hickman 1993), has a cli- evapotranspiration and cause local climates to be mesic, mate characterized by wet winters and dry summers. where summer marine air flow is strongest and fogs most Such climates are called “ Mediterranean” because simi- frequent. Such conditions reduce plant growth and re- lar climatic conditions occur in the Mediterranean Ba- sultant biomass, however, since they limit light and sin, but the San Francisco Bay Area’s Mediterranean cli- warmth. High biomass forest vegetation also seldom oc- mate is more extreme than much of its namesake since curs in areas directly exposed to salt-laden winds associ- it rarely receives any significant rainfall during the years’s ated with marine air flow (Holstein 1984a). warmest five months (Wernstedt 1972). Despite ample Summer water stress causes incomplete cover and water, plant growth is retarded in winter by low tempera- much bare ground in most Mediterranean climate veg- tures and short days. Growth is maximal in spring when etation. In parts of the San Francisco Bay Area, however, temperature and day length significantly increase and marine air flow and fog mitigate summer drought suffi- reserves of soil water from winter rains are still abundant ciently for occurrence of vegetation types like coastal (Walter 1979). scrub and prairie characterized by very complete cover The diversity of the San Francisco Bay Area climate and little bare ground despite relatively low biomass is explained, to a great extent, by variation in two fac- (Holstein 1984a). tors; winter precipitation and summer marine air flow. Summer marine air flow and fog arrive at the Pa- Both cause local climates to be relatively mesic, but their cific Coast predominantly from the northwest because maxima rarely coincide and do not identically affect veg- of anticyclonic origins, but a shallow semi-permanent etation. High winter precipitation makes abundant soil temperature inversion confines their movement into and moisture reserves available for rapid spring and early through the San Francisco Bay estuary to just a few low summer plant growth where low temperatures and fog altitude gaps in the Coast Range. By far, the most im- brought by marine air flow do not limit it. Since rapid portant of these is the Golden Gate (Gilliam 1962). plant growth increases biomass, high biomass vegetation Since marine air flow and fog suppress summer types like redwood and mixed evergreen forests are fre- temperatures, mean July temperature is a reliable indi- quently dominant in the Bay Area where rainfall is high- cator of their relative presence or absence in the San est. A popular myth contends redwoods (Seqouoia Francisco Bay Area. Not surprisingly, San Francisco’s sempervirens) require summer fog. What they actually July mean of 58.8°F is the lowest around the Estuary require (and are limited to) are places with high precipi- because of its location at the Golden Gate. Antioch’s July

Chapter 1 — Plant Communities 49 mean of 74.0°F is the highest of any Estuary station as microtopographic patterns arising from ground shak- since the low hills of northern Contra Costa County ing during earthquakes (Berg 1990) or interaction of lo- protect it from marine air flowing into the Central Val- calized soil processes and wind erosion (Abbott 1984). ley through the Carquinez Strait. Fairfield’s July mean Non-alluvial uplands around the Estuary consist of of 72.1°F indicates more direct exposure to that air flow uplifted hills underlain by a variety of pre-Holocene sedi-

Plants despite its more inland location. Mount Diablo State mentary and volcanic rocks. These include the Mesozoic Park’s entrance station has a July mean of 74.3°F because Franciscan formation and Great Valley Beds; Cenozoic of its location above the inversion that limits marine air sediments consisting of Paleocene, Eocene, Miocene, to low elevations. Most Estuary stations have July means Pliocene, and Pleistocene marine beds and Pliocene non- in the sixties, but a difference of just a few degrees within marine deposits; and the Pliocene Sonoma volcanic de- that range can profoundly effect summer climate. Ber- posits (Jennings 1977, Norris and Webb 1990). The in- keley (61.5° F), Richmond (62.0° F), and Oakland fluence of these rocks on vegetation is most frequently (62.4°F) have the lowest summer temperatures in the controlled by their clay content. Those with abundant Estuary next to San Francisco because of their location clay like Paleocene, Eocene, Miocene, and Pliocene sedi- directly east of the Golden Gate. Burlingame (62.3°F) ments weather to deep soils much like those on Holocene and the San Francisco Airport (62.7°F) are also relatively alluvium and predominantly support similar grassland low because of their location at the east end of the San vegetation. The Mesozoic deposits include areas where Bruno coast range gap (Gilliam 1962). Kentfield clay is abundant and others where it is scarce. As on other (65.9°F), in contrast, is relatively warm in July because clay-rich substrates, deep soils and grasslands dominate Mount Tamalpais protects it from summer fog as well the former in contrast to the thin soils and woody veg- as inducing its high winter rainfall. Distance from the etation types predominant where clay is scarce. The Pacific Coast is generally a poor predictor of summer Franciscan Formation, a melange of soft clay sediments marine air flow. Redwood City (67.9°F) on the west side and hard metamorphic rocks, has a particularly complex of the Bay, for example, is warmer than Newark (64.9°F) vegetation pattern since grass dominates the former and on the east side since the latter is more directly exposed trees the latter. Pleistocene marine beds and the Sonoma to air flow through the Golden Gate (Felton 1965, volcanics are relatively clay poor and consequently largely Gilliam 1962). Coastal scrub and coastal prairie, the support woody vegetation types like oak woodland and vegetation types most associated with summer fog, are mixed evergreen forest (Ellen and Wentworth 1995, common on the outer Pacific Coast but relatively scarce Critchfield 1971). in the San Francisco Bay Estuary because the parts of it Grass is dominant on clay soils because they have most exposed to summer fog were also those settled ear- a relatively high water holding capacity (Walter 1979). liest and urbanized most completely (Hoover et al. 1966, West of Cordelia in Solano County, for example, Dibble- Donley et al. 1979). Los Osos and Hambright loams occur on adjacent hills Geology – Holocene alluvium characterized by in the same climate. Dibble-Los Osos soils develop on abundant clay and level topography surrounds slightly clay-rich Eocene marine sediments and consequently over half the Estuary and is consequently the most abun- have B2t horizons containing accumulated clay and a dant geologic substrate beneath its adjacent non-tidal water-holding capacity of 5 to 7 inches. Hambright soils, vegetation (Jennings 1977, Wahrhaftig et al. 1993). Bay in contrast, develop on Sonoma volcanics, lack a B2t ho- Area uplands underlain by alluvium were farmed early rizon, and have a water holding capacity of only 2 to 3.5 and are now largely urbanized, but historic accounts and inches (Bates 1977). Despite identical precipitation, relict stands indicate open grassland was their over- Dibble-Los Osos soils support grassland and Hambright whelmingly dominant vegetation type before settlement soils support oak woodland dominated by coast live oak (Bryant 1848, McKelvey 1955). An exception was a few (Quercus agrifolia) because the former’s B2t retains soil oak savannas where widely spaced valley oaks (Quercus water that can be used by the shallow fibrous root sys- lobata) occurred in a grassland matrix. Such savannas tems of grasses. Since Hambright soils retain much less were most frequent around the northern part of the water, the excess infiltrates to the fractured rock below Estuary where rainfall was relatively high, but even there where it can be utilized by deep roots of trees but not they were most frequent in areas protected from sum- grasses. In May, evidence of the Dibble-Los Osos B2t’s mer marine air flow. water retention capacity is plain in the hills above A specialized feature of California Holocene and Cordelia since grass stays green there several weeks longer older alluvium with level topography is vernal pools, on Dibble-Los Osos soils than it does on the Hambright small closed basins that fill in winter and dry during despite the frequent shade of oaks. This phenomenon spring. They support a characteristic specialized flora rich illustrates that two very different vegetation types can be in annual forbs (Holland and Jain 1977). Vernal pools equally “ mesic” and that oak woodland and grassland are were long thought to result from gopher activity competitive enough within this region for slight soil dif- (Dalquest and Scheffer 1942), but are better explained ferences to shift dominance from one to the other.

50 Baylands Ecosystem Species and Community Profiles The geologic factor that most influences vegetation types. Numerous other local hydrological features around around the San Francisco Bay Estuary is the physical ef- the San Francisco Bay Estuary like springs, seeps, and

fect of clay on soil water holding capacity, but chemical shallow water tables are associated with distinctive local Plants effects are also locally important. Serpentinite, associated vegetation types. The relatively shallow water table un- with the Franciscan Formation and occurring at the der most valley oak savannas is a notable example. Estuary’s edge in Marin and San Francisco counties, is so chemically distinctive because of its high Mg/Ca ra- Ecotonal Plant Communities tio and frequent heavy metals that it supports unique vegetation types and many endemic plant species (Kruck- Plant communities surrounding the Baylands ecosystem eberg 1984). Soils beyond the limits of tides are also are here classified using the system of Holland and Keil usually much less saline than those under tidal influence, (1995). At present the most widely used and influential but salts can locally accumulate to high levels in non- classifications of California vegetation are derived from tidal areas where drainage is poor. Salt especially accu- Munz and Keck’s (1959) mixed system, which includes mulates in non-tidal areas where precipitation is low, taxonomic, physiognomic, and ecological information. relief is subdued, and Cretaceous Great Valley beds pro- Barbour and Major’s extensive (1977) review of Califor- vide a salt source (Chapman 1960; Johnson et al. 1993; nia vegetation, for example, was organized around a Harris 1991). Geology also strongly affects microclimate slightly modified and expanded version of Munz and wherever hills have been uplifted since their south slopes Keck’s system. The units of their classification were receive more sunlight, warmth, and resultant evapotrans- vegetationally ill-defined, however, since the plant spe- piration than their north slopes. Vegetation on Bay Area cies lists provided for each one lacked even estimates of hills is consequently relatively xeric on south slopes and relative dominance. Some very important plant commu- relatively mesic on north slopes (Bakker 1984). nities like riparian forests were also missing from both Hydrology – The influence of geology and climate Munz and Keck’s system and Barbour and Major’s sub- on soil water is discussed above. Streams also tend to sequent review. It is doubtful Munz and Keck intended increase in frequency and flow duration as rainfall in- their brief plant community synopsis to so profoundly creases. Since they provide water to plants in greater influence California vegetation science, however, since quantities and different seasons than local climates, they the primary purpose of their book was clearly floristic. support distinctive riparian vegetation types not found Its success at remaining California’s floristic standard for in upland areas. Not surprisingly, riparian and upland decades undoubtedly strongly contributed to the influ- vegetation become increasingly distinct as rainfall de- ence of its community classification. creases (Holstein 1984b). Streams and their associated Sawyer and Keeler-Wolf (1995) have recently tried riparian vegetation are usually narrowly linear landscape to overcome the Munz and Keck system’s problems by features, but they can broaden dramatically when streams developing a comprehensive alternative that excludes reach base level and form deltas. A broad willow-com- ecological information from community definitions ex- posite zone now removed by urbanization that report- cept in the case of certain specialized habitats like ver- edly once occurred around the southern edge of San nal pools. The Sawyer and Keeler-Wolf system presents Francisco Bay (Cooper 1926) undoubtedly represented its own new problems, however, since it lumps quite dif- covergent deltaic riparian vegetation of several creeks that ferent stable and successional communities when they flow into the Bay. are dominated by the same species. Excluding most eco- Alluvium in streambeds tends to be coarser and logical information also causes very different coastal and thus better aerated than interfluvial alluvium, and the alpine communities sharing only a generic relationship running water of streams is also relatively well-aerated. between their dominant species to be lumped into catch- Streamsides consequently provide suitable environments all groupings like “ Sedge series.” Many local dominance for roots of woody riparian vegetation. In freshwater types present in California’s complex vegetation are also marshes, however, standing water in poorly drained missing from their system despite its numerous series and interfluvial areas quickly causes anaerobic reducing con- apparent comprehensiveness. ditions to develop at such shallow depths that only her- Holland and Keil avoid these problems by greatly baceous vegetation with shallow, predominantly fibrous increasing the comprehensiveness and consistency of root systems can occur. The herbaceous freshwater Munz and Keck’s limited but fundamentally sound sys- marsh vegetation is consequently quite distinct from tem. The result is a system outstanding for simplicity, predominantly woody riparian vegetation (Holstein ease of use, and realistic description and classification of 1984a). California vegetation. Beginning with coastal sand dune Freshwater marsh vegetation grades into vernal vegetation and concluding with freshwater vegetation pool vegetation through a series of transitional seasonal and anthropogenic environments, the plant community marsh vegetation types and into moist grassland through descriptions below follow the system developed by Hol- a transitional series of lowland wet meadow and swale land and Keil.

Chapter 1 — Plant Communities 51 1. Coastal Sand Dune Vegetation – Sand is a dis- into Pleistocene deposits, the Aromas sand. Agricultural tinctive substrate for plants since water infiltrates it very development has removed some natural vegetation rapidly leaving little moisture available for plants with around Elkhorn Slough, but remaining relict stands are shallow root systems (Walter 1979). Sand differs from still numerous. Topographic features recorded prior to other substrates like fractured rock which have similarly development of the port of Oakland and Lake Merritt

Plants high infiltration rates, however, because of sand’s high resemble those along Elkhorn Slough (Wahrhaftig and subsurface homogeneity and lack of resistance to root Birman 1965). penetration. Large sand deposits are characteristic land- At Antioch, a sandy area is also present immedi- scape features of coasts and arid areas. In Holland and ately east of Broad Slough. It is less urban than Alameda, Keil’s (1995) system, followed here, vegetation on sand but most of its dune vegetation was lost to sand mining deposits of arid areas is classified as desert sand dune veg- prior to urbanization. A small protected remnant of such etation and consequently distinguished from vegetation vegetation at Antioch supports several state and feder- on coastal sands. In California, however, some dune ally listed rare animal and plant species (Sawyer and fields are located in areas neither coastal nor truly arid. Keeler-Wolf 1995). Antioch is significantly hotter and Examples occur on the Merced River alluvial fan in drier than the outer coast, and its sand probably origi- Merced County and at Antioch in Contra Costa County nated from nearby sand deposits that extend southward (Wahrhaftig et al. 1993). The former was produced by along the inner Coast Range. The affinity of its distinc- outwash from glacial erosion of granite in the Yosemite tive sand dune flora and vegetation is consequently closer Valley (Wahrhaftig and Birman 1965), but extensive to Holland and Keil’s (1995) desert sand dune commu- Eocene to Pliocene sandstone deposits in nearby hills nity than to either of his coastal dune communities. (Ellen and Wentworth 1995) are a likely source for the Because a rain shadow occurs along the inner Coast latter. Neither the Merced or Antioch dunes are dis- Range, the ranges of several plant and animal species cussed by Holland and Keil, but both occur in semi-arid with desert affinities, including the relatively well-known areas and share more floristic features with their desert San Joaquin kit fox (Vulpes macrotis ssp. mutica) (Zeiner sand dune vegetation type than their coastal sand dune et al. 1990), extend north along the western San Joaquin vegetation types. Valley to near Antioch. Pioneer dune vegetation occurs where significant 2. Coastal Scrub – Coastal scrub refers to com- aeolian movement of sand limits development of stable munities dominated by small shrubs in non-desert ar- soil and vegetation. eas of California. Coastal scrub typically develops on soil Ambrosia chamissonis is its characteristic dominant, and friable sediments rather than conglomerate or frac- and Abronia latifolia, Achillea millefolium, Atriplex tured hard rock and consists of shrubs with relatively californica, Atriplex leucophylla, Calystegia soldanella, shallow root systems. Camissonia cheiranthifolia, Lathyrus littoralis, Leymus Northern coastal scrub is a dense shrub-dominated mollis, and Lupinus chamissonis are frequent associated community which most frequently occurs on steep slopes species (Barbour and Johnson 1977). receiving strong prevailing onshore winds and at least 20 Dune scrub occurs where stable soil and vegetation inches of precipitation, but can also occur as an ecotone have developed on sand of dunes usually considerably between northern oak woodland and southern oak wood- older than those supporting pioneer dune vegetation. land on slopes with less wind. Most typically, however, Ericameria ericoides is the characteristic dominant of it occurs where precipitation and soils are adequate for dune scrub, and associated species include Artemisia development of forests, but tree growth is prevented by californica, Baccharis pilularis, Lotus scoparius, Lupinus strong onshore winds. Since moisture is not limiting, arboreus and Lupinus chamissonis (Barbour and Johnson cover is typically complete (Heady et al. 1977). 1977). Baccharis pilularis is the characteristic dominant, Sand is relatively rare around the San Francisco Bay but Mimulus aurantiacus, Rhamnus californica, and Toxi- estuary, but a significant deposit, the Pleistocene Merritt codendron diversilobum can also occasionally be locally sand, is present at Alameda and adjacent parts of Oak- dominant. Characteristic understory species include land (Radbruch 1957). Since the local climate is marine, Achillea millefolium, Anaphalis margaritacea, Eriophyllum some areas with surface deposits of Merritt sand prob- staechadifolium, Gaultheria shallon, Heracleum lanatum, ably once supported pioneer dune and dune scrub Polystichum munitum, Pteridium aquilinum, Rubus communities similar to those now occurring along the ursinus and Scrophularia californica. Northern coastal outer Pacific Coast. The sandy area at Alameda and Oak- scrub is most common along the outer Pacific Coast but land was one of the first places along the Bay to urban- also occurs at suitable sites around the San Francisco Bay ize, however, and any dune vegetation present there was Estuary near the Golden Gate, in the Berkeley Hills, and consequently eradicated before it could be described. A in San Mateo County. Baccharis pilularis frequently in- modern analogue with similar soils and climate is vades disturbed grasslands and forms communities which Elkhorn Slough (Monterey County), which is incised superficially resemble northern coastal scrub but lack

52 Baylands Ecosystem Species and Community Profiles most of its characteristic species. Eventually such recently quent on steep slopes but can also occur with relatively invasive B. pilularis stands may develop into stable coastal low relief on stone alluvial fans in valleys.

