Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California, May 2016 to March 2018

Open-File Report 2019–1057

U.S. Department of the Interior U.S. Geological Survey Cover. Landscape photograph of Coyote Creek, looking northeast over the southern San Francisco Bay. U.S. Geological Survey photograph by Fancis Parchaso, November 2, 2018. Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California, May 2016 to March 2018

By Kelly H. Shrader, Sarah A. Pearson, Francis Parchaso, and Janet K. Thompson

Open-File Report 2019–1057

U.S. Department of the Interior U.S. Geological Survey U.S. Department of the Interior DAVID BERNHARDT, Secretary U.S. Geological Survey James F. Reilly II, Director

U.S. Geological Survey, Reston, Virginia: 2019

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Suggested citation: Shrader, K.H., Pearson, S.A., Parchaso, F., and Thompson, J.K., 2019, Benthic community dynamics in Coyote Creek and Artesian Slough, southern San Francisco Bay, California, May 2016 to March 2018: U.S. Geological Survey Open- File Report 2019–1057, 93 p., https://doi.org/10.3133/ofr20191057.

ISSN 2331-1258 (online) iii

Contents

Executive Summary...... 1 Introduction...... 1 Methods...... 3 Results ...... 3 Community Composition...... 3 Temporal Trends in Community Composition...... 4 Spatial Trends in Community Composition...... 5 Artesian Slough Stations SB14 and SB15...... 6 Transitions in Benthic Community Function—As Consumers, as Prey, as Geochemical Enhancers...... 6 Conclusions...... 6 References Cited...... 7 Figures ...... 9 Tables ...... 22

Figures

1. Benthic sampling station locations in southern San Francisco Bay and sampling area in relation to San Francisco Bay proper...... 10 2. Time series graph showing abundance of major taxa at station SB03 in southern San Francisco Bay, May 2016–March 2018...... 11 3. Time series graph showing abundance of major taxa at station Alviso in Alviso Slough, May 2016–March 2018...... 11 4. Time series graph showing abundance of major taxa at station Mud in Coyote Creek, May 2016–March 201...... 12 5. Time series graph showing abundance of major taxa at station SB04 in Coyote Creek, May 2016–March 2018...... 13 6. Time series graph showing abundance of major taxa at station SB13 in Artesian Slough, May 2016–March 2018...... 13 8. Abundance of major taxa at six benthic sampling stations, measured in May of 2016...... 14 7. Time series graph showing abundance of major taxa at station Upcoy in Artesian Slough, May 2016—March 2018...... 14 9. Abundance of major taxa at six benthic sampling stations, measured in July of 2016...... 15 10. Abundance of major taxa at six benthic sampling stations, measured in August of 2016...... 15 11. Abundance of major taxa at six benthic sampling stations, measured in September of 2016...... 16 12. Abundance of major taxa at six benthic sampling stations, measured in November of 2016...... 16 iv

13. Abundance of major taxa at six benthic sampling stations, measured in January of 2017...... 17 14. Abundance of major taxa at six benthic sampling stations, measured in March of 2017...... 17 15. Abundance of major taxa at six benthic sampling stations, measured in May of 2017...... 18 6. Abundance of major taxa at six benthic sampling stations, measured in July of 2017...... 18 17. Abundance of major taxa at six benthic sampling stations, measured in September of 2017...... 19 18. Abundance of major taxa at stations SB14 and SB15. measured in June of 2017...... 19 19. Abundance of major taxa at stations SB14 and SB15, measured in December of 2017...... 20 20. Abundance of major taxa at six benthic sampling stations, measured in March of 2018...... 20 21. Time series graph showing abundance of major taxa at station SB14 in Artesian Slough, May 2016–March 2018...... 21 22. Time series graph showing abundance of major taxa at station SB15 in Artesian Slough, May 2016 – March 2018...... 21