scrub or oak woodland communities (Heady et al. 1977). Holland and Keil (1995) subdivide California Plants A protected example of northern coastal scrub occurs chaparral into 11 subclasses, of which six occur in San near the estuary at . Francisco Bay counties. These are not separately treated Southern coastal scrub is a relatively open shrub- here, however, since relatively little chaparral of any kind dominated community occurring most frequently on occurs in the Estuary’s immediate vicinity. steep, dry slopes. It is commonest in areas receiving un- Chaparral is dominated by shrubs in the genera der 20 inches of precipitation but can occasionally oc- Adenostoma, Arctostaphylos, Ceanothus, Cercocarpus, and cur in wetter areas on sunny south slopes. It typically Quercus, which form a functional group characterized by occurs where soils otherwise suitable for grassland are ex- deep root systems adapted for extracting water from deep cessively drained because of steepness. Because water is cavities in fractured rock. The sclerophyllous leaves of the primary limiting factor in southern coastal scrub, its chaparral shrubs are adapted for maintaining low levels dominant shrubs tend to be widely spaced, forming rela- of evapotranspiration and associated productivity dur- tively incomplete cover. In spring, when water stress is ing long growing seasons (Walter 1979, Mooney and briefly relieved, a diverse annual forb flora develops in Miller 1985). Discussions of chaparral ecology have long interstices between the dominant shrubs (Mooney emphasized its adaptation to fire since its shrubs use a 1977). variety of strategies to rapidly reoccupy burns and an as- Artemisia californica is the characteristic dominant, sociated functional group of annuals has seeds that re- and common associated species include Eriogonum nu- main dormant for decades and only germinate follow- dum, Eriophyllum lanatum, Lotus scoparius, Lupinus ing chaparral fires (Biswell 1974). Extensive research on albifrons, Mimulus aurantiacus and Nassella pulchra. Adenostoma-dominated chaparral suggesting a relatively Small stands of southern coastal sage scrub occur in hills short fire cycle my not be directly applicable to other around the Estuary and are especially frequent east of chaparral types, however, since some other kinds of chap- South San Fracisco Bay and south of Suisun Bay, where arral may have a much longer fire cycle (Keeley and precipitation is relatively low. An example occurs along Keeley 1988). the Estuary shore at Point Richmond. The nearest extensive chaparral to the Estuary oc- Sea-bluff coastal scrub occurs where persistent salt- curs in Marin County on the slopes of Mt. Tamalpais laden onshore winds suppress most other plant commu- two miles west of San Francisco Bay (Shuford 1993, nities. Such climatic conditions resemble those in north- Wieslander and Jensen 1945). While chaparral on allu- ern coastal scrub but are more extreme. In such sites the vial fans is rapidly disappearing but still fairly common only communities are sea-bluff coastal scrub and north- in parts of southern California (Smith 1980), it is virtu- ern coastal grassland. The former tends to occur on rocky ally unknown in central and northern California. Coo- sites with thin soils and the latter on deeper soils that per (1926), however, reported that chaparral that has tend to be heavier, but both frequently intermix in a since been extirpated formerly occurred near the south- complex mosaic (Holland and Keil 1995). ern end of San Francisco Bay on Los Gatos Creek’s al- Eriophyllum stachaedifolium is the characteristic luvial fan. dominant, and frequently associated species include Ar- 4. Grassland – Vegetation dominated by grasses temisia pycnocephala, Baccharis pilularis, Erigeron glaucus, and graminoid sedges was widespread along the shores Eriogonum latifolium and Lessingia filaginifolia. Salt- of the San Francisco Bay Estuary prior to urban devel- laden winds strong and persistent enough to support this opment and is still fairly common there (Bryant 1848, community enter the Estuary through the Golden Gate McKelvey 1955). It occurs in non-wetlands wherever but rapidly lose their intensely marine character as they soils with clay horizons thick enough to hold significant move inland. Havlik (1974) described small stands of this water near the soil surface and to exclude air from deeper community at , Brooks Island, Red horizons are directly exposed to solar radiation. Clay soils Rock, Point Richmond, Point Fleming, and Potrero San are particularly favorable for grasses and other graminoids Pablo, all places directly exposed to marine winds enter- because the near-surface water they hold is preferentially ing San Francisco Bay through the Golden Gate. available to the dense, relatively shallow fibrous root sys- 3. Chaparral – Chaparral refers to a widespread tems of such plants. In wet climates the most mesic con- and characteristic California community dominated by ditions occur on soils with high clay content because of large shrubs with evergreen sclerophyllous leaves. It is their high water holding capacity, but in arid areas that frequent in areas with precipitation between 10 and 20 pattern is reversed. In deserts clay holds much water from inches per year and occasional in wetter areas on sunny scarce precipitation near the soil surface, where solar south slopes. Chaparral occurs where rocky soils with radiation quickly evaporates it (Walter 1979). Condi- little clay permit rapid infiltration of water and air to tions intermediate between these extremes prevail in the relatively great depths. Such conditions are most fre- semiarid climate surrounding most of the Estuary. Clay

Chapter 1 — Plant Communities 53 soils are xeric and grass-covered on plains and south differ from it in the presence of more bare ground and slopes, where they are directly exposed to solar radiation, many species not occurring at the Estuary shore. Coo- but mesic and covered by forest and woodland on north per (1926) reported Hemizonia congesta and H. pungens slopes, where solar radiation is reduced. Grassland is were formerly dominant on similar soils near the south- most prevalent where annual precipitation is between 10 ern end of the Estuary that are now completely covered

Plants and 20 inches but becomes progressively scarcer as an- by urban development. The best presently extant ex- nual rainfall increases. Some grassland is usually present amples of alkaline grassland in the Estuary’s vicinity oc- even in very wet areas, however, wherever clay is directly cur near Livermore in Alameda County and near exposed to solar radiation. Soils with sufficient clay for Fairfield in Solano County. Other distinctive grassland grassland predominate on the recent alluvium that forms types of unusual substrates supporting rare species are the floors of virtually all San Francisco Bay Area valleys; serpentinite grassland and sandy soil grassland (Skin- they are also common on hillslopes where clay-rich sedi- ner and Pavlik 1994). ments have been uplifted (Ellen and Wentworth 1995). Native annual forbland. Wester (1981) presented While direct solar radiation usually keeps grassland free evidence that the southern San Joaquin Valley, an area of woody plants on valley floors and south-facing hill- traditionally considered former grassland, was dominated slopes, similar grassland frequently dominates understo- by annual forbs prior to European settlement. Califor- ries beneath the oak woodland that occurs on north nia vegetation classification has traditionally called all slopes because of less intense radiation (Holstein 1984a). upland vegetation dominated by herbs grassland, but Native perennial grassland. Frequent relict stands and Wester’s work suggests much of the area traditionally clear descriptions by early travelers leave little doubt that mapped as grassland (Kuchler 1964) was actually native most native grassland near the Estuary on both valley annual forbland. Since native annual forbland occurs floors and hillslopes was dominated by a rhyzomatous where rainfall is insufficient for most perennial grasses, and largely sterile hybrid between Leymus triticoides and it consequently was most extensive far south of the Es- L. condensatus (Stebbins and Walters 1949). Hybrids be- tuary in the southern San Joaquin Valley. Numerous tween these species have been called Leymus xmultiflorus, relict taxa suggest, however, that a narrow native annual but since the hybrid dominant around the Estuary is too forbland corridor extended north from there to near the small to match descriptions of xmultiflorus (Hickman Estuary shore in Contra Costa County because of a rain 1993), it is here included in L. triticoides. Two frequently shadow along the inner Coast Range’s eastern base. associated rhizomatous graminoids were Carex barbarae Forbland elements also probably occurred even more and C. praegracilis, the latter being especially frequent widely wherever local conditions like soil infertility and at upland-wetland ecotones. Nassella pulchra, a non-rhi- trampling by megafauna suppressed otherwise ubiqui- zomatous bunchgrass, has received more attention than tous perennial grasses. Even today wildflower displays any other species as a native grassland dominant. It fre- (i.e., annual forb dominance) are most spectacular locally quently dominated grassland but mostly did so only near where soil is relatively infertile (i.e., Bear Valley in Colusa ecotones with coastal scrub and oak woodland where County and Table Mountain in Butte County [Faber heavy clay grassland soils had begun to thin and dissi- 1997]) and most spectacular generally in years, as in pate or where specific substrates like serpentinite pre- 1991, when winter drought suppression of competitive vented development of typical grassland soils (Bryant grasses is followed by forb-promoting heavy spring rains. 1848, McKelvey 1955). Some forbland species like Eremocarpus setigerus have Native grassland had numerous local variations adapted well to anthropogenic land use changes but oth- ranging from topographic lows where soil water and clay ers have become rare (Convolvulus simulans, Madia ra- accumulated to topographic highs where clay was thin diata) or extinct (Eschscholzia rhombipetala). and water scarce. Species indicating topographic lows Non-native annual grassland. Introduction of graz- (locally called swales) included Juncus balticus, Juncus ing and agriculture during the nineteenth century caused xiphioides, Ranunculus californicus, and Sisyrinchium a dominance shift in almost all of California’s grasslands bellum, while N. pulchra and a variety of forbs indicated from native perennial graminoids to Eurasian non-na- the highs. Along the Estuary shore at ecotones with tidal tive annual grasses. Today dominance among such an- marsh, Distichlis spicata, another rhizomatous grass, was nuals changes spatially in a complex pattern reflecting particularly prominent (Heady 1977, Holland and Keil soil conditions. On catenas from thick, heavy clay soils 1995). to thinner, lighter ones a typical annual grass dominance A scarce native grassland type especially significant sequence Lolium multiflorum-Bromus hordeaceus-Avena for its many rare plants occurs on salt-affected soils as- fatua-Avena barbata replaces a simpler perennial se- sociated with inland basins and basin rims rather than quence Leymus triticoides-Nassella pulchra still occasion- coastal tidelands (Faber 1997). These inland alkaline ally extant on the same catenas. Another common domi- grasslands share features like the prominence of Distichlis nance sequence Bromus hordeaceus-Bromus spicata with the grassland-tidal marsh ecotone but often diandrus-Hordeum murinum reflects shifts in soil nitro-

54 Baylands Ecosystem Species and Community Profiles gen content from low to relatively high. The above spe- mountain ranges. Contrary to an enduring myth, red- cies are the most frequently dominant non-native annual woods are negatively rather than positively associated

grasses, but others also occasionally participate. Cynosurus with summer fog. Consequently, even at sites protected Plants echinatus, for example, frequently dominates annual from onshore winds they are almost completely absent grassland where rainfall is relatively high. Several exotic along the immediate coast wherever summer fog is fre- forbs are also becoming increasingly important compo- quent. Redwoods survive summer drought not because nents in a vast exotic herbaceous vegetation type that of fog drip but by storing surplus water from high win- may only temporarily be called grassland. Vicia villosa ter precipitation in their massive trunks, a strategy that ssp. varia is increasingly planted for forage in the Avena has produced only slightly less dramatic gigantism in zone; Picris echioides is important in the Lolium zone; other conifer species where large winter water surpluses and Centaurea solstitialis, especially, is a widespread in- occur with summer drought. As a consequence north- vader of the B. hordeaceus zone, where Erodium botrys is ern California and southern Chile, both areas with un- also important when soil fertility is particularly low usually wet winters and dry summers located at the outer (Heady 1977, Holland and Keil 1995). Grazing is par- periphery of more typical Mediterranean climate zones, ticularly important for maintaining replacement of na- are the world’s two greatest centers of tree gigantism tive perennial grasses with exotic annual species. At (Holstein 1984a, Zinke 1977). numerous sites around the Estuary, for example, domi- Shade is so intense in the redwood forest under- nance is shifting back from exotic annual grasses to story that only a few plant species survive there. Two that Leymus triticoides and Carex barbarae where expanding do, Oxalis oregana and Polystichum munitum, are usu- urbanization has at least temporarily caused the removal ally the sole understory dominants. of grazing. 6. Mixed Evergreen Forest – Coastal prairie. Where clay soils are directly ex- Central California mixed evergreen forest. Forests posed to marine air flow, a floristically distinct grassland dominated by a mix of broadleaf and conifer evergreen occurs that Holland and Keil (1995) call northern coastal trees are frequent in California where precipitation is grassland but is widely known in California as coastal relatively high and winter temperatures are mild. In prairie. Coastal prairie is most frequent along the outer northern California the trees most frequently dominat- coast, but small amounts also likely occur near the Es- ing such mixed evergreen forests are Arbutus menziesii, tuary where marine air flow is particularly direct. Lithocarpus densiflorus, Pseudotsuga menziesii, and Um- Much of California’s coastal prairie is now domi- bellularia californica. In central California the term mixed nated by two exotic perennial grasses, Anthoxanthum evergreen forest as presently used is somewhat anoma- odoratum and Holcus lanatus, but many distinctive na- lous, however, since it often designates forests solely tive perennial grasses like Agrostis pallens, Calamagrostis dominated by Umbellularia californica, the California nutkaensis, Danthonia californica, Deschampsia cespitosa, laurel. Such laurel-dominated forests are frequent around Festuca idahoensis and Festuca rubra can also frequently the Estuary where annual rainfall is between 20 and 40 be locally dominant. Two other distinctive plant species inches. At the dry end of that precipitation range laurel indicative of coastal prairie are Iris douglasiana and Juncus forests are entirely confined to very shady north slopes patens (Heady et al. 1977). and canyons, but they also occur on somewhat sunnier 5. Coastal Coniferous Forest – Forests dominated slopes as 40 inches is approached. Above that they are by large coniferous trees occur along the eastern Pacific almost entirely replaced by redwood forests (Sawyer et Coast in a high rainfall zone extending from central Cali- al. 1977, Wainwright and Barbour 1984). fornia to Alaska. Holland and Keil (1995) recognize two The most commonly associated tree species in cen- subdivisions of coastal coniferous forest, but only one of tral California’s laurel forests is a non-evergreen, Acer these, redwood forest, occurs near the Estuary. macrophyllum. Arbutus menziesii is also a frequent asso- Redwood forest. Extensive forests dominated by ciate but is almost entirely confined to the rockiest slopes. Sequoia sempervirens, the well-known redwood and the Shade is so intense beneath laurel forest canopies that world’s tallest tree species, occur on the southern slopes completely bare ground is common where drought is an of Mt. Tamalpais within 1.75 miles of the Estuary added stressor, but as 40 inches is approached Polysti- (Shuford 1993), but individual redwoods occur in mixed chum munitum often dominates the understory. Holo- evergreen forest much less than a mile from the shore discus discolor, a deciduous species, is commonly domi- of San Pablo Bay at China Camp State Park. Redwoods nant in shrubby openings frequent in laurel forests are common up to about 2,000 feet in the California (Safford 1995). Coast Range wherever annual precipitation is above 40 7. Oak Woodland – Vegetation with an overstory inches and soil is relatively fertile. Despite sufficient rain- dominated by oak trees is common throughout California’s fall, sensitivity to cold prevents their occurrence along Mediterranean climate zone including the Estuary’s vicin- the Oregon coast beyond a few miles north of the bor- ity. Such oak woodlands primarily vary in species and der, at high elevations in the Coast Range, or on inland spacing of their overstory oaks. Vegetation is called sa-

Chapter 1 — Plant Communities 55 vannah where oaks are widely spaced and forest where great vegetational difference is a result of the way in spacing is so close their canopies are closed. Woodland, which the two substrates respond to precipitation — rain as a term, describes vegetation with intermediate spac- rapidly infiltrates to deep levels on the fractured volcanics ing, but tree separation is so locally variable in where it can be utilized by oak roots, whereas it is held California’s oak-tree dominated vegetation it is appro- at the surface on the clay-rich Markley where it is more

Plants priate to use the traditional term oak woodland to refer available to grass roots. Rapid infiltration on the volcanics to all of it. That generalized oak woodland can then be causes such xeric conditions in its surface soils that its divided into subclasses based on its dominant species few stands of annual grassland cease productivity and dry (Griffin 1977). two weeks earlier than Markley grasslands dominated by Since woodland oaks and grassland grasses occur the same species (Bates 1977, Ellen and Wentworth in similar environmental conditions, they frequently 1995). compete directly for water and other soil resources. Spe- Coast live oak woodland differs from other oak cific aspects of that competition are discussed for each woodland subclasses in the relative rarity of annual subclass but a few of its consequences are general. Oaks grasses in its understory. The most frequent dominant only occur where water is present in deep soil horizons, there is Toxicodendron diversilobum, poison oak, but where it may arrive horizontally through shallow aqui- Rubus ursinus and Symphoricarpus mollis are also often fers or vertically when precipitation is abundant enough important (Safford 1995). to infiltrate past dense but relatively shallow grass root Valley oak woodland consists of several structur- systems. Grassland grasses, in contrast, only occur where ally diverse communities sharing dominance by Quercus solar radiation is direct because overstory trees are either lobata that include savannah and woodland on clay hill- absent or so widely spaced their canopies are not con- slopes and savannah, woodland, and closed canopy for- tiguous (Walter 1979). est on alluvial plains over shallow unconfined aquifers. Coast live oak woodland, which is dominated by Alluvial valley oak woodland often occurs on the outer Quercus agrifolia, is distinctive among oak woodland sub- edges of riparian forest corridors (see below) on relatively classes because it consists almost exclusively of closed fine, heavy soils distinct from the coarse alluvial soils canopy forests. As a consequence it is frequently treated under typical riparian stream bank vegetation. Tree spac- as a subclass of mixed evergreen forest rather than oak ing in alluvial valley oak woodland is related to water woodland. It is included here with oak woodland, how- stress since canopies closed when subsurface water is ever, because of the affinities of both its dominant tree abundant become progressively more open as water stress and the majority of its fauna (Griffin 1977). increases, resulting first in woodland and then savannah. Coast live oak woodland occurs widely around the Much alluvial valley oak forest was removed because it Estuary where annual precipitation is between 15 and coincided with highly desired agricultural soils, but a few 40 inches and continentality is at least partially moder- stands are extant in the Central Valley and elsewhere. ated by marine influences. Marine air flow through Alluvial valley oak woodland was probably always scarce Carquinez Strait even permits occurrence of coast live near the Estuary, however, since it is better adapted to oak woodland with two isolated Coast Range-related inland Califonia’s hot summers than to the outer Coast mammal populations (Sylvilagus bachmani riparius and Range’s relatively marine climate. One of the few ex- Neotoma fuscipes riparia) on the Central Valley floor near amples near the Estuary is located along Green Valley Lodi (Zeiner et al. 1990). Creek near Cordelia in Solano County. In hills on clay soils coast live oak woodland is fre- Valley oak woodland is most frequent near the quently present as an extensive ecotone between grass- Estuary on clay hillslopes with annual rainfall between land and mixed evergreen forest since it occurs on slopes 15 and 40 inches, where its range overlaps coast live oak shadier than the former but sunnier than the latter. On woodland and foothill woodland. It is less abundant than slopes where rockier substrates and lighter soils permit either but more tolerant of clay soils than the former and infiltration of more water to greater depths, however, less resistant to water stress than the latter. The under- coast live oak is less limited by solar exposure and can story of valley oak woodland’s savannah and woodland even occur on south slopes. North of Carquinez Strait, phases typically consists of non-native annual and occa- for example, adjacent ridges with identical microclimates sionally native perennial grassland. Vegetation beneath differ only in their substrates. Ridges underlain by sedi- closed canopy valley oak alluvial forest, however, can in- ments of the clay-rich Eocene Markley Formation are clude both grassland and features shared with riparian covered by grassland and have coast live oak woodland forest or coast live oak forest understories. Valley oak only on north slopes and in canyons, while those under- reproduction, often low because of competition with lain by hard but fractured rocks of the Pliocene Sonoma annual grass and predation of seeds and seedlings by a volcanics are covered by coast live oak woodland on all variety of herbivores, can be abundant in alluvial wood- exposures but north slopes and canyons, where Umbel- land when suppression of grass by flooding coincides lularia-dominated mixed evergreen forest occurs. The with large acorn crops. Urban fringes are also favorable

56 Baylands Ecosystem Species and Community Profiles sites for valley oak reproduction because their low live- Dudleya, the California genus with the most highly stock and wildlife populations result in lowered seed and adapted chasmophytes, has a few taxa near the Estuary

seedling predation (Holstein 1984b, Holland and Keil but is much more diverse in Southern California. Plants 1995). Plants of rock outcrops are less specialized than Foothill woodland is woodland and savannah veg- chasmophytes but may be rare since they occur in dis- etation wholly or partially dominated by Quercus dou- tinctive microenvironments that consequently are free glasii, blue oak, that is widespread on hillslopes surround- from competition with surrounding vegetation. Rock ing the Central Valley. Near the Estuary, foothill outcrops and cliffs are most likely to support rare plants woodland is largely confined to the inner Coast Range. when they are mineralogically different from surround- The foothill woodland environment has a relatively con- ing landscapes, and one mineral receiving particular at- tinental climate with cool to cold winters, very hot sum- tention because of its frequent association with rare mers, and annual rainfall from 15 to 40 inches. Winter plants is serpentine. Soil development is so retarded and cold reduces understory grass growth and consequently vegetation so distinctive on serpentine that its occur- permits infiltration of a large part of the wet season’s rences may be viewed as extended rock outcrops even water surplus to deep subsoil where it can be utilized by though they occasionally cover many square miles blue oaks during spring and summer. In summer high (Bakker 1984, Skinner and Pavlik 1994, Fiedler and temperatures and low humidity produce very low water Leidy 1987). potentials in blue oak leaves that permit withdrawal of 9. Riparian Vegetation – Riparian vegetation re- water tightly held by clay-rich subsoils. fers to the distinctive plant communities of streambanks Blue oak is usually the sole foothill woodland domi- and ecologically related habitats. Its most salient envi- nant on clay hillslopes, but on slopes with more rock and ronmental features are relatively coarse alluvial soils typi- thinner soils it often shares dominance with Pinus cally associated with streams and root zone water sup- sabiniana. Blue oaks occur on a wider range of slope ex- plies greater than the local climate provides. When posures than many other oak species, but foothill wood- mature, California riparian vegetation is closed canopy land dominance often shifts to Aesculus californicus on forest, but early successional riparian vegetation can be shaded north slopes. In canyons and around rock out- shrubby. crops Quercus wislizenii is also often a local dominant. Near the Estuary riparian vegetation is overwhelm- Because of foothill woodland’s open canopy its ingly dominated by three species, Acer negundo, Salix understory is almost universally dominated by non-na- lasiolepis and Salix laevigata, but others may dominate tive annual grassland. Native forbs like Holocarpha in specialized habitats. Populus fremontii and Salix good- virgata, however, are also usually frequent there. Com- dingii are important where climate becomes less marine petition is particularly intense between annual grasses and more continental near the Central Valley; Salix and blue oak seedlings before they develop roots long exigua is important on sandbars and other habitats where enough to reach subsoil water. Seedling mortality at this early successional riparian vegetation is developing; Alnus stage is so intense that much foothill woodland consists rhombifolia and Salix lucida ssp. lasiandra are important almost entirely of mature blue oaks that germinated in where, as at Niles Canyon, streams with rocky beds flow the 1860’s, a decade when severe overgrazing reduced perennially; and Platanus occidentalis and Baccharis much presumably native perennial grassland from viminea dominate where ones with sandy and rocky beds California’s rangelands. Subsequent increase of non- flow intermittently. native annual grassland has severely restricted reproduc- Typical Acer negundo-Salix lasiolepis-Salix laevigata tion of foothill woodland developing at that time (Grif- riparian vegetation also is common where ecological con- fin 1977, Holland and Keil 1995). ditions simulate streambank environments, as at lake- 8. Cliffs and Rock Outcrops -Vegetation of cliffs shores and a variety of places with shallow water tables. and rock outcrops is usually virtually ignored in surveys On the outer coast non-streambank riparian vegetation of California vegetation including that of Holland and is frequent in dune slacks, but around the Estuary it at Keil (1995) because its areal extent is small and it con- least formerly was most frequent in sausals, microdeltas sists largely of non-vegetated surfaces. It is particularly occurring where stream channels and their subsurface important, however, as a habitat for rare plant species. water tables spread laterally as they entered tidal marsh. Cliffs are unique environments where soil and compe- Most sausals have been lost to urbanization of the tition with other plants is very limited and solar radia- Estuary’s periphery, but a small example occurs at China tion is often abundant. Plants adapted to cliffs (chasmo- Camp State Park. phytes) resemble epiphytes in producing small easily Common riparian understory plants near the Es- dispersed seeds in such great numbers that the likelihood tuary include Baccharis douglasii, Euthamia occidentalis, of reaching rare suitable germination habitats is in- Rosa californica, and Rubus ursinus. For a short distance creased. Seeds reaching these light-rich habitats can af- these can also replace riparian trees as dominants at the ford to be small because they require little stored food. ecotone with tidal marsh where a veneer of coarse stream-

Chapter 1 — Plant Communities 57 side alluvium deposited on tidal mud thins as it nears Soils beneath freshwater marshes may be mineral the Estuary. Like sausals, however, such riparian-tidal or organic. Despite otherwise similar vegetation fresh- marsh ecotones have almost entirely disappeared around water marshes with organic soils are technically fens. the Estuary because of urbanization (Holland and Keil Since organic soils derived from Scirpus acutus rhizomes 1995, Holstein 1984b). were general beneath the Delta’s tidal freshwater

Plants 10. Freshwater Vegetation – Freshwater wetland marshes, they once constituted a single vast fen (Atwater vegetation occurs where land surfaces are saturated by and Belknap 1980). Mineral soils, however, generally freshwater or shallowly covered by it. Its two main phases occur beneath the many small freshwater marshes near the Estuary, freshwater marshes and vernal pools, around the Estuary. Marshes develop most readily on are very distinctive but also united by intermediate com- fine, heavy mineral soils since these exclude air and cre- munities. ate the anaerobic conditions suitable for marsh vegeta- Freshwater marsh refers to vegetation dominated tion more readily than the coarse and readily aerated by plant species emergent from at least semi-permanent sediments common on streambanks beneath riparian shallow freshwater. The most frequently dominant fresh- forests. Since waterbirds quickly transport propagules water marsh species near the Estuary is Scirpus acutus, permitting establishment of freshwater marsh plants at but Scirpus americanus, Scirpus californicus, Typha angus- sites with suitable hydrological conditions regardless of tifolia, Typha domingensis, and Typha latifolia can also their climatic and geological environments, freshwater be important there as dominants. The Typha spp., in marshes are among the easiest plant communities to particular, are often dominant in early successional and restore (Kusler and Kentula 1990). nitrogen-enriched freshwater marshes. Continua exist between semi-perennial marshes Climate and geology have less influence on the dis- and both moist grassland swales (see above) and vernal tribution of freshwater marsh than they do on the oc- pools (see below). Vegetation of areas with hydrology in- currence of other plant communities. When vegetation termediate between freshwater marshes and vernal pools is primarily limited by precipitation, temperature, and pond longer than the latter but shorter than the former. light, its distribution is controlled by climate, and when These are most frequently dominated by Eleocharis limited by mineral nutrition and soil texture, its distri- macrostachya with normal winter wet season inundation bution is controlled by geology. The primary limiting but can also be dominated by Cyperus eragrostis when factor in freshwater marshes, however, is air, which, ponding resulting primarily from agricultural and urban while superabundant at the marsh surface, falls to such runoff occurs in the warm season. Vegetation arising low concentrations a short distance beneath it that en- from both kinds of seasonal ponding is properly called vironments too anoxic, reduced, and toxic for root seasonal marsh, but wildlife managers also frequently use growth are frequent there. All freshwater marsh domi- the term to describe non-tidal mudflat environments nants in California are consequently , extremely important for shorebird foraging. Such non- which have shallow fibrous root systems readily supplied tidal mudflats have little vegetation and once commonly with air by aerenchyma-rich stems. Many dicotyledons occurred where flooding temporarily suppressed normal including most trees and shrubs, in contrast, have solid grassland development on stream terraces. Streamflow stems and deep, non-fibrous root systems poorly adapted control and terrace urbanization, however, have greatly to anoxic conditions. California consequently lacks reduced traditional episodically flooded shorebird habi- swamps, vegetation in semi-permanent shallow water tat around the Estuary. Most non-tidal seasonal marshes dominated by woody plants, since it has no native trees presently occurring there consequently result from sea- or shrubs capable of completing life cycles in flooded sonal drawdowns of artificial ponds and floodways (SFEP environments. Buttonbush, Cephalanthus occidentalis, 1991a,b). and several species of Salix can tolerate extended flood- Limnetic vegetation refers to floating or submerged ing, however, and frequently occur at the ecotone be- vegetation occurring in open freshwater too deep or oth- tween freshwater marsh and riparian vegetation (Holland erwise unsuitable for marsh vegetation. Important na- and Keil 1995, Holstein 1984a,b). tive components of submerged limnetic vegetation near Both tidal and non-tidal freshwater marshes are fre- the Estuary include Ceratophyllum demersum, Najas quent around the Estuary, but the former are most im- guadalupensis, Potamogeton pectinatus and Potamogeton portant in the Sacramento-San Joaquin Delta immedi- pusillus, while important floating elements are Azolla ately upstream from the true estuary. The Delta filiculoides, Lemna gibba and Lemna minor. Non-native consisted almost entirely of tidal freshwater marsh be- species like Egeria densa and Mytiophyllum aquaticum are fore it was largely converted to agricultural land, but a now also extremely significant and often predominant few remnant tidal freshwater marshes still occur there. elements of submerged limnetic vegetation near the Small non-tidal freshwater marshes often resulting from Estuary, but the floating component consists almost en- human alteration of hydrologic conditions are also wide- tirely of extremely widespread and readily dispersed na- spread around the estuary (Bowcutt 1996). tive species except in and near the Delta, where non-na-

58 Baylands Ecosystem Species and Community Profiles tive Eichornia crassipes is important (Holland and Keil hydrologically resembling vernal pools but lacking their 1995). characteristic biota because of elevated salinity also oc-

Vernal pool vegetation refers to a distinctive plant cur. They are called playas when their surrounding sa- Plants community dominated by annual and short-lived peren- line environment is inland (Chapman 1960, Waisel nial forbs that occurs in microtopographic basins flooded 1972) and pans when it is coastal (Adam 1990, in the wet season and dry the rest of the year. Vernal pool Chapman 1960, Long and Mason 1983, Waisel 1972). plants are consequently adapted for beginning their life Both occur in San Francisco Bay Area counties but only cycle like submerged limnetic species but completing it the latter near the Estuary shore (SFEP 1991a). Today as terrestrial plants in completely dry environments. The vegetated pans near the Estuary are ubiquitously domi- vernal pool environment has led to adaptive radiation of nated by Cotula coronopifolia, an exotic annual that may numerous species primarily in the genera Downingia, have replaced a now extinct native annual Plagiobothrys Eryngium, Lasthenia, Navarretia, Plagiobothrys, and glaber. Psilocarphus, and it is these that dominate its vegetation. 11. Anthropogenic Environments – Anthropo- Plagiobothrys bracteatus, in particular, is the most fre- genic environments must be briefly considered because quent dominant of vernal pool vegetation around the they collectively now dominate non-tidal uplands around Estuary. Upland vegetation around vernal pools is almost the Estuary. The anthropogenic typology used here fol- invariably non-native annual grassland (Holland 1977). lows Mayer and Laudenslayer, Jr. (1988) rather than the The origin of vernal pool basins is obscure but may more complex one of Holland and Keil (1995). result from seismic activity or interaction of wind ero- Agricultural environments historically surrounded sion and soil processes (see above). To pond water and much of the Estuary but have become increasingly scarce create an environment suitable for vernal pool vegeta- because of displacement by urbanization. Structurally tion, however, an aquaclude or barrier to water infiltra- and physiologically different elements like orchards, vine- tion that may be a clay horizon, duripan, or bedrock yards, and both irrigated and dry farmed cropland are must be present immediately beneath the basin. Most included here, but all share low plant and animal diver- vernal pools and the plants adapted to them occur en- sity. Irrigated nursery crops are most important near the tirely or almost entirely in California, and few hydrologic southern part of the Estuary; and vineyards, irrigated features resembling vernal pools occur outside North pastures, and dry farmed oats (Avena sativa) predomi- America even in otherwise similar Mediterranean cli- nate near the northern part. mates (Thorne 1984). Urban and suburban environments now over- Vernal pools are at risk even in the Central Valley whelmingly dominate non-tidal uplands around the where they are most common because virtually all hu- Estuary. They often structurally resemble extended and man activities except rangeland grazing destroy the mi- unusually diverse riparian zones since irrigated non-na- crotopography and aquacludes that create the vernal pool tive trees predominantly in the genera Acacia, Eucalyp- environment. Around the Estuary they are even more tus, and Pinus are ubiquitously present above an even threatened since they are extremely rare near southern more diverse understory of ornamental shrubs and herbs. San Francisco Bay and only slightly more frequent north As a consequence, urban-suburban communities are of San Pablo and Suisun bays. Vernal pools north of Sui- probably the landscape unit near the Estuary with the sun Bay are particularly environmentally significant be- highest plant diversity but the fewest native plants. Some cause they are often partially dominated by Lasthenia native bird species have adapted to using urban areas as conjugens, a federally listed endangered species extinct habitat and become common, but far fewer terrestrial throughout much of its range (Skinner and Pavlik 1994). species are able to do so. Artificially created basins often sufficiently re- semble natural vernal pools to be colonized by a few Rare Plants of Ecotonal Plant Communities wide-ranging and extremely tolerant pool species. More rarely a few rare species may be present in such artificial Table 1.4 lists rare plant species found in the nine Bay sites. The full suite of vernal pool taxa including the Area counties. The table is organized using the same rarest species almost never develops in such environ- classification system (Holland and Keil) as was used in ments, however, because soil characteristics of natural the previous section. It includes, for each species, the pools can rarely be replicated. As a consequence creation state and federal listing status, as well as the status de- of artificial vernal pools has been the least successful of rived from the California Native Plant Society (CNPS) all wetland restoration efforts (Ferren and Gevirtz 1990, inventory (Skinner and Pavlik 1994). The CNPS inven- Kusler and Kentula 1990). tory is more complete than the state or federal listings Vernal pools typically are freshwater environments and is organized on the following lists: since their primary water source is precipitation (Hanes 1a. Presumed extinct et al. 1990). However, salt from underlying 1b. Rare, threatened, or endangered in California soils causes some to be slightly brackish. Seasonal pools and elsewhere.

Chapter 1 — Plant Communities 59 2. Rare, threatened, or endangered in California local floras since these are full of observations by bota- but more common elsewhere. nists with deep knowledge of their region’s plants and 3. Possibly rare, but more information is needed. habitats. Tragically, however, a number of plants near 4. Distribution limited: a watch list. the Estuary went extinct or became extremely rare in an Plants with the greatest need for protection are on older era when little or no ecological information was

Plants list 1b, and 1a (presumed extinct) plants are placed there provided when plants were collected. We can only specu- if rediscovered. The CNPS inventories rare plants by late regarding the niches of these taxa. county. To prepare Table 1.4, each of the CNPS-iden- Many species are rare because they occur in rare tified rare species was assigned to a modal plant com- ecological niches. Historically, these have not been the munity or ecotone based on information provided by focus of plant community classification, which is most state and local floras. An effort was made to place each concerned with the commonest kinds of vegetation. taxon in the plant community it most frequently (but While there was an effort to include some of the rarer not necessarily exclusively) occurs(ed) in, however, fre- niches occurring near the Estuary in Table 1.4, it is not quently reference materials regarding a taxon were con- comprehensive, and rare niches distant from the Estu- tradictory. In these cases I sought to develop a consen- ary are not included. Rare plants that occur primarily in sus view, and weighted local floras and my own field plant communities distant from the Estuary were not in- experience most heavily. cluded in the narrative community descriptions. The greatest constraint in preparing this table was It is hoped this table will generate discussion and the frequent sparsity of ecological information regard- suggestions for its improvement. ing rare species. Preparation was easiest in areas with

60 Baylands Ecosystem Species and Community Profiles Table 1.4 Rare Plant Species* Found in the Nine Counties Adjacent to the San Francisco Bay Estuary,

by Plant Community or Ecotone Plants 1. Sand dune vegetation Arctostaphylos montaraensis - FSC Arctostaphylos pallida - FPT, SE A. Pioneer coastal dune vegetation Arctostaphylos stanfordiana ssp. decumbens 1b. Abronia umbellata ssp. breviflora - FSC Ceanothus confusus - FSC Ceanothus divergens - FSC B. Coastal dune scrub Ceanothus foliosus var. vineatus - FSC 1b. Agrostis blasdalei - FSC Ceanothus masonii - FSC, SR Chorizanthe cuspidata var. cuspidata - FSC Ceanothus sonomensis - FSC Chorizanthe cuspidata var. villosa Malacothamnus hallii Chorizanthe robusta var. robusta - FE Plagiobothrys uncinatus - FSC Collinsia corymbosa 3. Calyptridium parryi var. hesseae Erysimum ammophilum - FSC +Arctostaphylos manzanita ssp. elegans Horkelia cuneata ssp. sericea - FSC Horkelia marinensis - FSC 4. Ceanothus purpureus Layia carnosa - FE, SE Dichondra occidentalis Lessingia germanorum - FE, SE Lomatium repostum Lupinus tidestromii - FE, SE Malacothamnus arcuatus +Gilia capitata ssp. chamissonis Malacothamnus helleri +Gilia millefoliata Orobanche valida ssp. howellii Plagiobothrys myosotoides 4. undulata A. Chaparral burns C. Inland dune vegetation 4. Calandrinia breweri 1b. Erysimum capitatum ssp. angustatum - FE, SE +Malacothrix phaeocarpa Oenothera deltoides ssp. howellii - FE, SE 2. Coastal scrub 4. Grassland A. Native perennial grassland A. Northern coastal scrub 1b. Amsinckia grandiflora - FE, SE 1b. Delphinium bakeri - FPE, SR Astragalus clarianus - FE, ST Lilium maritimum - FC Blepharizonia plumosa ssp. plumosa +Lupinus latifolius var. dudleyi pluriflora - FSC 3. Lupinus eximius - FSC Tracyina rostrata 4. Cirsium andrewsii Trifolium amoenum - FE Collinsia multicolor +Calochortus argillosus Piperia michaelii 3. Lessingia hololeuca Sanicula hoffmannii 4. Androsace elongata ssp. acuta B. Southern coastal scrub Fritillaria agrestis C. Sea-bluff coastal scrub +Allium peninsulare var. franciscanum 1b. Cirsium occidentale var. compactum - FSC +Microseris paludosa Grindelia hirsutula var. maritima - FSC Alkaline grassland Phacelia insularis var. continentis - FSC 1a. Tropidocarpum capparideum - FSC Silene verecunda ssp. verecunda - FSC 1b. Astragalus tener var. ferrisiae - FSC +Agrostis clivicola var. punta-reyesensis Astragalus tener var. tener +Gilia capitata ssp. tomentosa Atriplex cordulata - FSC +Piperia elegans ssp. decurtata Atriplex depressa 4. Arabis blepharophylla Atriplex joaquiniana - FSC Ceanothus gloriosus var. gloriosus Cordylanthus mollis ssp. hispidus - FSC Erysimum franciscanum - FSC Cordylanthus palmatus - FE, SE Hesperevax sparsiflora var. brevifolia Delphinium recurvatum - FSC +Agrostis clivicola var. clivicola Hemizonia parryi ssp. congdonii - FC Isocoma arguta – FSC 3. Chaparral +Trifolium depauperatum var. hydrophilum 1b. Arctostaphylos auriculata 3. Hordeum intercedens Arctostaphylos densiflora - FSC, SE Arctostaphylos imbricata - FPT, SE 4. Atriplex coronata var. coronata Arctostaphylos manzanita ssp. laevigata Thelypodum brachycarpum

* Derived from the inventory of the California Native Plant Society (CNPS) (Skinner and Pavlik 1994) Key to CNPS list codes: Key to Federal and State List Codes: 1a. Presumed extinct FE Federally listed as endangered SE State listed as endangered 1b. Rare, threatened, or endangered in California and elsewhere. FT Federally listed as threatened ST State listed as threatened 2. Rare, threatened, or endangered in California but more common FC Federal listing candidate SR State listed as rare elsewhere. FPE Proposed for Federal listing as endangered 3. Possibly rare, but more information is needed. FPT Proposed for federal listing as threatened 4. Distribution limited: a watch list FSC Federal species of special concern + Proposed new addition to the CNPS inventory

Chapter 1 — Plant Communities 61 Table 1.4 (continued) Rare Plant Species* Found in the Nine Counties Adjacent to the San Francisco Bay Estuary, by Plant Community or Ecotone

Sandy soil grassland 4. Piperia candida 1a. Eriogonum truncatum Pityopus californicus +Galium muricatum