Tables

1. Species list and abundance at sampling station SB03, southern San Francisco Bay, California, May 2016–March 2018...... 23 2. Species list and abundance at sampling station Alviso, Alviso Slough, California, May 2016–March 2018...... 32 3. Species list and abundance at sampling station Mud, Coyote Creek, California, May 2016–March 2018...... 41 4. Species list and abundance at sampling station SB04, Coyote Creek, California, May 2016–March 2018...... 50 5. Species list and abundance at sampling station SB13, Artesian Slough, California, May 2016–March 2018...... 59 6. Species list and abundance at sampling station Upcoy, Artesian Slough, California, May 2016–March 2018...... 68 7. Species list and abundance at sampling station SB14, Artesian Slough, California, May 2016–March 2018...... 77 8. Species list and abundance at sampling station SB15, Artesian Slough, California, May 2016–March 2018...... 85 v

Conversion Factors

International System of Units to U.S. customary units Multiply By To obtain Length millimeter (mm) 0.03937 inch (in.) meter (m) 3.281 foot (ft) meter (m) 1.094 yard (yd) Area square meter (m2) 0.0002471 acre square meter (m2) 10.76 square foot (ft2)

Supplemental Information

Water year is the 12-month period from October 1 through September 30 and is designated by the calendar year in which it ends.

Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California, May 2016 to March 2018