Plants 4. Cryptantha hooveri Linanthus grandiflorus 6. Mixed evergreen forest Serpentinite grassland A. Central California mixed evergreen forest 1b. Acanthomintha duttonii - FE, SE 1b. +Quercus parvula var. tamalpaisensis Calochortus tiburonensis - FT, ST 3. +Viburnum ellipticum Castilleja affinis ssp. neglecta - FE, ST Fritillaria biflora var. ineziana 4. Cypripedium montanum Lessingia arachnoidea - FSC Dirca occidentalis Streptanthus niger - FE, SE Ribes victoris 3. Eriogonum luteolum var. caninum 7. Oak woodland 4. Astragalus breweri A. Coast live oak woodland Linanthus ambiguus 1b. Clarkia concinna var. automixa Moist grassland 4. Amsinckia lunaris 1a. Plagiobothrys hystriculus Isocoma menziesii var. diabolica 1b. Pleuropogon hooverianus - FSC, SR B. Valley oak woodland Sidalcea oregana ssp. hydrophila C. Foothill oak woodland 2. Carex californica 8. Cliffs and rock outcrops 4. Perideridia gairdneri ssp. gairdneri - FSC A. Cliffs B. Native annual forbland 3. +Streptanthus tortuosus var. suffrutescens 1a. Eschscholzia rhombipetala - FSC 4. Arabis modesta 1b. Madia radiata B. Rock outcrops 4. Convolvulus simulans 1b. Arctostaphylos virgata +Erodium macrophyllum Coreopsis hamiltonii - FSC C. Non-native annual grassland Penstemon newberryi var. sonomensis D. Coastal prairie Phacelia phacelioides - FSC Sanicula saxatilis - FSC, SR 1b. Blennosperma nanum var. robustum - FSC, SR Streptanthus callistus - FSC chorizanthe valida - FE, SE Streptanthus glandulosus var. hoffmanii - FSC Erigeron supplex - FSC Streptanthus hispidus - FSC Fritillaria lanceolata var. tristulis Fritillaria liliacea - FSC 3. Erigeron biolettii Holocarpha macradenia - FC, SE Monardella antonina ssp. antonina Limnanthes douglasii ssp. sulphurea - FSC, SE 4. Antirrhinum virga Plagiobothrys diffusus - FSC, SE Arabis oregona Sanicula maritima - FSC, SR Arctostaphylos hispidula Triphysaria floribunda - FSC Navarretia subuligera 3. Hemizonia congesta ssp. leucocephala Serpentinite outcrops Plagiobothrys chorisianus var. chorisianus 1a. Arctostaphylos hookeri ssp. franciscana - FSC 5. Coastal coniferous forest 1b. Allium sharsmithae A. Redwood forest Arctostaphylos bakeri ssp. bakeri - SR Arctostaphylos bakeri ssp. sublaevis 4. Elymus californicus Arctostaphylos hookeri ssp. montana - FSC B. Closed-cone coniferous forest Arctostaphylos hookeri ssp. ravenii - FE, SE 1b. Ceanothus gloriosus var. porrectus - FSC Astragalus rattanii var. jepsonianus Cupressus goveniana ssp. pigmaea - FSC Calochortus raichei - FSC Pinus radiata - FSC Campanula sharsmithiae - FSC C. North coast coniferous forest Ceanothus ferrisae - FE Chlorogalum pomeridianum var. minus 2. Boschniakia hookeri Clarkia franciscana - FE, SE

* Derived from the inventory of the California Native Plant Society (CNPS) (Skinner and Pavlik 1994) Key to CNPS list codes: Key to Federal and State List Codes: 1a. Presumed extinct FE Federally listed as endangered SE State listed as endangered 1b. Rare, threatened, or endangered in California and elsewhere. FT Federally listed as threatened ST State listed as threatened 2. Rare, threatened, or endangered in California but more common FC Federal listing candidate SR State listed as rare elsewhere. FPE Proposed for Federal listing as endangered 3. Possibly rare, but more information is needed. FPT Proposed for federal listing as threatened 4. Distribution limited: a watch list FSC Federal species of special concern + Proposed new addition to the CNPS inventory

62 Baylands Ecosystem Species and Community Profiles Table 1.4 (continued) Rare Plant Species* Found in the Nine Counties Adjacent to the San Francisco

Bay Estuary, by Plant Community or Ecotone Plants Cordylanthus nidularius - FC, SR Volcanic outcrops Cordylanthus tenuis ssp. capillaris - FE, SR 1b. Eriastrum brandegeae - FSC Cryptantha clevelandii var. dissita Dudleya setchellii - FE 4. Madia nutans Erigeron angustatus 9. Riparian vegetation Erigeron serpentinus 1b. Juglans californica var. hindsii - FSC Eriogonum nervulosum - FSC +Triteleia lugens Fritillaria falcata - FSC Hesperolinon bicarpellatum - FSC 4. Astragalus rattanii ssp. rattanii Hesperolinon breweri - FSC 10. Freshwater vegetation Hesperolinon congestum - FT, ST Hesperolinon drymarioides - FSC A. Freshwater marsh Hesperolinon serpentinum 1a. Castilleja uliginosa - FSC, SE Lessingia micradenia var. glabrata - FSC 1b. Alopecurus aequalis var. sonomensis - FE Lessingia micradenia var. micradenia - FSC Arenaria paludicola - FE, SE Madia hallii - FSC Campanula californica - FSC Navarretia rosulata Carex albida - FE, SE Sidalcea hickmanii ssp. viridis - FSC Lilium pardalinum ssp. pitkinense - FE, SE Streptanthus albidus ssp. albidus - FE Potentilla hickmanii - FPE, SE Streptanthus albidus ssp. peramoenus - FC Rhynchospora californica - FSC Streptanthus batrachopus - FSC Sidalcea calycosa ssp. rhizomata Streptanthus brachiatus ssp. brachiatus - FC Sidalcea oregana ssp. valida - FE, SE Streptanthus brachiatus ssp. hoffmanii - FC Streptanthus glandulosus ssp. pulchellus 2. Calamagrostis crassiglumis - FSC Streptanthus morrisonii ssp. elatus - FC Carex comosa Streptanthus morrisonii ssp. hirtiflorus - FC Carex leptalea Streptanthus morrisonii ssp. kruckebergii - FSC Rhynchospora globularis var. globularis Streptanthus morrisonii ssp. morrisonii - FSC 3. Equisetum palustre +Hoita strobilina 4. Calamagrostis bolanderi +Streptanthus breweri var. hesperidis Rhynchospora alba 3. Cardamine pachystigma var. dissectifolia +Zigadenus micranthus var. fontanus +Streptanthus glandulosus var. sonomensis B. Limnetic vegetation 4. Acanthomintha lanceolata 2. Potamogeton filiformis Asclepias solanoana Potamogeton zosteriformis Aspidotis carlotta-halliae 4. Azolla mexicana Calamagrostis ophitidis Ranunculus lobbii Calyptridium quadripetalum Campanula exigua C. Vernal pools Clarkia breweri 1b. Blennosperma bakeri - FE, SE Collomia diversifolia Gratiola heterosepala - SE Cordylanthus tenuis ssp. brunneus Lasthenia burkei - FE, SE Eriogonum argillosum Lasthenia conjugens - FE Eriogonum ternatum Legenere limosa - FSC Eriogonum tripodum Limnanthes vinculans - FE, SE Fritillaria purdyi Navarretia leucocephala ssp. bakeri Galium andrewsii ssp. gatense Navarretia leucocephala ssp. pauciflora - FE, ST Lomatium ciliolatum var. hooveri Navarretia leucocephala ssp. plieantha - FE, SE Navarretia jepsonii Neostapfia colusana - FT, SE +Ceanothus jepsonii var. albiflorus Tuctoria mucronata - FE, SE +Streptanthus barbiger 2. Downingia pusilla Granite and sandstone outcrops 3. Myosurus minimus ssp. apus - FSC 4. Arctostaphylos regismontana Pogogyne douglasii ssp. parviflora

* Derived from the inventory of the California Native Plant Society (CNPS) (Skinner and Pavlik 1994)

Key to CNPS list codes: Key to Federal and State List Codes: 1a. Presumed extinct FE Federally listed as endangered SE State listed as endangered 1b. Rare, threatened, or endangered in California and elsewhere. FT Federally listed as threatened ST State listed as threatened 2. Rare, threatened, or endangered in California but more common FC Federal listing candidate SR State listed as rare elsewhere. FPE Proposed for Federal listing as endangered 3. Possibly rare, but more information is needed. FPT Proposed for federal listing as threatened 4. Distribution limited: a watch list FSC Federal species of special concern + Proposed new addition to the CNPS inventory

Chapter 1 — Plant Communities 63 Table 1.4 (continued) Rare Plant Species* Found in the Nine Counties Adjacent to the San Francisco Bay Estuary, by Plant Community or Ecotone

4. Eryngium aristulatum var. hooveri - FC Lilium rubescens Psilocarphus brevissimus var. multiflorus Monardella viridis ssp. viridis Psilocarphus tenellus var. globiferus

Plants D. Mixed evergreen-serpentinite outcrops D. Thermal springs 4. Calochortus umbellatus 1b. Dichanthelium lanuginosum var. thermale - FSC, SE E. Rock outcrops-riparian - FE, ST napensis - FP, SE 1b. Delphinium californicum ssp. interius - FSC 4. Trichostema rubisepalum 11. Anthropogenic environments F. Serpentinite outcrops-riparian (including serpentine A. Agricultural seeps) B. Urban-suburban 1b. Cirsium fontinale var. campylon - FSC 12. Coastal marsh Cirsium fontinale var. fontinale - FE, SE Cirsium hydrophilum var. vaseyi - FSC A. Brackish marsh 4. Astragalus clevelandii 1b. Aster lentus - FSC Cypripedium californicum Cirsium hydrophilum var. hydrophilum - FE Delphinium uliginosum Cordylanthus mollis ssp. mollis - FE, SR Helianthus exilis Lathyrus jepsonii var. jepsonii - FSC Mimulus nudatus Lilaeopsis masonii - FSC, SR Senecio clevelandii var. clevelandii 2. Limosella subulata G. Coastal coniferous forest-riparian B. Saltmarsh 1b. Pedicularis dudleyi - FSC, SR 1b. Castilleja ambigua ssp. humboldtiensis - FSC 4. Cypripedium fasciculatum - FSC Cordylanthus maritimus ssp. palustris - FSC Pleuropogon refractus Suaeda californica - FE H. Oak woodland-serpentinite outcrops 3. Polygonum marinense - FSC 1b. Eriophyllum latilobum - FE, SE 4. Eleocharis parvula Grindelia stricta var. angustifolia I. Oak woodland-chaparral 13. Ecotones 1b. Calochortus pulchellus 4. Eriophyllum jepsonii A. Grassland-oak woodland J. Alkaline grassland-pans 1b. Helianthella castanea - FSC Monardella villosa ssp. globosa 1a. Plagiobothrys glaber Plagiobothrys mollis var. vestitus - FSC 4. Linanthus acicularis K. Coastal coniferous forest-coastal prairie B. Grassland-rock outcrops 1b. Sidalcea malachroides 1b. Balsamorhiza macrolepis var. macrolepis Clarkia concinna ssp. raichei - FSC L. Freshwater marsh-riparian Layia septentrionalis 1b. Sagittaria sanfordii - FSC Pentachaeta bellidiflora - FE, SE 2. Hibiscus lasiocarpus Stebbinsoseris decipiens - FSC M. Grassland-southern coastal scrub 4. Micropus amphibolus 2. Senecio aphanactis C. Mixed evergreen-chaparral N. Coastal prairie-northern coastal scrub 1b. Arctostaphylos andersonii - FSC Arctostaphylos canescens ssp. sonomensis 1b. Delphinium luteum - FPE, SR Cupressus abramsiana - FE, SE O. Grassland-chaparral Eriogonum nudum var. decurrens 1b. Clarkia imbricata - FE, SE Lupinus sericatus Horkelia tenuiloba Penstemon rattanii var. kleei P. Northern coastal scrub-riparian 4. Calystegia collina ssp. oxyphylla - FSC Erythronium helenae 4. Veratrum fimbriatum

* Derived from the inventory of the California Native Plant Society (CNPS) (Skinner and Pavlik 1994)

Key to CNPS list codes: Key to Federal and State List Codes: 1a. Presumed extinct FE Federally listed as endangered SE State listed as endangered 1b. Rare, threatened, or endangered in California and elsewhere. FT Federally listed as threatened ST State listed as threatened 2. Rare, threatened, or endangered in California but more common FC Federal listing candidate SR State listed as rare elsewhere. FPE Proposed for Federal listing as endangered 3. Possibly rare, but more information is needed. FPT Proposed for federal listing as threatened 4. Distribution limited: a watch list FSC Federal species of special concern + Proposed new addition to the CNPS inventory

64 Baylands Ecosystem Species and Community Profiles References Ellen, S. D. and C. M. Wentworth. 1995. Hillside ma- terials and slopes of the San Francisco Bay region.

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Chapter 1 — Plant Communities 65 Hoover, M. B., H. E. Rensch, E. G. Rensch, and W. N. the San Francisco Estuary. Oakland: San Francisco Abeloe. Historic spots in California, 3rd edition. Estuary Project. Stanford, Calif.: Stanford Univ. Press. ______. 1991b. Status and trends report on wildlife Jennings, C. W. 1977. Geologic map of California. of the San Francisco Estuary. Oakland: San Fran- Reston, Va.: US Geological Survey. cisco Estuary Project.

Plants Johnson, S; G. Haslam; and R. Dawson. 1993. The great Sawyer, J. O.; D. A. Thornburgh; and J. R. Griffin. Central Valley: California’s heartland. Berkeley: UC 1977. Mixed evergreen forest. In: M. Barbour and Press. J. Major (eds). Terrestrial vegetation of California. Keeley, J. E. and S. C. Keeley. 1988. Chaparral. In: M. New York: Wiley. pp. 359-381. Barbour and W. Billings (eds). North American Sawyer, J. O. and T. Keeler-Wolf. 1995. A manual of terrestrial vegetation. Cambridge, UK: Cambridge California vegetation. Sacramento: Calif. Native Univ. Press. pp. 165-207. Pant Society. Kruckeberg, A. R. 1984. California serpentines: flora, Shuford, W. D. 1993. The Marin County breeding bird vegetation, geology, soils, and management prob- atlas: a distributional and natural history of coastal lems. Berkeley: UC Press. California birds. Bolinas, Calif.: Bushtit Books. Kuchler, A. W. 1964. Potential natural vegetation of the Skinner, M. W. and B. M. Pavlik. 1994. California Na- United States. American Geographical Society Spe- tive Plant Society’s inventory of rare and endan- cial Publication # 36. New York: American Geo- gered vascular plants of California, Special Publi- graphical Society. cation #1, 5th ed. Sacramento: Calif. Native Plant Kusler, J. A. and M. E. Kentula (editors). 1990. Wet- Society. land creation and restoration: The status of the Smith, R. L. 1980. Alluvial scrub vegetation of the San science. Covelo, Calif.: Island Press. Gabriel River floodplain, California. Madrono 27: Long, S. P. and C. F. Mason. 1983. Saltmarsh ecology. 126-138. Glasgow: Blackie. Stebbins, G. L. and M. S. Walters. 1949. Artificial and Louderback, G. D. 1951. Geologic history of San Fran- natural hybrids in the Gramineae, tribe Hordeae. cisco Bay. In: O. Jenkins (ed). Geologic guidebook III. Hybrids involving Elymus condensatus and E. of the San Francisco Bay counties: Calif. Division triticoides. American Journal of Botany: 36: 291- of Mines Bulletin 154. San Francisco: Calif. Divi- 301. sion of Mines. pp. 75-94. Thorne, R. F. 1984. Are California’s vernal pools unique? Mayer, K. E. and W. F. Laudenslayer, Jr. 1988. A guide In: Jain, S. and P. Moyle (eds). Vernal pools and to wildlife habitats in California. Sacramento: Ca- intermittent streams: A symposium sponsored by lif. Dept. Fish and Game. the Institute of Ecology University of Calif., Davis McKelvey, S. D. 1955. Botanical exploration of the May 9 and 10, 1981, Institute of Ecology Publica- Trans-Mississippi West: 1790-1850. Jamaica Plain, tion #28. Davis, Calif.: UC Davis Institute of Ecol- Mass.: The Arnold Arboretum of Harvard Univ. ogy. pp. 1-8. Mooney, H. A. 1977. Southern coastal scrub. In: M. Wahrhaftig, C. and J. H. Birman. 1965. The Quater- Barbour and J. Major (eds). Terrestrial vegetation nary of the Pacific Mountain System in Califor- of California. New York: Wiley. pp. 471-489. nia. In: H. Wright and D. Frey (eds). The Qua- Mooney, H. A. and P. C. Miller. 1985. Chaparral. In: B. ternary of the United States. Princeton, NJ: Chabot and H. Mooney (eds). Physiological ecol- Princeton Univ. Press. pp. 299-340. ogy of North American plant communities. Lon- Wahrhaftig, C.; S. W. Stine; and N. K. Huber. 1993. don: Chapman and Hall. pp. 213-231. Quaternary geologic map of the San Francisco Bay Munz, P. A. and D. D. Keck. 1959. A California flora. 4" x 6" quadrangle, United States. Denver: US Berkeley: UC Press. Geological Survey. Norris, R. M. and R. W. Webb. 1990. Geology of Cali- Wainwright, T. C. and M. G. Barbour. 1984. Charac- fornia, 2nd edition. New York: Wiley. teristics of mixed evergreen forest in the Sonoma Radbruch, D. H. 1957. Areal and engineering geology Mountains of California. Madrono 31: 219-230. of the Oakland West Quadrangle, California. Mis- Waisel, Y. 1972. Biology of halophytes. New York: Aca- cellaneous gelogical investigations map 1-239. demic Press. Washington DC: US Geological Survey. Walter, H. 1979. Vegetation of the earth and ecological Safford, H. D. 1995. Woody vegetation and succession systems of the geo-biosphere, 2nd edition. New in the Garin Woods, Hayward Hills, Alameda York: Springer-Verlag. County, California. Madrono: 42: 470-489. Wernstedt, F. L. 1972. World climatic data. Lemont, San Francisco Estuary Project (SFEP). 1991a. Status and Pa.: Climatic Data Press. trends report on wetlands and related habitats in Wester, L. 1981. Composition of native grasslands in the San Joaquin Valley, California. Madrono 28:

66 Baylands Ecosystem Species and Community Profiles 231-241. Wieslander, A. E. and H. A. Jensen. 1945. Vegetation

types of California. Berkeley, Calif.: US Forest Ser- Plants vice. Zeiner, D. C.; W. F. Laudenslayer, Jr.; K. E. Mayer; and M. White. California’s wildlife: Volume III: Mam- mals. Sacramento: Calif. Dept. Fish and Game. Zinke, P. J. 1977. The redwood forest and associated north coast forests. In: M. Barbour and J. Major (eds). Terrestrial vegetation of California. New York: Wiley. pp. 679-698.

Chapter 1 — Plant Communities 67 Plants

68 Baylands Ecosystem Species and Community Profiles 2

Estuarine Fish and Associated Invertebrates Fish

Food and Feeding Opossum Shrimp The diet of N. mercedis varies with size. At release, young Neomysis mercedis shrimp eat mostly phytoplankton and rotifers. Adult Bruce Herbold diets include phytoplankton and rotifers but the diet shifts more to copepods, particularly Eurytemora affinis General Information (Herbold et al. 1992). The opossum shrimp is a native mysid shrimp that is an Distribution important food for many estuarine fish, especially young striped bass. Since 1994, their role of dominant plank- N. mercedis is found in greatest abundance in Suisun Bay tonic shrimp has been overwhelmed by the introduced and the western Delta, although it occurs as far upstream species, Acanthomysis (Orsi and Mecum 1996). as Sacramento, the lower reaches of the Mokelumne

River, and in the San Joaquin River to above Stockton. Pl Reproduction Population Status and Influencing Factors The common name of the opossum shrimp derives from the fact that females carry their eggs and young in a During most of the 1980s, the opossum shrimp popu- pouch at the base of the last two pairs of legs. Young are lation varied considerably, but remained at a lower level released at a well-developed stage. Fecundity is related of abundance than existed in the early 1970s. Opossum both to adult size and season (Heubach 1969). shrimp abundance fell dramatically after 1986 and re- Reproduction is continuous but the rate is strongly mained at very low levels from 1990 to 1993 (CDFG controlled by temperature and food supply. Thus, the 1994). As a general trend, opossum shrimp populations rate is high during spring and summer months and slows have declined substantially in Suisun Bay, yet they have down as temperature and insolation decline. The win- occasionally rebounded to high levels (BDOC 1993). tertime population is composed largely of large adults, Reasons for the system-wide declines of several whose greater fecundity allows rapid development of zooplankton taxa in the Bay-Delta Estuary are not high densities as temperatures and phytoplankton den- known. Although the declines occurred at about the sities rise. The autumn decline in density has been vari- same time as declines in phytoplankton and various fish ously attributed to seasonal changes in high temperature, species, no cause-and-effect relationships have been es- low dissolved , predation, and food supply tablished (CDWR 1992). However, several factors have (Turner and Heubach 1966, Heubach 1969, Siegfried been identified which are believed to have some influ- et al. 1979, Orsi and Knutson 1979). ence on the decline of zooplankton in the Estuary. Decrease in food supply has been associated with the decline in abundance of rotifers and the copepod, E. affinis. The decline of rotifers in the Delta appears to be strongly associated with declining concentrations of chlorophyll a, which formerly characterized the areas of greatest rotifer abundance (Herbold et al. 1992). How- ever, chlorophyll and many zooplankton species have similar spatial distributions, and correlations between the two groups can arise through movement of the entrap-

ARO, M. Roper ment zone in the Estuary. Also, while it is commonly

Chapter 2 — Estuarine Fish and Associated Invertebrates 69 assumed that chlorophyll is a good measure of food avail- a higher rate of loss to resident zooplankton populations ability for zooplankton, E. affinis can subsist on detrital than export pumping. matter and requires larger particles than those that make Pollutants may be another factor in the decline of up total chlorophyll. In addition, small zooplankton zooplankton in the upper Estuary. For example, rice her- could provide food for many of the larger zooplankton bicides have been shown to be toxic to opossum shrimp species (Kimmerer 1992). Consistently low E. affinis (CDWR 1992). However, rice herbicides are largely con- abundance in recent years has been named as a factor fined to the Sacramento River, not the entire Estuary. that has probably contributed to the decline of opossum No Estuary-wide decline in planktonic crustaceans have shrimp (Herbold et al. 1992). been associated with the timing of herbicide occurrence Introduced species have also been named as a po- in the river (NHI 1992). tential cause for the decline in zooplankton abundance.

Fish For example, the introduction of Sinocalanus has been Trophic Levels identified as a possible cause of the decline in abundance of E. affinis (Kimmerer 1992), although the introduced The opossum shrimp is a primary and secondary con- copepod does not have the same habitat requirements sumer. as the native copepods (NHI 1992). However, based on the known feeding habits of a related species of Sinocala- Proximal Species nus, S. doerrii may prey on native copepods (Herbold et al. 1992). In addition, predation by the introduced Asian Predators: Striped bass, longfin smelt, splittail. clam, Potamocorbula amurensis, has been suggested as a Prey: Various copepods, various phytoplankton. factor in the decline of rotifer (Herbold et al. 1992) and Competitors: Potamocorbula amurensis, Acanthomysis spp. E. affinis populations. E. affinis abundance in Suisun Bay decreased substantially when the clam became abundant Good Habitat there in 1988 (CDWR 1992). Since 1994 Neomysis abundance has dropped to less than that of an introduced Good habitat appears to be similar to that of Delta smelt; species of mysid shrimp which has increased in abun- a well-dispersed area of open water with salinities in the dance (Orsi 1996). Competition with both the clam and range of 2 to 6 ppt for most of the year and clean, non- new shrimp are likely to prevent re-establishment of toxic over-wintering habitat in freshwater through the Pl Neomysis at the levels of their former abundance. winter and early spring. Dead-end sloughs both in Sui- ants

Reptiles The decline in the abundance of opossum shrimp sun Marsh and upstream apparently serve as important

Amphibians & and other zooplankton species (e.g., E. affinis) that are refuges from predation during the annual period of low found in the entrapment zone in relatively high abun- abundance and slow growth. With the advent of newly dances has been correlated with Delta outflow. It is pre- introduced competitors in the open waters of the Estu- sumed that low outflow reduces opossum shrimp abun- ary it is possible that such refugia will become impor- dance by: (1) restricting the entrapment zone to deeper, tant for the year-round maintenance of opossum shrimp. more upstream channels which are less likely to promote high densities of opossum shrimp; and (2) producing References weaker landward currents along the bottom so that the ability of opossum shrimp transported downstream to Bay-Delta Oversight Council (BDOC). 1993. Draft return to the entrapment zone is reduced. It has also been briefing paper on biological resources of the San presumed that larger numbers of opossum shrimp may Fran. Bay/Sac.-San Joaquin Delta Estuary. Septem- be exported through the Central Valley Project and State ber 1993. 42 pp. plus appendices. Water Project pumps as a result of the increased propor- California Department of Fish and Game (CDFG). tion of inflow diverted during drought years when the 1994. Comments on key issues of the State Water entrapment zone is upstream in the Estuary. The loca- Resources Control Board’s June workshop for re- tion of the entrapment zone within the lower river chan- view of standards for San Francisco Bay/Sacra- nels during dry years increases the vulnerability of opos- mento-San Joaquin Delta Estuary. Presented by sum shrimp to such displacement (Herbold et al. 1992). Perry L. Herrgesell, Chief of Bay-Delta and Spe- However, analyses by Kimmerer (1992) suggest that ex- cial Water Projects Division, June 14, 1994. 68 ports by the water projects are not a major source of pp. losses for opossum shrimp and E. affinis populations, pri- California Department of Water Resources (CDWR). marily due to the small percentage of entrapment zone 1992. Bay-Delta fish resources. Ca. Dept. of Wa- volume (and entrapment zone organisms) diverted. De- ter Res. Sacramento, Ca. July 1992. 46 pp. pending on the timing, location, and quantity of with- (WRINT-DWR-30) drawals, in-Delta water diversions, whose net consump- Herbold, B., P.B. Moyle and A. Jassby. 1992. Status and tion is on the same order of export flows, may result in trends report on aquatic resources in the San Fran-

70 Baylands Ecosystem Species and Community Profiles cisco Estuary. San Francisco Estuary Project. Pub- lic Report. March 1992. 257 pp. plus appendices. Dungeness Crab Heubach, W. 1969. Neomysis awatchschensis in the Sa- cramento-San Joaquin Estuary. Linmol. Oceanogr. Cancer magister 14: 533-546. Robert N. Tasto Kimmerer, W. 1992. An evaluation of existing data in the entrapment zone of the San Francisco Bay Es- General Information tuary. Interagency Ecological Studies Program for the Sac./San Joaquin Estuary. Tech. Rept. 33. Sep- Dungeness crab has been the object of an immensely tember 1992. FS/BIO-IATR/92-93. 49 pp. popular commercial and recreational fishery in the San Fish Natural Heritage Institute (NHI). 1992. Causes of de- Francisco region since 1848. The San Francisco fishery, cline in estuarine fish species. Presented to the State which occurs exclusively outside the Golden Gate, was Wat. Res. Contr. Bd. Water Rights Phase of the long a mainstay of statewide commercial landings. How- Bay Delta Estuary Proceedings. St. Wat. Res. ever, beginning in the early 1960s, it underwent a se- Contr. Bd. exhibit WRINT-NHI-9. 29 p plus ap- vere and longterm decline which persisted until the pendices. mid-1980s. The principal causes of the decline have been Orsi, J.J. and A.C Knutson. 1979. The role of mysid related to changes in ocean climate, increased predation, shrimp in the Sacramento-San Joaquin Estuary and and possibly pollution (Wild and Tasto 1983). Landings factors affecting their abundance and distribution. in the past decade have rebounded to some extent and In: T.J. Conmos (ed). San Francisco Bay: The ur- are generally able to accomodate local market demand, banized estuary, Pac. Div., Am. Assoc. Adv. Sci., but the northern California fishery (Eureka and Cres- San Francisco, Ca. pp. 401-408. cent City) continues to be the major provider of Dunge- Orsi, J.J. and W.L. Mecum. 1996. Food limitation as ness crabs throughout the rest of California. The value the probable cause of a long-term decline in the of the Dungeness crab resource extends beyond the tra- abundance of Neomysis mercedis, the opossum ditional economic return to the fishermen, seafood pro- shrimp, in the Sacramento-San Joaquin estuary. cessors, and retail markets, as it is an important element

In: J.T. Hollibaugh (ed). San Francisco Bay: The in the tourism industry of San Francisco. Pl ecosystem. Pacific Division, Amer. Assoc. for the California commercial and recreational fishing Advancement of Science, San Francisco, Ca. pp. regulations pertaining to Dungeness crab have been de- 375-402, signed to protect this species from over-harvesting. The Siegfried, C.A., M.E. Kopache and A.W. Knight. 1979. standard commercial fishing gear is a baited 3.5-foot The distribution and abundance of Neomysis diameter metal trap, weighing 60 to 120 pounds (Warner mercedis in relation to the entrapment zone in the 1992). California regulations set a 6.25-inch carapace western Sacramento-San Joaquin Delta. Trans. Am. width (cw) size limit, prohibit the take of female crabs, Fish. Soc. 108: 262-270. and, like most states, have established a specific fishing Turner, J.L. and W. Heubach. 1966. Distribution and season to protect reproducing and egg-bearing crabs. A concentration of Neomysis awatchschensis in the limited recreational fishery allows the take of female crabs Sacramento-San Joaquin Delta. In: D.W. Kelley and has a smaller size restriction (5.75 inches cw); a (ed). Ecological studies of the Sac.-San Joaquin 10-crab bag limit is placed on the sportfishers. Recre- Delta. Ca. Dept. Fish and Game, Fish Bull. No. ational gear consists of a variety of traps, hoops, and nets 133: 105-112. of different sizes, shapes, and materials. It is currently CDFG

Chapter 2 — Estuarine Fish and Associated Invertebrates 71 illegal to catch Dungeness crab of any size in San Fran- nile fish, and bivalves (Gunderson et al. 1990). By com- cisco Bay. parison to other cancrid crabs, the small chelae of C. magister are better suited for soft-bodied, mobile prey Reproduction found on sandy bottoms (Oresanz and Gallucci 1988). One study has suggested that size-specific feeding on Mating occurs in nearshore coastal waters, from March clams in the laboratory was due to an attempt to mini- through May, between hard-shelled males and recently mize handling time of the prey in a competitive situa- molted, soft-shelled females. Fertilized eggs are extruded tion (Palacios and Armstrong 1990). in the fall and lay protected beneath the female’s abdomi- The most common predators on juvenile crabs nal flap in a -like mass until hatching occurs from within the San Francisco Estuary include bottom-feeding late December to mid-January (Wild and Tasto 1983). fishes such as starry flounder, English sole, Pacific tom-

Fish Fecundity ranges from 500,000 to 2,000,000 eggs, de- cod, Pacific staghorn sculpin, white croaker, pile perch, pending upon the size of the female (Warner 1992). C. sturgeon, and several elasmobranchs (sharks, skates, and magister is capable of about four broods over its repro- rays) (Reilly 1983a). The principal predator on young- ductive life span (Hines 1991). -of-the-year Dungeness crab in Gray’s Harbor Estuary was found to be the Pacific staghorn sculpin (Fernandez Growth and Development et al. 1993a). In addition, cannibalism is reported to oc- cur among all age groups (Warner 1992). Dungeness crab life stages include the egg, larval, juve- nile, and adult. Dungeness crab eggs range in diameter Distribution from 0.016 to 0.024 inches (Warner 1992). There are a total of six larval stages (five zoeae and one megalopa) Dungeness crab range from the Aleutian Islands to Santa which spend about 3 to 4 months in both nearshore and Barbara, but are rare south of Point Conception (Warner offshore coastal waters; larval timing is believed to coin- 1992). The pelagic larval forms are found distributed cide with peak plankton production (Hines 1991). widely in both nearshore and offshore waters, but return Late-stage megalopae, which have returned to the coast, to the coast, bays, and estuaries where the juvenile and bays, and estuaries via ocean currents and other mecha- adult stages are mostly found from the intertidal zone nisms, settle onto relatively open sandy areas (Oresanz to approximately 300 feet (Hatfield 1983, Reilly 1983b, Pl and Gallucci 1988) and subsequently metamorphose to Warner 1992). San Francisco Bay, as is the case with ants

Reptiles the first bottom-dwelling instar stage generally between other coastal estuaries, is an important nursery area for

Amphibians & April and June. It is at this stage that the young crabs the offshore stock. The vast majority of individuals in enter San Francisco Bay in large numbers, relative to the Bay are juveniles of a single year-class, having entered year-class strength, seemingly aided by strong bottom in the spring of one year and exited approximately 1 year currents (Tasto 1983). San Francisco Bay-reared crabs later (Tasto 1983, McCabe et al. 1988). Juveniles are molt more frequently than those juveniles found in the often found in tidal and navigational channels early in near coastal environment and reach sexual maturity (ap- summer, but spread out over mudflats and into protected proximately 4 inches wide) after nearly one year (Wild shoreline areas as they develop over the year (Figures 2.1 and Tasto 1983). This rate of growth is substantially and 2.2). greater than that found in open areas along the Pacific coast and may be due to increased availability of food Population Status and Influencing Factors and/or overall warmer temperatures of estuaries (Tasto 1983, Gunderson et al. 1990, Wainwright and Arm- Few population estimates have been made on individual strong 1993). It is believed that the large number of Dungeness crab stocks along the Pacific coast because molts necessary to reach sexual maturity in an estuarine there is significant variation in year-class strength, pur- environment is due, in large part, to the demands of os- portedly due to environmental conditions and density- moregulation (Oresanz and Gallucci 1988). -dependent factors (Botsford and Hobbs 1995). How- ever, commercial crab landings, monitored annually Food and Feeding by state and, in some instances, federal resource agen- cies, appear to be a reliable indicator of relative abun- Larval Dungeness crab in the water column are plank- dance. tivorous, whereas the juvenile and adult crabs are oppor- The most important factors affecting overall popu- tunistic foragers on larger bottom-dwelling organisms. lation numbers in the San Francisco area (i.e., Half In the San Francisco Estuary, juvenile crabs have been Moon Bay to Bodega Bay) include ocean temperatures shown to feed on clams, crustaceans, and small fishes (hatching success), ocean currents (larval drift), preda- (Tasto 1983). In Grays Harbor, Washington, juvenile tion, commercial fishing, and, possibly, pollution of crab diets consisted primarily of Crangon shrimp, juve- nursery habitat (Wild and Tasto 1983). Although labo-

72 Baylands Ecosystem Species and Community Profiles

Fish Pl

Figure 2.1 Seasonal Distribution of Juvenile Dungeness Crab Within San Francisco Bay (Tasto 1983)

ratory results show that cannibalism may be an impor- (McConnaughey and Armstrong 1990). Within the San tant determinant in the abundance and structure of some Francisco Estuary, juvenile abundance varies consid- populations (Fernandez et al. 1993b), year-class strength erably from year to year, but is often highest in San and recruitment to the fishery do not appear to be de- Pablo Bay and lowest in south Bay (Tasto 1983, pendent upon success of any particular “ critical” stage CDFG 1987).

Chapter 2 — Estuarine Fish and Associated Invertebrates 73

Fish

Pl ants

Reptiles

Amphibians &

Figure 2.2 Annual Distribution of Juvenile Dungeness Crab Within the San Francisco Bay – Caught by Otter Trawl, May-December (CDFG 1987)

Trophic Levels Proximal Species

Larvae are planktivores making them primary consum- Predators: Chinook and coho salmon* (prey on late lar- ers (phytoplankton) and secondary consumers (zoop- val stages); Carcinonemertes errans* (predator worm on lankton). Juveniles and adults are higher order con- egg masses); Dungeness crab (cannibalism by larger in- sumers. stars, principally females, on small juveniles), starry

74 Baylands Ecosystem Species and Community Profiles flounder, English sole, Pacific tomcod, Pacific staghorn ness crab recruitment. Ecological Monographs, 65 sculpin, white croaker, brown smoothhound shark, and (2): 193-216. skate (prey on juveniles); and humans (commercial and Emmett, R.L., S.L. Stone, S.A. Hinton and M.E. Mo- recreational fishing for adults*). naco. 1991. Distribution and abundance of fishes * Generally takes place outside of San Francisco Bay. and invertebrates in west coast estuaries, Volume Prey: Crustaceans, bivalves (clams), small fishes. II: species life history summaries. ELMR Rep. No. 8 NOAA/NOS Strategic Envir. Ass. Div., Rockville, MD. 329 pp. Good Habitat Fernandez, M.E., O. Iribarne and D.A. Armstrong. 1993a. Habitat selection by young-of-the-year Fish Juvenile crabs appear to prefer sandy or sandy-mud sub- Dungeness crab Cancer magister Dana and preda- strate, but can be found on almost any bottom type (e.g., tion risk in intertidal habitats. Mar. Ecol. Prog. shell debris). Structurally complex habitats that provide Ser., Vol. 92: 171-177. protection from predation (e.g., high relief shell, eel Fernandez, M.E., D.A. Armstrong and O. Irbarne. grass, drift macroalgae, etc.) are favored over bare mud 1993b. First cohort of young-of-the-year Dunge- or open sand (Fernandez et al. 1993a, Iribarne et al. ness crab (Cancer magister) reduces abundance of 1995, Eggleston and Armstrong 1995, McMillan et al. subsequent cohorts in intertidal shell habitats. Can. 1995). J. Fish. Aquat. Sci. 50: 2100-2105. Chemical and physical characteristics of the water Gunderson, D.R., D.A. Armstrong, Y.-B. Shi and R.A. column and sediment are also important habitat features. McConnaughey. 1990. Patterns of estuarine use Juvenile Dungeness crab in the San Francisco Estuary by juvenile English sole (Parophrys vetulus) and seem to be somewhat intolerant of salinities lower than Dungeness crab (Cancer magister). Estuaries 13(1): 10 ppt (Tasto 1983, CDFG 1987). Maximum growth 59-71. appears to occur at 15°C or above (Kondzela and Shirley Gutermuth, F. Brandt and D.A. Armstrong. 1989. 1993, McMillan et al. 1995); and studies in Washing- Temperature-dependent metabolic response of ju- ton State have shown that juvenile crab have stable meta- venile Dungeness crab (Cancer magister Dana): eco- bolic rates at elevated estuarine temperatures (e.g., 14 logical implications for estuarine and coastal popu- Pl to 16°C), whereas older crabs were more stable at colder lations. J. Exp. Mar. Biol. Ecol. 126: 135-144. temperatures (Gutermuth and Armstrong 1989). This Hatfield, S.E. 1983. Intermolt staging and distribution is consistent with the tendancy for juvenile crabs to of Dungeness crab, Cancer magister, megalopae. emigrate out of estuaries into colder coastal waters as they In: Wild and Tasto (eds). Life history, environment, approach sexual maturity. and mariculture studies of the Dungeness crab, Although no single pollutant, or suite of pollutants, Cancer magister, with emphasis on the central Cali- has been shown to significantly affect Dungeness crab, fornia fishery resource. Ca. Dept. Fish and Game, various studies on different life stages have shown sen- Fish Bull. (172): 85-96. sitivity to oiled sediments, dissolved oxygen levels below Hines, A.H. 1991. Fecundity and reproductive output 5 ppm, low ammonia concentrations, pesticides, and in nine species of Cancer crabs (Crustacea, chlorinated wastewater (Wild and Tasto 1983, Emmett Brachyura, Cancridae). Can. J. Fish. Aquat. Sci. et al. 1991). Juvenile crab abundance in the Bay has been 48: 267-275. shown to be negatively correlated to Delta outflow Iribarne, O., D. Armstrong and M. Fernandez. 1995. (CDFG 1987). Environmental impact of intertidal juvenile Dungeness crab enhancement: effects on bivalves References and crab foraging rate. J. Exp. Mar. Biol. Ecol. 192: 173-194. Botsford, L.W. and R.C. Hobbs. 1995. Recent advances Kondzela, C.M. and T.C. Shirley. 1993. Survival, feed- in the understanding of cyclic behavior of Dunge- ing, and growth of juvenile Dungeness crabs from ness crab (Cancer magister) populations. ICES Mar. southeastern Alaska reared at different tempera- Sci. Symp., 199: 157-166. tures. Jour. of Crust. Biol., 13 (1): p. 25-35. California Department of Fish and Game (CDFG). McCabe, G.T. Jr., R.L. Emmett, T.C. Coley and R.J. 1987. Delta outflow effects on the abundance and McConnell. 1988. Distribution, density, and distribution of San Francisco Bay fish and inverte- size-class structure of Dungeness crabs in the brates, 1980-85. Exhibit 60. State Wat. Res. Ctrl. river-dominated Columbia River Estuary. North- Bd., Wat. Qual./Wat. Rights Proc. on San Fran. west Science 62(5): 254-262. Bay/Sac.- San Joaquin Delta. 337 pp. McConnaughey, R.A. and D.A. Armstrong. 1990. A ju- Eggleston, D.B. and D.A. Armstrong. 1995. Pre- and venile critical stage in the Dungeness crab (Cancer post-settlement determinants of estuarine Dunge- magister) life history. Abstracts of the 1990 annual