By Kelly H. Shrader, Sarah A. Pearson, Francis Parchaso, and Janet K. Thompson

Executive Summary Deviations from this relation are usually related to an extreme increase or decrease in the number of Benthic invertebrate communities are monitored because individuals of a particular species. the composition of those communities can affect and be • Species abundance at stations within the sloughs affected by the water quality of an aquatic system. Benthic was higher than the abundance at stations within communities use and sometimes regulate the cycling of essen- the southern San Francisco Bay or Coyote Creek. tial elements (for example, carbon). Benthic invertebrate taxa However, grand abundance—the sum of all taxa at all may also indicate acute and chronic stressors in an environ- stations—was higher at all stations in 2016 compared ment because they accumulate contaminants and can respond to 2017 and 2018. Annelids were prominent across (sometimes substantially) to low or high phytoplankton all stations, whereas bivalves were prominent in biomass as well as low oxygen conditions. Benthic communi- southern San Francisco Bay and Coyote Creek, and ties affect water quality by grazing pelagic food resources and amphipods were prevalent in the sloughs. increasing the rate of nutrient regeneration through feeding and bioturbating sediments. • Bivalves were not the most numerically abundant taxon The southern San Francisco Bay is a system dependent at stations in Coyote Creek but still represented a on phytoplankton as the base to the food web. Despite abun- sizeable proportion of the total abundance during dant nutrients, southern San Francisco Bay has had limited 2016 sampling and decreased during 2017 and 2018. phytoplankton production in the last several decades owing The lack of grazing pressure caused by observed to poor light conditions caused by high turbidities, and high decreases in these taxa starting in 2017 may have grazing losses from the water column by benthic invertebrates allowed the sloughs to become larger sources of and zooplankton. However, the balance of biogeochemical phytoplankton in spring. Potamocorbula amurensis conditions during spring of most years accommodates a short (Schrenck 1861) and Gemma gemma (Totten 1834), phytoplankton bloom in the southern San Francisco Bay. This the most commonly occurring bivalves observed in balance between available light, nutrients, and grazing has this study, are shallow-burrowing bivalves and hence maintained the phytoplankton biomass in the southern San are easy prey for bottom-feeding predators. The Francisco Bay at low levels relative to other high-nutrient quantitative importance of such predator-prey rela- urban estuaries. The role of benthic invertebrates during tionships on phytoplankton dynamics warrants further episodic spring events, as well as in other seasons, remains investigation. There were also more amphipods in the of great interest to water-quality and biological resource sloughs from May 2016 to May 2017; this group is managers. another potential contributor to the benthic-pelagic Our primary objective in this study is to quantify current biomass balance as they also consume phytoplankton (2016–18) benthic-community structure and function in the in suspension and serve as prey for small fish. southern San Francisco Bay, and to compare those communi- ties to the communities in the neighboring sloughs. The study area is inclusive of the area south of the Dumbarton Bridge including Coyote Creek and Artesian Slough. Introduction The following results are highlighted in this report: • Benthic communities of Coyote Creek and Artesian Benthic communities are monitored because the individu- Slough were dominated by different species but simi- als are indicators of the water quality of a system, and because lar functional groups from May 2016 to March 2018. they use and sometimes control available element resources such as carbon. Benthic communities are also a good indica- • Total number of individuals and the total number tor of acutely and chronically stressful environments because of species in this study are positively correlated. they are stationary, may accumulate contaminants, and 2 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California respond—sometimes markedly—to low or high phytoplank- The Sacramento River is the largest river and watershed ton biomass as well as low oxygen conditions (Cloern, 2001; system in California, and drains the slopes from parts of the Richman and Lovvorn, 2004; Thompson and others, 2008). Coast Range, Mount Shasta, the Cascade, and the Sierra Benthic communities can affect water quality by graz- Nevada Ranges. San Francisco Bay receives nearly all of its ing pelagic food resources and increasing the rate of nutrient freshwater from the Sacramento watershed, and the amount of regeneration through feeding and bioturbating the sediment freshwater flowing through the mouth of the Sacramento River (Caffrey, 1995; Thompson and others, 2008). Southern San can impact salinity throughout the San Francisco Bay (Kim- Francisco Bay is a system dependent on phytoplankton as the merer, 2002). The Sarcramento watershed has experienced base to the food web (Jassby and others, 1993). Despite abun- below normal rainfall and dry conditions with sporadic wet dant nutrients, southern San Francisco Bay has had limited years for the past decade. However, heavy rainfall in water phytoplankton production in the last