Chapter 2 — Estuarine Fish and Associated Invertebrates 75 meeting of the National Shellfisheries Assoc. Williamsburg, VA. p. 133-134. Rock Crabs McMillan, R.O., D.A. Armstrong and P.A. Dinnel. 1995. Comparison of intertidal habitat use and Cancer antennarius and Cancer productus growth rates of two northern Puget Sound cohorts Robert N. Tasto of 0+ age Dungeness crab, Cancer magister. Estu- aries 18(2): 390-398. General Information Oresanz, J.M. and V.F. Gallucci. 1988. Comparative study of postlarval life-history schedules in four The brown rock crab (Cancer antennarius) is found along sympatric species of Cancer (Decapoda: Brachyura: the west coast of North America from Washington State Cancridae). Jour. Crust. Biol. 8(2): 187-220. to Baja California; the red rock crab (Cancer productus)

Fish Palacios, R. and D.A. Armstrong. 1990. Predation of has a slightly more northerly distribution, i.e., Alaska to juvenile soft-shell clam (Mya arenaria) by juvenile San Diego (Carroll and Winn 1989). A small recreational Dungeness crab. Abstracts of the 1990 annual fishery exists for brown and red rock crabs in central San meeting of the National Shellfisheries Assoc. Francisco Bay and parts of south Bay and San Pablo Bay. Williamsburg, VA. p. 445-446. Most rock crabs in this fishery are caught from piers and Reilly, P.N. 1983a. Predation on Dungeness crabs, Cancer jetties by a variety of baited hoop nets and traps. A mod- magister, in central Califirnia. In: Wild and Tasto est commercial fishery also occurs throughout Califor- (eds). Life history, environment, and mariculture nia waters, with the vast majority of the catch taking studies of the Dungeness crab, Cancer magister, place from Morro Bay southward (Parker 1992). Ex-ves- with emphasis on the central California fishery re- sel value for the commercial fishery approached $2 mil- source. Ca. Dept. Fish and Game, Fish Bull. (172): lion in the mid-1980s (Carroll and Winn 1989) and 155-164. appears to be unchanged since then. Unlike their close ______. 1983b. Dynamics of Dungeness crab, Cancer relative, the Dungeness crab, which has a significant magister, larvae off central and northern Califor- amount of muscle tissue in the body, rock crabs, gener- nia. In: Wild and Tasto (eds). Life history, envi- ally, have been sought after for their claws only. In re- ronment, and mariculture studies of the Dunge- cent years, however, live whole crabs have become a ness crab, Cancer magister, with emphasis on the larger part of the retail market. California Department Pl central California fishery resource. Ca. Dept. Fish of Fish and Game regulations prohibit the commercial ants

Reptiles and Game, Fish Bull. (172): 57-84. take of crabs less than 4.25 inches carapace width (cw),

Amphibians & Tasto, R.N. 1983. Juvenile Dungeness crab, Cancer mag- require that sport-caught crabs must be 4.0 inches cw ister, studies in the San Francisco Bay area. In: Wild or greater, and impose a bag limit of 35 crabs per day. and Tasto (eds). Life history, environment, and mariculture studies of the Dungeness crab, Can- Reproduction cer magister, with emphasis on the central Califor- nia fishery resource. Ca. Dept. Fish and Game, Mating takes place between a soft-shelled (recently Fish Bull. (172): 135-154. molted) female and hard-shelled male. Male brown rock Wainwright, T.C. and D.A. Armstrong. 1993. Growth crabs have been reported to outnumber females by a ra- patterns in the Dungeness crab (Cancer magister tio of 1.6/1 (San Mateo County coast) during all seasons Dana): synthesis of data and comparison of mod- (Breen 1988), although studies by Carroll (1982) at els. Jour. Crust. Biol. 13(1): 36-50. Diablo Cove showed that females were more abundant Warner, R.W. 1992. Dungeness crab, p. 15-18. In: W.S. in the fall, with no other seasonal trends for either sex. Leet, C.M. Dewees and C.W. Haugen (eds). Unfertilized eggs remain within the female for approxi- California’s living marine resources. Ca. Sea Grant mately three months, following mating, and then are Publ. UCSGEP-92-12, 257 pp. fertilized by the stored sperm as they are released (Parker Wild, P.N. and R.N. Tasto. 1983. Life history, environ- 1992). The fertilized eggs are then carried until hatch- ment, and mariculture studies of the Dungeness ing (6 to 8 weeks) in a sponge-like mass beneath the crab, Cancer magister, with emphasis on the cen- female’s abdominal flap (Parker 1992). Female body size tral California fishery resource. Ca. Dept. Fish and is the principal determinant of reproductive output and Game, Fish Bull. (172): 352 pp. fecundity, with red rock crab having 172,600 to 597,100 eggs per brood and brown rock crab having 156,400 to 5,372,000 eggs per brood (Hines 1991). Like the Dungeness crab, ovigerous female rock crabs have been observed buried in the sand at the base of rocks in shal- low waters protecting their eggs (Reilly 1987). Also, some red rock crab females have been detected emigrating out

76 Baylands Ecosystem Species and Community Profiles of estuaries prior to spawning to avoid osmotic stress ovigerous red rock crab as small as 3.7 inches cw. Brown (Oresanz and Gallucci 1988). rock crabs have reached a maximum 6.5 inches cw and Hatching takes place in spring and early summer red rock crabs, the larger of the two species, at 8 inches in central California (Carroll 1982). The planktonic lar- cw (Carroll and Winn 1989, Parker 1992). Maximum vae then settle to the bottom before beginning the ju- life span of the brown rock crab has been estimated at venile stage. Juvenile abundance is highest in San Fran- 5-6 years (Carroll 1982). cisco Bay during the summer months (CDFG 1987). Much like other cancrids, larval release in spring coin- Food and Feeding cides with peak plankton production, and settlement in the summer is optimal for growth (Hines 1991). The re- Rock crabs are both nocturnal predators and scavangers Fish productive life span for the red rock crab is approximately and have been shown to feed upon hard-shelled organ- four years with four broods, and for the brown rock crab isms such as clams, snails, and barnacles (Parker 1992). it is approximately seven years with up to 10 broods The large chelae of these crabs is well-suited to forage (Hines 1991). on the hard shells of more sedentary prey of their rocky habitats (Oresanz and Gallucci 1988). Red rock crab feed Growth and Development upon intertidal mussels and barnacles (Robles et al. 1989). Juvenile rock crabs are preyed upon by other mac- Brown rock crabs are known to go through 10 to 12 roinvertebrates and demersal fishes, whereas adults are molts before reaching sexual maturity at about 3 inches prey items for marine mammals (Carroll 1982). Very cw, and will likely molt one to two times per year there- little is known about the specific food habits of, or preda- after (Parker 1992). The average number of red rock crab tors upon, these two species of rock crabs within San Fran- instars is 13 over the total life span (Oresanz and Gallucci cisco Bay; however, the sportfishery within the Bay accounts

1988). Studies in Humboldt Bay (O’Toole 1985) found for the loss of an indeterminate number of adult crabs. Pl CDFG CDFG

Brown Rock Crab, Cancer antennarius. Red Rock Crab, Cancer productus. Top and bottom: Views of 5 in. male crab. Top: top surface of 6.5 in. male. Bottom: under surface of 5.75 in. female.

Chapter 2 — Estuarine Fish and Associated Invertebrates 77 Distribution (Carroll 1982, Breen 1988). Small, local populations of rock crab can be overfished, although there is no evi- Both rock crab species inhabit the low intertidal zone dence suggesting that overfishing occurs in the Bay. Data to depths of 300 feet or more (Parker 1992) and, al- from the Interagency Ecological Study Program indicate though their microhabitat utilization patterns are simi- that there is a negative relationship between abundance lar, they appear to be different in how they utilize estu- of both rock crab species and outflow from the Delta aries (Oresanz and Gallucci 1988). The brown rock crab (CDFG 1987). is principally a marine species and does not osmoregulate well in brackish waters, whereas the red rock crab can Trophic Levels successfully inhabit brackish areas. All stages of the red and brown rock crab have been collected in San Fran- Rockcrab larvae are planktivores and, as such, are both

Fish cisco Bay, including larvae and ovigerous females (Tables primary consumers (phytoplankton) and secondary con- 2.1 and 2.2). Areas of peak abundance appear to be in sumers (zooplankton). Juveniles and adults are higher Central Bay, the northern portion of South Bay, and the order consumers. southern portion of San Pablo Bay, with the red rock crab having a somewhat greater distribution than the Proximal Species brown rock crab (CDFG 1987). In general, rock crab movement is local (Breen 1988, Carroll and Winn Predators: Marine mammals, humans (recreational fishery). 1989). At Fitzgerald Marine Reserve along the San Prey: Bay mussels, barnacles. Mateo County coast, studies demonstrated that juvenile brown rock crab are most abundant in July, although no Good Habitat seasonal trend in the settlement of early instars was evi- dent (Breen 1988). In Santa Barbara County, Reilly Not surprisingly, both species have been shown to pre- (1987) found all stages of rock crabs to be most abun- fer rocky shore, subtidal , or coarse gravel and sand dant in the fall. substrate (Carroll and Winn 1989). Opportunity for con- cealment appears to be an important feature of red rock crab habitat in British Columbia studies (Robles et al.

Population Status and Influencing Factors Pl 1989). Juvenile brown rock crab, when settling from the There are no known estimates of the overall population last larval stage, appear to accept both sand and rock as ants

Reptiles size or knowledge of recruitment mechanisms for San suitable substrate (Carroll and Winn 1989), and red rock

Amphibians & Francisco Bay rock crabs. Most studies have shown that crab also tend to settle out onto structurally complex population densities of rock crabs were well below 1/m2 substrates (Oresanz and Gallucci 1988).

Table 2.1 Annual Abundance of Rock Crabs Caught by Otter Trawl (crabs/tow) in the San Francisco Estuary (CDFG 1987) Species and Size Class 1980 1981 1982 1983 1984 1985 1986

C. antennarius (all sizes) 0.101 0.047 0.010 0.015 0.071 0.033 0.007 C. antennarius (<50mm) 0.098 0.037 0.005 0.015 0.067 0.024 0.007 C. gracilis (all sizes) 0.035 0.103 0.044 0.182 0.333 0.240 0.174 C. gracilis (<20mm) 0.003 0.005 0.034 0.080 0.079 0.064 0.095 C. productus (all sizes) 0.014 0.032 0.005 0.010 0.055 0.071 0.088 C. productus (<50mm) 0.014 0.027 0.002 0.005 0.040 0.050 0.081

Table 2.2 Annual Abundance of Rock Crabs Caught by Ring Net (crabs/tow) in the San Francisco Estuary (CDFG 1987) Species and Size Class 1980 1981 1982* 1983 1984 1985 1986

C. antennarius (all sizes) - - 0.113 0.095 0.296 0.491 0.407 C. antennarius (<50mm) - - 0 0.009 0.028 0.009 0.176 C. gracilis (all sizes) - - 0.014 0.019 0.037 0.009 0.130 C. productus (all sizes) - - 0.155 0.067 2.509 4.315 0.806 C. productus (<50mm) - - 0 0 0.185 0.148 0.157 * Ring net survey started in May 1982

78 Baylands Ecosystem Species and Community Profiles Rock crabs appear to be influenced by both tem- Sulkin, S.D. and G. McKeen. 1994. Influence of tem- perature and salinity. In various laboratory studies, both perature on larval development of four co-occur- brown and red rock crab were adversely affected by ex- ring species of the brachyuran genus Cancer. Ma- posure to water temperatures above 20°C (Carroll and rine Biology. 118: 593-600. Winn 1989, Sulkin and McKeen 1994). The brown rock crab is considered primarily a marine species, whereas red rock crabs can osmoregulate in more brackish wa- ter; although the latter have been shown to be adversely affected by salinities below 13 ppt (Oresanz and Gallucci

Bat Ray Fish 1988, Carroll and Winn 1989). Myliobatus californica References Kurt F. Kline

Breen, R.T. 1988. Sizes and seasonal abundance of rock General Information crabs in intertidal channels at James V. Fitzgerald Marine Reserve, California. Bull. Southern Ca. The bat ray is a member of the family Myliobatidae Acad. Sci. 87(2): 84-87. (eagle rays). The family is found worldwide in tropical California Department of Fish and Game (CDFG). and temperate shallow seas. Bat rays are very common 1987. Delta outflow effects on the abundance and and are found in sandy and muddy bays and sloughs, as distribution of San Francisco Bay fish and inverte- well as in rocky areas and kelp beds. In shallow bays they brates, 1980-85. Exhibit 60. State Wat. Res. Ctrl. can be found feeding in the intertidal zone during high tide. Bd., Wat. Qual./Wat. Rights Proc. on San Fran. Bay/Sac.-San Joaquin Delta. 337 pp. Reproduction Carroll, J.C. 1982. Seasonal abundance, size composition, and growth of rock crab, Cancer antennarius Stimpson, off Mating occurs during the summer months followed by central California. J. Crust. Biol. 2: 549-561. an estimated gestation period of nine to 12 months (Mar- Carroll, J.C. and R.N. Winn. 1989. Species profiles: tin and Cailliet 1988). The young are born alive at 220 Pl life histories and environmental requirements of to 356 mm wing width and weigh about 0.9 kg (Baxter coastal fishes and invertebrates (Pacific South- 1980, Martin and Cailliet 1988). Males are mature at west)—brown rock crab, red rock crab, and yel- 450 to 622 mm wing width and two to three years, while low crab. U.S. Fish Wildl. Serv. Biol. Rep. 50% of the females are mature at 881 mm wing width 82(11.117). U.S. Army Corps of Engineers, TR and five years. EL-82-4. 16 pp. Hines, A.H. 1991. Fecundity and reproductive output Growth and Development in nine species of Cancer crabs (Crustacea, Brachyura, Cancridae). Can. J. Fish. Aquat. Sci. The growth of juvenile bat rays is not well documented, 48: 267-275. but is likely at least 100 mm per year. They can grow to Oresanz, J.M. and V.F. Gallucci. 1988. Comparative study of postlarval life-history schedules in four sympatric species of Cancer (Decapoda: Brachyura: Cancridae). Jour. Crust. Biol. 8(2): 187-220. O’Toole, C. 1985. Rock crab survey of Humboldt Bay. U.C. Coop. Ext., Sea Grant Mar. Adv. Prog., Eu- reka, Ca., Interim Rep. 14 pp. Parker, D. 1992. Rock Crabs. In: W.S. Leet, C.M. Dewees and C.W. Haugen (eds). California’s liv- ing marine resources. Ca. Sea Grant Publ. UCSGEP-92-12, 257 pp. Reilly, P.N. 1987. Population studies of rock crab, Can- cer antennarius, yellow crab, Cancer anthonyi, and Kellet’s whelk, Kelletia kelletii, in the vicinity of little Coho Bay, Santa Barbara County, California. Ca. Dept. Fish and Game. 73: 88-98. Robles, C., D.A. Sweetnam and D. Dittman. 1989. Diel varia- tion of intertidal foraging by Cancer productus L. in Brit-

ish Columbia. Jour. Nat. Hist. 23: 1041-1049. CDFG

Chapter 2 — Estuarine Fish and Associated Invertebrates 79 a wingspan of six feet (>2000 mm) though individuals Good Habitat this large are uncommon. The largest bat ray reported was a 95 kg female from Newport Bay (Baxter 1980). Sandy to muddy shallow bottoms with abundant mol- lusk and polychaete populations. Food and Feeding References Bat rays are opportunistic bottom feeders, feeding pri- marily upon benthic and epibenthic invertebrates. In Baxter, J.L. 1980. Inshore fishes of California. Ca. Dept. Elkhorn Slough, bat rays feed primarily on clams and the Fish and Game. 72 pp. echiuroid worm, Urechis caupo; in La Jolla kelp beds, they Flemming, R. 1999. Elasmobranchs. In: J. Orsi (ed). feed on shellfish including abalone and snails; and in Report on the 1980-1995 fish, shrimp, and crab

Fish Tomales Bay, they feed on polychaete worms, large clams sampling in the San Francisco Estuary, California. and echiuroid worms (Karl and Obrebski 1976, Karl IEP Technical Report 63. 1979, Talent 1982). Studies done along the southern Karl, S.R. 1979. Fish feeding habit studies from Toma- California coast (Van Blaricom 1982) found that pits dug les Bay, California. M.S. Thesis, Univ. of Pacific, by feeding bat rays were an important controlling factor of Stockton, Ca., 44 pp. infaunal community organization, opening areas for infauna Karl, S.R. and S. Obrebski. 1976. The feeding biology recolonization and uncovering food items for other fish. of the bat ray, Myliobatis californica, in Tomales Bay, California. In: C.A. Simsenstad and S.J. Distribution Lipovsk (eds). Fish food habits studies, 1st Pacific Northwest Technical Workshop, Workshop Pro- The bat ray ranges from the Gulf of California to Or- ceedings, October 13- 15. Washington Sea Grant, egon, and is found from shallow subtidal water to 46 m. Div. Mar. Res., Univ. of Washington HG :30, Se- It is common in bays and shallow sandy areas along the attle, pp. 181-186. coast (Miller and Lea 1976). Martin, L.K. and G.M. Cailliet 1988. Age and growth determination of the bat ray, Myliobatis californica Gell, in Central California. Copeia 3: 763 773.

Population Status and Influencing Factors Pl Miller, D.J. and R.N. Lea. 1972. Guide to the coastal The current status of the bat ray in San Francisco Bay marine fishes of California. Ca. Dept. Fish and ants

Reptiles is unknown. Its distribution is likely influenced by sa- Game Fish Bull. 157, 249 pp.

Amphibians & linity; it has occaisionally been collected in San Pablo Bay Talent, L.G. 1982. Food habits of the gray smooth- at salinities lower 20 ppt (Flemming 1999). hound, Mustelus californicus, the brown smooth- hound, Mustelus henlei, the shovelnose guitarfish, Trophic Levels Rhinobatos productus, and the bat ray, Myliobatis californica, in Elkhorn Slough, California. Ca. Bat rays are primary consumers, feeding primarily on Dept. Fish and Game 68(4): 224-234. benthic invertebrates. They are taken by fishermen us- Van Blaricom, G.R. 1982. Experimental analyses of ing cut fish as bait, however natural feeding on fishes structural regulation in a marine sand community has not been documented. exposed to oceanic . Ecological Monographs 52: 283-305. Proximal Species

Prey: Benthic mollusks, polychaetes, crustaceans, Urechis caupo.