several decades owing to year 2017 (October 2016 to September 2017) ended a five- poor light conditions and high losses from grazing. Thus, the year drought and set the record for California’s wettest year system has rarely experienced anoxia that is usually associated since 1983 (California Department of Water Resources, 2017). with high nutrient systems (Cloern, 2001). Our conceptual A large influx of freshwater from heavy, persistent rains can model for phytoplankton growth in southern San Francisco have similar impacts on the benthic community as a potential Bay includes a delicate balance between light availability, wastewater treatment plant malfunction, but on a potentially grazing losses (primarily in the shallow water), and physical much larger and farther-reaching scale. The severity and dura- mixing of the water column (Lucas and others, 2009). During tion of a potential change in the benthic community as a result spring of most years, the balance of biogeochemical condi- of this increase in freshwater is still unknown, yet it is unlikely tions accommodates a short phytoplankton bloom in southern for such a drastic change in salinity as this to go unnoticed. San Francisco Bay. This balance has maintained phytoplank- The role of benthic invertebrates during episodic spring ton biomass in southern San Francisco Bay at low levels rela- events, as well as in other seasons, remains of great interest to tive to other high-nutrient urban estuaries (Cloern, 2001). water-quality and biological resource managers. The autumn/winter reduction in filter-feeding bivalves Nichols and Thompson (1985a) described a 10-year data- in the shallow water is one of the primary triggers that allows set for an intertidal location in the southern San Francisco Bay a spring phytoplankton bloom to develop in the southern San and summarized the state of our knowledge on the bay benthos Francisco Bay (Cloern and others, 2007). During autumn, pre- in 1985 (Nichols and Thompson, 1985b). In both papers, the dation by migratory and resident birds (Thompson and others, authors acknowledged the high percentage of non-indigenous 2008), fish, and invertebrates (Cloern and others, 2007) greatly species in the benthic community and how the traits of those diminishes the shallow water bivalve communities in both San species might determine community structure and persis- Pablo Bay and southern San Francisco Bay (fig. 1) (Poulton tence. The 15 most common species in the 10-year study were and others, 2002, 2004; Richman and Lovvorn, 2004). The non-indigenous. Nichols and Thompson also stressed the elimination of bivalve grazing in the shallow water allows the importance of understanding the role of physical and possi- phytoplankton to grow if light and water-column residence bly chemical disturbance in maintaining populations of these time are not limiting (Thompson and others, 2008). Bivalves opportunistic species (1985a), and the importance of seasonal in the shallow water are thus essentially an annual species with weather and hydrologic extremes in controlling the seasonal larvae settling each spring followed by rapid growth, which patterns of growth, reproduction, and mortality of individual allows them to become a controlling factor on phytoplankton species (1985b). biomass by late spring and summer. Despite the variability that they observed in time and Changes in the benthic community structure are common. space, the authors concluded that benthic communities Benthic species distributions are dependent on the physical sampled “during the past three decades in San Francisco Bay habitat (substrate and depth), physiological limits (such as, provide no evidence that the qualitative distribution of benthic salinity; Lee and others, 2003), and predators (Cloern and oth- macroinvertebrate species in the bay had(s) changed percepti- ers, 2007). Therefore, seasonal and interannual differences in bly” (Nichols and Thompson, 1985b, p. 134). Lee and others freshwater flow result in both seasonal and episodic changes (2003) analyzed more recent benthic community data from in species abundance and community composition. Episodic four monitoring programs (two in the southern San Francisco events such as wastewater treatment plant malfunctions are Bay) and concluded that the introduction of Potamocorbula likely to have short-term effects, whereas other events such as amurensis (Schrenck 1861) (Carlton and others, 1990) had the introduction of non-native species can have lasting effects rapidly changed the benthic community structure from the on the benthic community (Nichols and Thompson, 1985a, period of the Nichols and Thompson studies and that their 1985b). Contaminants can also restrict the success of some conclusion needed to be revisited. After its introduction, P. species (Hornberger and others, 2000). Therefore, when a ben- amurensis changed the composition of the benthic community thic community that was dominated by filter feeders changes in the northern bay (Nichols and others, 1990) and reduced to one dominated by surface deposit feeders, many factors the biomass of phytoplankton (Alpine and Cloern, 1992) and could be responsible for such a change. zooplankton (Kimmerer and others, 1994). It is not apparent Results 3 that the introduction of Potamocorbula resulted in large community data are needed from shallow sloughs and deeper benthic community changes in the southern San Francisco Bay channels, because bivalves in the channel are