80 Baylands Ecosystem Species and Community Profiles Males mature earlier and at smaller sizes than females. Leopard Shark Growth rates are slow. In San Francisco Bay tagged leop- ard sharks grew 1.4 cm/yr (Smith and Abramson 1990). Triakis semifasciata Michael F. McGowan Food and Feeding

General Information Primary foods of the leopard shark are benthic and epibenthic crustaceans, clam siphons, echinuroid worms, The leopard shark (Family: Elasmobranchs) is one of the and small fishes. most common sharks in California bays and estuaries Fish (Talent 1976). It is the most abundant shark in San Fran- Distribution cisco Bay (Ebert 1986) being found especially around piers and jetties (Emmett et al. 1991). The leopard shark The leopard shark is found from Mazatlan, Mexico in- is an important recreational species in San Francisco Bay cluding the Sea of Cortez to Oregon (Miller and Lea and a limited commercial long-line fishery has targeted 1976). In California it is most common in estuaries and it in the bay (Smith and Kato 1979). Juveniles and adults bays south of Tomales Bay (Monaco et al. 1990). Leop- are demersal and sometimes rest on the bottom (Feder ard sharks are apparently resident in San Francisco Bay, et al. 1974). Although other elasmobranchs occur in although some move out in fall and winter (Smith and euhaline bays and estuaries of the U. S. Pacific coast, the Abramson 1990) and several size classes appear in the leopard shark was the only shark or ray included among California Department of Fish and Game length data. 47 fish and invertebrate species in the life history sum- maries of west coast estuarine species prepared by the Population Status and Influencing Factors National Oceanic and Atmospheric Administration’s Estuarine Living Marine Resources (ELMR) program The leopard shark probably has no predators except (Emmett et al. 1991). These species were selected on the larger sharks and humans. Its broad dietary range should basis of commercial value, recreational value, indicator protect it from food limitation. Heavy fishing mortality species of environmental stress, and ecological impor- poses a threat to the leopard shark, as it does to all sharks, Pl tance. That the leopard shark was selected is an indica- because of its slow growth, long time to maturity, and tion of its importance in estuaries in general and in San low fecundity. The minimum size limit recommended Francisco Bay where it is the most abundant shark. by Smith and Abramson (1990) for sustainable fishing in San Francisco Bay was 100 cm (40 in). Areas of high Reproduction freshwater input causing low salinity are largely avoided by leopard sharks. The leopard shark is a live bearer with internal fertiliza- tion, but no yolk-sac placenta. Mating occurs in the Trophic Levels spring, primarily during April and May soon after the females give birth to from 4-29 pups (Compagno 1984). Juveniles and adults are secondary and higher carnivores. Pupping can occur from March through August with a peak in April or May (Ackerman 1971). In San Fran- Proximal Species cisco Bay leopard sharks pup almost exclusively in South Bay (CDFG Bay Trawl data). The center of abundance Predators: Larger sharks, humans. of pups <300 mm long is south of, and just north of the Prey: Yellow shore crab, Urechis caupo, ghost shrimp, Dumbarton Bridge. rock crabs, octopus, shiner perch, arrow goby, Pacific herring, northern anchovy, topsmelt. Growth and Development Cohabitors: Smoothhound sharks form mixed schools with leopard sharks. Embryonic development is direct and internal and takes 10-12 months. At birth pups are 18-20 cm long. Females Good Habitat mature when 12-14 years old at a length of 110-129 cm. Leopard sharks are primarily a marine species which occu- pies bays and estuaries unless freshwater flows lower salin- ity excessively. Sandy and muddy bottom areas are pre- ferred, although they may be found near rocky areas and kelp beds along the coast. Estuaries are used as pupping and rearing areas for young sharks. Shallow mud and sand flats

CDFG are used for foraging during high tide (Compagno 1984).

Chapter 2 — Estuarine Fish and Associated Invertebrates 81 References Pacific Herring Ackerman, L.T. 1971. Contributions to the biology of the leopard shark, Triakis semifasciata (Girard) in Clupea pallasi Elkhorn Slough, Monterey Bay, California. M.A. Robert N. Tasto Thesis, Sacramento State College, Sacramento, CA, 54 pp. General Information Compagno, L.J. 1984. FAO species catalogue. Vol. 4. Sharks of the world. An annotated and illustrated The Pacific herring (Family: Clupeidae) resource in the catalogue of shark species known to date. Part 2. San Francisco Estuary is widely recognized for its com- Carcharhiniformes. FAO Fish. Synop. 125(4): 433- mercial, recreational, and ecological values. The com-

Fish 434. mercial fishery concentrates on ripe females for their roe Ebert, D.A. 1986. Observations on the elasmobranch (eggs) which are then exported to Japan, although there assemblage of San Francisco Bay. Ca. Dept. Fish is some limited effort for the fresh fish market and for and Game 72(4): 244-249. live bait by recreational salmon trollers (Spratt 1981, Emmett, R.L., S.L. Stone, S.A. Hinton and M.E. Mo- Lassuy 1989). Fishermen traditionally catch herring in naco. 1991. Distribution and abundance of fishes nearshore areas of the Bay with gillnets or in deeper wa- and invertebrates in west coast estuaries, Volume ters with round-haul nets, and there also is a relatively II: species life history summaries. ELMR Rep. N. new roe-on-kelp fishery operated from rafts (Spratt 1981, 8. NOAA/NOS Strategic Environmental Assess- CDFG 1992). The economic value of the fishery based ments Div., Rockville, MD, 329 pp. upon ex-vessel prices paid to the fishermen in 1995-96 was Feder, H.M., C.H. Turner and C. Limbaugh. 1974. approximately 16.5 million dollars (CDFG, unpub. data). Observations on fishes associated with kelp beds in southern California. Ca. Dept. Fish Game, Fish Reproduction Bull. 160, 144 pp. Miller, D.J. and R.N. Lea. 1976. Guide to the coastal Adult herring congregate outside of San Francisco Bay marine fishes of California. Fish Bull. 157, Ca. before entering and generally spend about 2 weeks in the Dept. Fish and Game , Sacramento, Ca.. Sea Grant Bay before spawning (CDFG 1987). Spawning takes Pl reprint of 1972 edition with addendum added place from early November through March, with peak ants

Reptiles 1976. activity in January (Spratt 1981, CDFG 1992). The tim-

Amphibians & Monaco, M.E., R.L. Emmett, S.A. Hinton and D.M. ing of spawning is believed to coincide with increased Nelson. 1990. Distribution and abundance of levels of plankton production as a food source for larvae fishes and invertebrates in West Coast estuaries, (Lassuy 1989), as well as the presence of freshwater flows volume I: data summaries. ELMR Report No. 4. (Emmett et al. 1991). Pacific herring spawn primarily Strategic Ass. Div., NOS/NOAA, Rockville, Mary- on vegetation, rock rip-rap, pier pilings, and other hard land. 240 pp. substrates in intertidal and shallow subtidal waters Smith, S.E. and N. J. Abramson. 1990. Leopard shark (Spratt 1981, Lassuy 1989, Emmett et al. 1991). Spawn- Triakis semifasciata distribution, mortality rate, ing occurs in waves of 1 to 3 days, occasionally up to a yield, and stock replenishment estimates based on week in length, and often at night in conjunction with a tagging study in San Francisco Bay. Fish. Bull high tides (Spratt 1981). Waves are separated by one to 88: 371-381. several weeks over the length of the season with larger Smith, S.E. and S. Kato. 1979. The fisheries of San fish tending to spawn first (Lassuy 1989). The number Francisco Bay: past, present and future. In: T.J. and size of the waves is related to the distribution of the Conmos (ed). San Francisco Bay: The urbanized dominant year classes (CDFG 1992). estuary, Pac. Div., Am. Assoc. Adv. Sci., San Fran- Egg-deposition is thought to be facilitated by the cisco, Ca. pp. 445-468. brushing of the female’s vent up against the substrate, Talent, L.G. 1976. Food habits of the leopard shark, and, while there is no pairing of the sexes, the spawn- Triakis semifasciata, in Elkhorn Slough, Monterey ing area will be white with milt from the males so that Bay, California. Ca. Fish Game 62(4): `286-298. the rate of fertilization is usually high (Hart 1973). Pa- CDFG

82 Baylands Ecosystem Species and Community Profiles cific herring eggs adhere to the substrate in amounts vertebrates and various fishes, while juveniles and adults ranging from a few eggs to as many as eight layers thick are consumed by a variety of fishes (e.g., spiny dogfish (Spratt 1981). The fecundity of herring is approximately shark, Chinook salmon, Pacific staghorn sculpin, and 4,000 to 134,000 eggs per female, depending upon its striped bass), seabirds (e.g., Brandts cormorants, brown distribution and size (Hart 1973, Emmett et al. 1991). pelicans, and western gulls), and marine mammals, such As with spawning, most hatching takes place at night, as harbor seals (Hart 1973, Lassuy 1989, Emmett et al. and will occur in 10 to 15 days under 8.5° to 10.7°C 1991). Predation is considered to be the greatest source temperatures; longer if the water is colder (Emmett et of natural mortality for juvenile and adult Pacific her- al. 1991). The average in San Francisco Bay is 10.5 days ring (CDFG 1992). at 10.0°C (CDFG 1992). Fish Distribution Growth and Development Major populations exist in the eastern Pacific between Pacific herring eggs are approximately 1.0 mm in diam- San Francisco Bay and central Alaska (Hart 1973). eter, and 1.2 to 1.5 mm after fertilization (Hart 1973). Within San Francisco Bay, the principal spawning ar- A newly hatched larva, with yolk sac, is about 6 to 8 mm eas are found along the Marin County coastline (i.e., total length (TL) and will develop swimming powers at Sausalito, Tiburon Penninsula, and Angel Island), at the about 20 mm TL (CDFG 1992). Metamorphosis to the San Francisco waterfront and Treasure Island, on the east juvenile stage occurs from 25 to 35 mm TL and takes side of the Bay from the Port of Richmond to the Naval place over two to three months (Emmett et al. 1991). Air Station at Alameda, and on beds of vegetation in They are free-swimming at this stage and begin to form Richardson Bay and South Bay (Figure 2.3) (Spratt shoreline-oriented schools (CDFG 1992). Juveniles are 1981, CDFG 1992). After hatching, the larvae are 35 to 150 mm TL depending upon regional growth clumped and controlled largely by tidal factors, and fol- rates, which in turn are affected by population size and lowing disappearance of the yolk sac and the onset of environmental conditions (Emmett et al. 1991). In the feeding, their distribution becomes patchy (CDFG Bay Area, there are no apparent differences in the growth 1992). Larvae and young juveniles are found in the Bay rates of males and females (Spratt 1981). Adults range between November and April and their greatest densi- Pl in size from 130 to 260 mm TL, and locally it takes two ties are in the shallow waters of upper South Bay, Cen- to three years to reach maturity (Spratt 1981, Emmett tral Bay, and San Pablo Bay. Juveniles are found in the et al. 1991). The San Francisco Bay population ranges deeper areas of the Bay (peak in Central Bay) between from 110 to 250 mm TL (CDFG 1992; Ken Ota, Pers. April and August, and, for the most part, have left the Comm.) It is possible that some Pacific herring in more Bay by late June at sizes that approach 80 mm TL northern climates may exceed 15 years in age, but few (CDFG 1987). They eventually move to offshore or have been noted to live longer than nine years (Emmett nearshore areas and do not return to the Bay until they et al. 1991). are mature and ready for spawning. There is conflicting evidence of a strong correlation between juvenile abun- Food and Feeding dance, as measured by young-of-the-year surveys, and re- cruitment to the adult spawning population two years Pacific herring larvae, juveniles, and adults are selective later (Herbold et al. 1992) pelagic planktonic feeders and move toward the water’s surface to feed at dusk and dawn (Emmett et al. 1991). Population Status and Influencing Factors Generally, prey items will change with growth and geo- graphic distribution. Larvae feed on diatoms, inverte- San Francisco Bay population levels fluctuate widely and brate and fish eggs, crustacean and mollusc larvae, have ranged between approximately 6,000 tons and bryzoans, rotifers, and copepods (Hart 1973). Juveniles 100,000 tons spawning biomass, as measured by spawn consume a variety of crustaceans, as well as mollusc and deposition surveys and hydroacoustic monitoring of fish fish larvae; while adults eat mostly planktonic crustaceans schools (CDFG 1992). 1995-96 season estimates were and fish larvae (Hart 1973, Emmett et al. 1991). In approximately 99,000 tons, second highest on record winter, there is an overall reduction in adult Pacific her- (CDFG, unpub. data). Year-class strength is often de- ring feeding as stored energy is used for ripening repro- termined in the first six months of life (Hart 1973, ductive products and, during their spawning migration Lassuy 1989, Emmett et al. 1991). Egg mortalities can and inshore “ holding” period, herring may severely limit result from tidal exposure and dessication, abrubt or se- or stop feeding entirely (Lassuy 1989). vere temperature or salinity changes, low oxygen levels, Herring eggs are eaten by various species of fish wave action, suffocation by high egg densities or silt- (e.g., sturgeon), ducks (e.g., surf scoter), and gulls ation, pollution, and predation (Lassuy 1989, Emmett (CDFG 1992). Larvae are often prey for large pelagic in- et al. 1991). Factors related to natural mortality of larvae

Chapter 2 — Estuarine Fish and Associated Invertebrates 83 Figure 2.3 Traditional Pacific Herring Spawning Areas in Central San Francisco Bay

Fish

Pl ants

Reptiles

Amphibians &

in the Bay include competition and other density depen- Larvae predators: Young salmonids, pelagic inverta- dent mechanisms, as well as starvation during their initial brates. feeding period and changes in dispersal patterns. Juveniles Juvenile Predators: California halibut, young salmo- and adult survival is affected by competition, predation, dis- nids, harbor seals, harbor . ease, spawning stress, and fishing (Emmett et al. 1991). Adult Predators: California halibut, California sea lion, Predation appears to be the single most important harbor seals, harbor porpoise. factor affecting population levels (Lassuy 1989). In ad- Habitat: Eel grass (spawning substrate). dition to commercial and recreational fishing, humans Prey: Striped bass, copepods. influence herring survival by impacting water and habi- tat quality. Spawning habitat quantity and Delta out- Good Habitat flows are not thought currently to be limiting factors in determining the Bay’s herring population size (CDFG It is frequently stated that herring prefer sea grasses (e.g., 1987 and 1992). Zostera marina) or algae (e.g., Gracilaria sp.) as spawn- ing substrate (Lassuy 1989, Emmett et al. 1991); how- Trophic Levels ever, a variety of seemingly less attractive surfaces have proven to be very successful in the Estuary. Rigidity, Larvae are planktivores (primary and secondary consum- smooth texture, and the absence of sediment appear to ers). Juveniles and adults are primary and higher order be important components of suitable substrates (Lassuy consumers. 1989). Larvae and juveniles need quiescent and produc- tive shallow subtidal areas as rearing habitat. Proximal Species In northern waters, the optimal salinity range for spawning is reported to be 8 to 22 ppt and 13 to 19 ppt Egg Predators: Gulls, diving ducks, white sturgeon, for eggs and larval survival (CDFG 1987). Also in these atherinids (topsmelt and jacksmelt), surf perches, rock crabs. areas, temperatures in the range of 5.5 to 8.7° C have

84 Baylands Ecosystem Species and Community Profiles been shown to be best for egg development (Emmett et al. 1991); however, 10 to 12°C temperatures are about Northern Anchovy average for the spawning grounds in San Francisco Bay (Lassuy 1989). Optimal temperatures for juveniles and Engraulis mordax adults appear to be a few degrees higher than for eggs Michael F. McGowan or larvae (Lassuy 1989). It has been suggested that eggs need a minimum dissolved oxygen concentration of 2.5 General Information mg/L at the surface and, therefore, eggs elevated from the bottom on vegetation or other structures avoid silt- The northern anchovy (Family: Engraudidae) has the ation and receive better circulation for waste removal and largest biomass and is the most abundant fish in San Fish oxygenation (Lassuy 1989). Water quality is an impor- Francisco Bay (Aplin 1967). It is an important forage tant factor as eggs are vulnerable to high levels of sus- species for larger predators and consumes substantial pended particulate matter, particularly if the sediments amounts of phytoplankton and zooplankton (McGowan are laden with contaminants (e.g., dredged material from 1986). There is a bait fishery for northern anchovy at urban ports). Additionally, larvae have been shown to the mouth of the Bay. Most of the stock occurs outside be sensitive to the water-soluble fraction of hydrocarbons the Bay in the California Current. Although north- from spilled oil or other sources (Lassuy 1989). ern anchovy can be found inside the bay throughout the year, their seasonal peak is generally April to Oc- References tober. The spring influx may be associated with the onset of coastal upwelling (P. Adams, pers. comm.). California Department of Fish and Game (CDFG). Their exodus in the autumn may be linked to cool- 1987. Delta outflow effects on the abundance and ing water temperatures inside the bay (McGowan distribution of San Francisco Bay fish and inverte- 1986). brates, 1980-85. Exhibit 60. State Wat. Res. Ctrl. Bd., Wat. Qual./Wat. Rights Proc. on San Fran. Reproduction Bay/Sac.-San Joaquin Delta. 337 pp. ______. 1992. Pacific herring commercial fishing regu- Northern anchovy spawn oval, pelagic eggs approxi- Pl lations. Draft environmental document. 183 pp. mately 1.5 x 0.75 mm in size. Peak spawning is Emmett, R.L., S.L. Stone, S.A. Hinton and M.E. Mo- thought to occur at night at about 10 pm. Females naco. 1991. Distribution and abundance of fishes can produce up to 130,000 eggs per year in batches and invertebrates in West Coast estuaries, Volume of about 6,000. The eggs hatch in approximately 48 II: species life history summaries. ELMR Rep. No. hours depending on temperature. Larvae were col- 8 NOAA/NOS Strategic Environmental Ass. Div., lected in Richardson Bay within San Francisco Bay by Rockville, MD, 329 pp. Eldridge (1977). Spawning was documented in San Hart, J.L. 1973. Pacific herring. In: Pacific fishes of Francisco Bay in 1978 by collections of eggs and lar- Canada. Fisheries Research Bd. of Canada, Bull. vae from south of the Dumbarton Bridge to San Pablo 180: 96-100. Bay (McGowan 1986). Based on differential distribu- Herbold, B., A.D. Jassby and P.B. Moyle. 1992. Status tions of eggs and larvae, spawning occurs in the chan- and trends report on aquatic resources in the San nels while larvae seek out the productive shallows. Francisco Estuary. U.S. Env. Prot. Agency, San Although the biomass of northern anchovy within the Fran. Est. Proj. 368 pp. bays is small relative to that in the California Current, Lassuy, D.R. 1989. Species profiles: life histories and the bay is a favorable habitat for reproduction because environmental requirements of coastal fishes and of ample food for adults to produce eggs, abundant invertebrates (Pacific Northwest)—Pacific herring. zooplankton prey for larvae, and protection of eggs U.S. Fish and Wildl. Serv. Biol. Rep. 82 (11.126). and larvae from offshore transport to less productive U.S. Army Corps of Engrs., TR-EL-82-4. 18 pp. areas by coastal upwelling. Spratt, J.D. 1981. Status of the Pacific herring, Clupea harengus pallasii, resource in California, 1972 to 1980. Ca. Dept. Fish and Game, Fish Bull. (171). 107 pp.