the source of because data are sparse before 1988, but it is possible that the recruits (animals less than or equal to [≤] 2.5 millimeters [mm] benthic community today in South Bay is a result of competi- in length) following the autumn predation on the bivalves. tion with and facilitation from P. amurensis. The result of reduced grazing pressure on the phytoplank- ton has contributed to an upward trend and development of autumnal increases of phytoplankton biomass; however, that Methods these trends occur in conjunction with changes in turbidity is also of great importance to phytoplankton biomass, and its Eight stations were sampled in southern San Francisco effects cannot be overlooked (Cloern and others, 2007). As Bay, Coyote Creek and Artesian Slough (fig. 1). Samples were shown by this example, trends in phytoplankton biomass are collected from May 2016 to March 2018. Each station was not solely linked to grazing, and understanding the ecologi- sampled at least once every season (total of 13 times) from cal dynamics of the southern San Francisco Bay is not always May 2016 to March 2018. straightforward. This is a cautionary story, as it is important Samples were provided to the U.S. Geological Survey that we not misinterpret changes in phytoplankton standing (USGS) by the San José-Santa Clara Regional Wastewater stock to be solely due to changing water-quality conditions Facility staff. Samples were collected with a 0.05-square meter when there may be equally, if not more impactful biotic (m2) weighted Van Veen grab that was hand deployed in all changes. but the deep-water stations. Samples were sieved through a Predation on benthic bivalves is important, but other 0.5-mm screen, preserved in 10-percent buffered formalin, benthic invertebrates are also a substantial prey resource for and transferred to 70-percent ethyl alcohol with rose bengal many fish species and are considered a component of essential dye. Samples were sorted, and well-known species were fish habitat (The Magnuson-Stevens Fishery Conservation and enumerated at the USGS Benthic Laboratory in Menlo Park. A Management Act, 16 U.S.C. 1801–1891(d)). Our conceptual quality-assurance procedure was used whereby samples were model for maintaining appropriate benthic prey for fish and double sorted/identified depending on the difficulty and the bird species is based on understanding what prey character- number of organisms in the sample. All species were identified istics and habitat are important for the predator. The effect and enumerated to the lowest taxon possible. of species swaps within benthic communities as previously noted (Nichols and Thompson, 1985a and 1985b) may be very important to predators. For example, a surface-dwelling Results bivalve like P. amurensis has a soft shell, is highly caloric, is easy to capture, and has been shown to be valuable prey in San Francisco Bay (Richman and Lovvorn, 2004). A deep- burrowing tube-dwelling worm such as Sabaco elongatus Community Composition (Verill 1873), which is common in the southern San Francisco Bay (Lee and others, 2003), is unlikely to be fed upon by Species were classified into one of six taxa for further either fish or birds. Two prominent amphipod species,Mono - anaylses: annelida, amphipoda, bivalvia, cumacea, isopoda, corophium acherusicum (Costa 1853) and Americorophium and ostracoda. Bivalves, annelids, and amphipods represented spinicorne (Stimpson 1857), are relatively mobile and spend a substantial portion of the community composition and are time burrowed into the benthos; M. acherusicum lives in silky subsequently the focus of this report. Cumaceans, isopods, and tubes and leaves to forage and mate, whereas A. spinicorne ostracods remained negligible throughout most of the sam- burrows into soft sediment to forage and avoid predators pling period. (Bousfield and Hoover, 1997). Like the annelidS. elongatus, Bivalves in the southern San Francisco Bay and adjacent these amphipods make it challenging for predators to consume sloughs are filter feeders or deposit feeders with one species them. For this reason, analysis of the benthic community capable of feeding both ways (Poulton and others, 2004; Jones needs to include abundance and functional ecology (feeding and others, 2009). Many bivalves are broadcast spawners with mode, habitat, motility, and structures such as tubes and shells, external fertilization except for Gemma gemma (Totten 1834), which may impede predation) of each species. which broods its young. Except for small surface-dwelling Our primary objective is to quantify the current (2016– species (G. gemma, approximately 5 mm in length, and juve- 18) community structure and function in the benthic commu- nile P. amurensis), bivalves are usually stationary once they nity in the sloughs connected to southern San Francisco Bay settle and are thus easily captured by predators. This combined and to compare those communities to the benthic community with their high caloric value distinguishes bivalves as impor- in the southern San Francisco Bay. The study area (fig. 1) is tant prey for demersal fish and birds (Richman and Lovvorn, inclusive of the area south of the Dumbarton Bridge, includ- 2004). The large size of bivalves relative to the rest of the ben- ing Coyote Creek and Artesian Slough. To fully understand thic community means they consume a substantial amount of how the benthic community changes seasonally, benthic the available carbon in the water column