Personal Communications

Ken Ota. Ca. Dept. of Fish and Game, Pacific Herring Research Project, 1996. CDFG

Chapter 2 — Estuarine Fish and Associated Invertebrates 85 Growth and Development ton, fish eggs, and fish larvae, depending on food con- centrations. Larvae and older stages should be consid- Larvae grow from 2.5 to 25 mm in about two months, ered as secondary and higher consumers. at which time they are considered juveniles. Growth is rapid within the warm productive bay environment. Proximal Species Based on analysis of length frequencies, some juveniles that were spawned late in the summer overwinter in the Predators: California halibut, Chinook and coho bay (McGowan 1986). The others apparently depart at salmon; rockfishes, yellowtail, tunas, sharks, and almost the same time as the adults in autumn. all California current fish; harbor seal; northern fur seal; sea lions; common murre; brown pelican; sooty shear- water; cormorant spp. Fish Food and Feeding Potential Competitors: Sardine. Jacksmelt, topsmelt, Larvae eat dinoflagellates and zooplankton, while adults and other schooling planktivores are potential competi- filter-feed in dense patches of large phytoplankton or tors and predators on young life stages. small zooplankton, but selectively pick larger zooplank- ters from the water (O’Connell 1972). Good Habitat Distribution Northern anchovy occupy near surface waters where the water temperature should be between 10° and 25° C. The northern anchovy occurs from Queen Charlotte Is- Eggs tend to be in water with salinities from 32-35 ppt, lands, Canada to Cabo San Lucas, Baha California and but juveniles and adults are abundant in fresher bays and into the Sea of Cortez. It can be found in all estuaries estuaries as well as marine waters. Spawning in San Fran- within this range. There is a subpopulation which oc- cisco Bay occurs at higher temperatures and lower sa- cupies the Columbia River plume, an “ offshore estuary.” linities than spawning in coastal areas. Northern anchovy In San Francisco Bay, they occur from Suisun Bay to are typical species of areas with high production such as South Bay, but are most abundant downstream of the coastal upwelling regions and estuaries. Carquinez Strait (Herbold et al. 1992). There is a sea-

sonal influx of northern anchovy into the bay in spring Pl References ants when water temperatures and plankton production be-

Reptiles gin to rise in the bay and when nearshore upwelling gen- Aplin, J.A. 1967. Biological survey of San Francisco Bay

Amphibians & erally begins. Adults exit the bay in autumn, but some 1963-1966. Report for Ca. Dept. Fish and Game, late-spawned juveniles may overwinter within the bay. MRO, Sacramento, Ca. Ref. 67-4. 131pp. Eldridge, M.B. 1977. Factors influencing distribution Population Status and Influencing Factors of fish eggs and larvae over eight 24-hour sam- plings in Richardson Bay, California. Ca. Dept. Northern anchovy populations off California range in Fish Game 63: 101-106. the hundreds of thousands of tons. Their biomass in- Herbold, B., A.D. Jassby and P.B. Moyle. 1992. Status creased dramatically following the decline of the sardine and trends report on aquatic resources in the San stock, suggesting that competitive interactions might Francisco estuary. The San Francisco Estuary control population fluctuations. Historical records of fish Project, Oakland, Calif., 257 pp. plus apps. scales in sediments suggests that large fluctuations in McGowan, M.F. 1986. Northern anchovy, Engraulis both anchovy and sardine populations have occurred in mordax, spawning in San Francisco Bay, Califor- the past and were not strongly correlated with each other. nia 1978-1979, relative to hydrography and zoop- Variable survival of eggs and larvae due to environ- lankton prey of adults and larvae. Fish. Bull., U.S. mental factors probably influences population size more 84(4):879-894. than predation or fishing. Active research into the causes O’Connell, C.P. 1972. The interrelation of biting and of northern anchovy population dynamics has contrib- filtering in the feeding activity of the northern an- uted immensely to our understanding but without re- chovy (Engraulis mordax). J. Fish. Res. Board Can. solving whether starvation, predation, advection, or other 29:285-293. cause is the key limiting factor. Personal Communications Trophic Levels P. Adams, National Marine Fisheries Service, Tiburon. First-feeding larvae may eat phytoplankters, larger lar- vae selectively pick copepods and other zooplankters from the water, juveniles and adults pick or filter plank-

86 Baylands Ecosystem Species and Community Profiles Mature splittail eggs are 1.3 to 1.6 mm in diam- Sacramento Splittail eter with a smooth, transparent, thick chorion (Wang 1986 cited in CDWR and USBR 1994). The eggs are Pogonichthys macrolepidotus adhesive or become adhesive soon after contacting wa- Ted R. Sommer ter (Bailey 1994). The eggs appear to be demersal and it is assumed that they are laid in clumps and attach to General Information vegetation or other submerged substrates. Under labo- ratory conditions, fertilized eggs incubated in fresh wa- The Sacramento splittail (Family: Cyprinidae) is one ter at 19°C (±0.5°C) start to hatch after approximately of California’s largest native minnows and is the only 96 hours. Asynchronous hatching of egg batches from Fish surviving member of its genus. In 1994 it was proposed single females has been observed in preliminary cultur- for listing as a Threatened species by U.S. Fish and Wild- ing tests. life Service based on concerns about reduced abundance Early hatched larvae are 6 mm long, have not de- and distribution (Meng and Kanim 1994, Meng and veloped eye pigment, and are physically underdeveloped. Moyle 1995). The species supports a small sport fishery The last larvae to hatch have developed eye pigmenta- in winter and spring, when it is caught for human con- tion and are morphologically better developed. Larvae are sumption and live bait for striped bass angling. 7.0 to 8.0 mm total length (TL) when they complete yolk-sac absorption and become free swimming; postlar- Reproduction vae are up to 20 mm (±4.2 mm) TL. First scale forma- tion appears at lengths of 22 mm standard length (SL) Adult splittail generally reach sexual maturity at about or 25 mm to 26 mm TL. It is unknown when exogenous 2 years of age (Caywood 1974). Some males mature at feeding actually begins, but preliminary observations the end of their first year and a few females mature in indicate that newly hatched larvae may have undeveloped their third year. An upstream spawning migration occurs mouths. Well-developed mouths are observed in post- November through May, with a typical peak from larvae between 8.1 mm and 10.4 mm TL. January-March. Spawning is thought to peak during Sacramento splittail are a relatively long-lived February-June, but may extend from January-July. minnow, reaching ages of 5, and possibly, up to 7 years. Pl Although submerged vegetation is thought to be the pre- Studies from Suisun Marsh indicate that young-of-the- ferred spawning substrate, egg samples have not yet been year (YOY) grow approximately 20 mm per month (mm/ collected on any substrate. Reproductive activity appears month) from May through September and then decrease to be related to inundation of floodplain areas, which to < 5 mm/month through February (Daniels and Moyle provides shallow, submerged vegetation for spawning, 1983). In their second season they grow at about 10 rearing and foraging (Caywood 1974, Sommer et al. mm/month until the fall when somatic growth declined 1997). Splittail have high fecundity like most cyprinids. and gonadal development began. The adult growth rate Reported fecundities range from 5,000 to 266,000 ranges from 5 to 7 mm/month. During gonad develop- eggs per female, depending on age (Daniels and Moyle ment, which occurs primarily between September and 1983). Generally, female splittail will have more than February, the growth rate slows to less than 5 mm/ 100,000 eggs each year. month. The largest recorded splittail measured between 380 mm and 400 mm. Growth and Development Food and Feeding The morphological characteristics of splittail eggs, larvae, and juveniles have been described and recent culturing Feeding studies describe splittail as opportunistic benthic studies (Bailey 1994) are providing preliminary informa- foragers. Splittail feeding appears highest in the morn- tion on early life history requirements and development. ing and early afternoon. Studies from the Sacramento Very little is known about factors that influence splittail River found that their diets were dominated by oligocha- egg and larval development. etes, cladocerans, and dipterans (Caywood 1974). Samples from the lower San Joaquin River included copepods, dipterans, detritus and algae, clams (Corbicula) and amphipods (Corophium spp.). Copepods were the dominant food items. These findings were similar to results of feeding studies from Suisun Marsh (Daniels and Moyle 1983), where the diet consisted predomi- nantly of detritus in both percent frequency of occur- rence (74%) and percent volume (57%). A smaller por-

Ted Sommer tion of the stomach contents (41% by volume) consisted

Chapter 2 — Estuarine Fish and Associated Invertebrates 87 of animal matter, mostly crustaceans (35% by volume). ing and draining activities during the past century prob- Opossum shrimp (Neomysis mercedis) were the dominant ably represents the greatest reduction in habitat. crustacean food item (37% frequency; 59% volume less Within the San Francisco Estuary, splittail were detritus) both daily and seasonally for splittail in Suisun collected from southern San Francisco Bay and at the Marsh. Other minor prey items included molluscs, in- mouth of Coyote Creek in Santa Clara County around sects, and fish. the turn of the century. To our knowledge, no other Food selection studies from Suisun Marsh suggest splittail have been collected in this part of San Francisco that splittail specifically select Neomysis as their main Bay (Aceituno et al. 1976). However, splittail are caught prey item in the Estuary (Herbold 1987). Fullness in- in San Francisco Bay and San Pablo Bay in wet years. dices data indicate that condition factors of splittail are Adults and young are abundant in two tributaries to San linked to Neomysis abundance. Splittail did not switch Pablo Bay, the Napa and Petaluma rivers. The core of

Fish to alternate and more prevalent food items, as was ob- distribution of adult splittail during summer appears served for other native resident species. to be the region from Suisun Bay to the west Delta. Splittail are also present in some of the smaller tributar- Distribution ies and sloughs of Suisun Bay, including Peyton Slough, Hastings Slough, and Pacheco Creek. The historical range of splittail included all low gradi- ent portions of all major tributaries to the Sacramento Population Status and Influencing Factors and San Joaquin rivers, as well as some other freshwa- ter tributaries to San Francisco Bay (Meng and Moyle Abundance estimates for YOY and adult splittail were 1995). A confounding issue is that the collection sea- developed recently (Sommer et al. 1997) from several son and life stage for most of the early observations Interagency Ecological Program surveys. The survey are unknown, so the relative importance of each lo- equipment for the Program includes otter trawls, mid- cation to different age classes of splittail cannot be es- water trawls, beach seines, and townets. tablished. Abundance of YOY declined in the Estuary dur- Splittail are presently most common in the brack- ing the six-year drought, which commenced in 1987 ish waters of Suisun Bay, Suisun Marsh, and the Sacra- (Figure 2.4). There was a strong resurgence in YOY mento-San Joaquin Delta. The data suggest that splittail in 1995, when abundance estimates were the highest Pl inhabit much of their historical range and have been lo- on record for State Water Project, Central Valley ants

Reptiles cated in previously unreported sites (Table 2.3). Much Project, beach seine, Outflow/Bay otter trawl, and

Amphibians & of the loss of splittail habitat is attributable to migration Outflow/Bay study midwater trawl. The midwater trawl barriers, but loss of floodplain and wetlands due to dik- index was the second highest on record. The response

Table 2.3 Historical and Recent Collections of Splittail(a)

River Distance (km) from Mouth of River Distance (km) to first dam to Collection Site Rutter (1908) Caywood (1974) Sommer et al. (1997)

Sacramento 483 387 331 387 (Red Bluff) Feather 109 (b) 94 109 (Oroville) American 49 37 19 37 (Nimbus) San Joaquin 435(c) (b) 201 295 (Sack) Mokelumne n/a 25 63 63 (Woodbridge) Napa n/a 21 10 n/a Petaluma n/a 25 8 16(d) (a) For the purposes of comparing present and historical distribution, we assumed that collection of any life stage of splittail constituted evidence that a given location was part of the range of the species. The results should be considered as the minimum range only; there had not been sufficient sampling in sites farther upstream to conclusively show that they were not present. To illustrate the fact that much of the loss of channel habitat is attributable to migration barriers, the location of the first dam on each river is included. (b) Records indicate that splittail were collected, but it is unclear where. (c) Rutter (1908) was cited by FWS (1994) as the source of an observation of splittail at Fort Miller (km 435), near the current site of Friant Dam on the San Joaquin River . However, Rutter’s distribution was based on Girard (1854), who reported two Pogonichthys species, P. symetricus and P. inaquilobus in the San Joaquin system. P. symetricus, collected from Fort Miller, is unlikely to have been a splittail (P. macrolepidotus) because Girard reported the “ lobes of the caudal fin are symmetrical” . Girard’s description of P. inaequilobus had an asymmetrical tail and other features similar to that of splittail, but the collection location is listed as “ San Joaquin River” with- out reference to a specific site. (d) Dam was removed in 1994.

88 Baylands Ecosystem Species and Community Profiles

Fish Pl

Figure 2.4 Trends in Age-0 Splittail Abundance for 1975-1995 as Indexed by Eight Independent Surveys. The first data point in each series is marked with a circle. Dry years are identified with asterisks above the data points— all other years are wet.

was not as dramatic for the Suisun Marsh, Chipps Floodplain inundation appears to be a key factor Island, or townet surveys, but there was a clear in- responsible for strong year classes, based on both statis- crease in abundance for each relative to the previous tical and limited observational data (Sommer et al. nine years. 1997). Higher flows increase inundation of floodplain There appears to be no consistent decline in adult areas, such as the Yolo Bypass, which provides spawn- abundance for most of the surveys (Figure 2.5). How- ing, rearing, and foraging habitat. The species has little ever, both the Suisun Marsh and surveys or no stock recruitment relationship. This is best illus- show significantly lower abundance in the early to trated from data collected in 1995, when exceptionally mid-1980s (Sommer et al. 1997). large numbers of young splittail were produced by a stock

Chapter 2 — Estuarine Fish and Associated Invertebrates 89

Fish

Pl ants

Reptiles

Amphibians &

Figure 2.5 Trends in Adult Splittail Abundance for 1976-1995 as Indexed by Six Independent Surveys. The first data point in each series is marked with a circle. Dry years are identified with asterisks above the data points— all other years are wet.

that should have been depleted by drought conditions Prey: Oligochaetes, zooplankton (cladocerans and cope- in seven of the previous eight years. pods), terrestrial , opossum shrimp (Neomysis Attributes that help splittail respond rapidly to mercedis), mollusks. improved environmental conditions include a relatively long life span, high reproductive capacity, and broad en- Good Habitat vironmental tolerances (Sommer et al. 1997). Additional factors that may affect population levels include habitat Sacramento splittail are one of the few freshwater loss, recreational fishing, entrainment, and toxic com- cyprinids that are highly tolerant of brackish water. Al- pounds. though they have been collected at salinities as high as 18 ppt, abundance is highest in the 0-10 ppt salinity Trophic Levels range (Sommer et al. 1997). Physiological studies show that splittail have critical salinity maxima of 20-29 ppt Splittail are secondary consumers. (Young and Cech 1996). Splittail also tolerate a wide range (7-33° C) of water temperatures in the labora- Proximal Species tory, which fits well with thermal fluctuations asso- ciated with its habitat. Depending upon the acclima- Predators: Striped bass, centrarchids. tion temperature (range 12-20° C), critical thermal

90 Baylands Ecosystem Species and Community Profiles maxima ranged from 22-33° C. As further evidence of the general hardiness of the species, splittail appear Chinook Salmon to be tolerant of low dissolved oxygen levels and strong water currents. Oncorhynchus tshawytscha Splittail are numerous within small dead-end Lt. Dante B. Maragni sloughs, those fed by freshwater streams, and in the larger sloughs such as Montezuma and Suisun (Daniels General Information and Moyle 1983). Juveniles and adults utilize shallow edgewater areas lined by emergent aquatic vegetation. The Chinook salmon (Family: Salmonidae) is morpho- Submerged vegetation provides abundant food sources logically distinguished from other Oncorhynchus species Fish and cover to escape from predators. Shallow, seasonally of the northern Pacific Ocean by its large size, small black flooded vegetation is also apparently the preferred spawn- spots on both caudal fin lobes, black pigment along the ing habitat of adult splittail (Caywood 1974). base of the teeth (McPhail and Lindsey 1970 as cited in Healey 1991), and varying shades of flesh color from References white through shades of pink and red (Healey 1991). The Chinook salmon life history (Figure 2.6) is char- Aceituno, M.E., M.L. Caywood, S.J. Nicola and W.I. acterized by adult migration from the ocean to natal Follett. 1976. Occurrence of native fishes in freshwater streams to spawn, and juvenile migration Alameda and Coyote Creeks, California. Ca. Dept. seaward as smolts in their first year of life. During the Fish and Game 62(3):195-206. smoltification process, juvenile Chinook salmon undergo Bailey, H. 1994. Culturing studies on splittail. physiological, morphological, and behavioral changes IEP Newsletter, Summer 1994. p. 3. that stimulate emigration and prepare them for life in Caywood, M.L. 1974. Contributions to the life history of the marine environment (Healey 1991). the splittail Pogonichthys macrolepidotus (Ayres). The Sacramento-San Joaquin Chinook salmon of Master’s thesis. Ca. State Univ., Sacramento. California exists as four races—winter, spring, fall, and Daniels, R.A. and P.B. Moyle. 1983. Life history of late-fall—as defined by the timing of adult spawning mi- the splittail (Cyprinidae: Pogonichthys macrolepidotus gration (Mason 1965, Frey 1971, Moyle 1976, Healey Pl (Ayres)) in Sacramento-San Joaquin estuary. U.S. 1991). In 1989, the Sacramento River winter-run Chi- Natl. Marine Fish. Bull. 81: 647-654. nook salmon was listed as threatened under the federal California Department of Water Resources and U.S. Bu- Endangered Species Act by the National Marine Fish- reau of Reclamation (CDWR and USBR). 1994. eries Service (NMFS) (54 FR 32085). NMFS reclassi- Effects of the Central Valley Project and State fied the winter-run as endangered in 1994 (59 FR 440) Water Project on Delta smelt and Sacramento based on: 1) the continued decline and increased vari- splittail. Prepared for U.S. Fish and Wildl. Serv., ability of run sizes since its listing as a threatened spe- Ecol. Services, Sacramento, CA. cies in 1989, 2) the expectation of weak returns in cer- Herbold, B. 1987. Patterns of co-occurrence and resource tain years as a result of two small year classes (1991 and use in a non-coevolved assemblage of fishes. Ph.D. 1993), and 3) continuing threats to the population. The dissertation. Univ. of Ca., Davis. State of California listed the winter-run as endangered Meng, L. and N. Kanim. 1994. Endangered and threat- under the California Endangered Species Act in 1989. ened wildlife and plants; proposed determination In 1995, the Oregon Natural Resources Council and R. of threatened status for the Sacramento splittail. Nawa petitioned NMFS to list Chinook salmon along Fed. Reg. 59:004: 862-868. the entire West Coast, including the States of Califor- Meng, L. and P.B. Moyle. 1995. Status of splittail in nia, Idaho, Oregon, and Washington, under the federal the Sacramento-San-Joaquin estuary. Transactions Endangered Species Act (54 FR 32085). The State of of the Amer. Fisheries Society 124: 538- 549. California presently includes on its list of species of spe- Sommer, T.R., R. Baxter and B. Herbold. 1997. The cial concern the late-fall (Class 2– special concern) and resilience of splittail in the Sacramento-San Joaquin the spring-run (Class 1– qualified as threatened or endan- Estuary. Transactions of the Amer. Fisheries Soci- gered) Chinook salmon. Spring-run Chinook salmon ety 126: 961-976. Young, P.S. and J.J. Cech. 1996. Environmental toler- ances and requirements of splittail. Transactions of the Amer. Fisheries Society 125: 664-678. Moyle 1976

Chapter 2 — Estuarine Fish and Associated Invertebrates 91 Figure 2.6 Life History of Chinook Salmon (USFWS 1995)

Fish

have also been given a special category by the state and that mature early in freshwater) (Miller and Brannon are considered a “ monitored” species. 1982). Pl Chinook salmon support commercial, recreational, Chinook salmon can be grouped into two types ants

Reptiles and tribal subsistence fisheries. However, due to the state based on variations in their life histories: stream-type and

Amphibians & of Pacific Coast Chinook salmon populations, the U. S. ocean-type. Stream-type Chinook salmon populations Department of Commerce declared the U.S. Pacific are most commonly found north of 56°N latitude along Coast salmon commercial fishery, excluding Alaska, a the North American coast and characterized by long disaster and has provided emergency relief funding for freshwater residence as juveniles (1+ years). Ocean-type displaced fisherman in 1995 and 1996 (59 FR 51419, Chinook salmon populations are most commonly found 60 FR 5908). Also, the federal Central Valley Project south of 56°N latitude and characterized by short fresh- Improvement Act requires restoration actions to double water residence as juveniles (2-3 months). Chinook the Chinook salmon population in the Sacramento-San salmon of the Sacramento-San Joaquin River system are Joaquin River system in California by the year 2002 es- predominantly ocean-t