and in the sediment 4 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California surface. Their large size also allows them to “wait out” periods increased slightly above the annelids by 50 individuals/0.05 of unfavorable water quality and low food availability and m2. Though consistently dominant, annelid abundance peaked respond very quickly once conditions change. Therefore, they during summer and winter because of increases in the abun- are formidable competitors with pelagic filter feeders such as dance of Streblospio benedicti Webster 1879. Amphipods zooplankton, which must reproduce and grow populations in exhibited relatively low abundance throughout sampling, but response to increased food availability. experienced small peaks during summer 2016 and summer to Annelids present throughout the southern San Francisco autumn 2017 related to changes in M. acherusicum abundance. Bay and adjacent sloughs are suspension and deposit feeders Bivalves and annelids made up much of the abundance in that feed on phytoplankton and detritus in the water column Alviso Slough at station Alviso, whereas amphipods, iso- and on the sediment surface. The most abundant species of pods, cumaceans, and ostracods accounted for less than 25 annelids in this study were opportunistic tube-dwellers or percent of total abundance (fig. 3, table 2). At the beginning burrowers with a wide range of temperature and salinity toler- of sampling in May 2016, bivalves were the most abundant ances, a characteristic of estuarine species. Annelids were taxa. Bivalves peaked May and September of 2016 at about often present in high abundance across all stations and were 1,000 and 850 individuals/0.05 m2, respectively, then sharply temporally and spatially the most abundant taxa on average. decreased in November 2016 and never recovered above 150 As a result, annelids represent important prey sources for ben- individuals/0.05 m2. Following a loss of G. gemma in Novem- thic predators, including shorebirds and fish. The annelid spe- ber 2016, bivalve abundance decreased, and annelids became cies commonly occurring in southern San Francisco Bay and the most abundant taxa from November 2016 until March Coyote Creek preferred more marine environments whereas 2018 when sampling concluded. Annelid abundance fluctuated the annelid species occurring in Alviso and Artesian Sloughs slightly between about 100 and 150 individuals per 0.05 m2 were more comfortable in brackish or fresh waters. from May 2016 to November 2016 before decreasing until the The most common amphipods are tube-dwelling filter following summer. From July 2017 to March 2018, annelid feeders. They are oviparous/viviparous (brood their young) abundance remained around 150 individuals per 0.05 m2 with and release their young as juveniles. Because most amphipods a decrease in September to 16 and a spike in November to as with these traits can swim, rapidly leave an area when chal- much as 250 individuals/0.05 m2. These fluctuations resulted lenged, and rapidly invade an area to reestablish their tubes from abundance changes of S. benedicti and Oligochaetes. and burrows; they are considered opportunistic species despite Amphipods started out as the second most abundant taxa in producing a relatively low number of juveniles. They feed on May 2016 at about 290 individuals/0.05 m2, then decreased pelagic food sources (phytoplankton is common) and sediment to 9 individuals/0.05 m2 in July 2016 and never reached more surface detritus and bacteria. Amphipods occur in high num- than 30 individuals/0.05 m2 from July 2016 to March 2018. bers of individuals at some locations, which results in the con- This 2016 reduction was due to decreases in Ampelisca abdita sumption of a noticeable amount of the pelagic food. In most Mills 1964, Grandidierella japonica Stephensen 1938, and M. cases, however, they still have an order of magnitude (or less) acherusicum. effect on the phytoplankton biomass relative to the bivalves Annelids, amphipods and bivalves all peaked during (Jones and others, 2009). Amphipods are common prey for fall 2016 and then substantially decreased in March 2017 at fish and birds, mainly shore birds and ducks (Stenzel and oth- station Mud in Coyote Creek (fig. 4, table 3). Annelids and ers, 1976; Feyrer and others, 2003). Pelagic and demersal fish bivalves greatly recovered in June 2017, but amphipod abun- feed on amphipods as some species vacate their tubes at night dance remained low. Annelids somewhat followed bivalve and actively swim, making them available to pelagic feeders. abundance patterns until bivalves decreased in August 2017 and failed to recover. The changes in total annelid abundance Temporal Trends in Community Composition marked the changes in abundance of S. benedicti and Oligo- chaete species, while bivalve seasonal fluctuations consisted Here we refer to taxa as dominant when their abundance of changes in P. amurensis abundance, and to a lesser extent to represents more than 50 percent of the total abundance at a G. gemma abundance changes. Amphipods and bivalves had given station and month, and taxa are considered prominent opposing abundance levels throughout the sampling period; when their abundance represents between 10 and 50 percent when one was high the other tended to be low. Bivalves were of the total abundance at a given station and month. At station more abundant than amphipods during spring and summer SB03 in the southern San Francisco Bay, all taxa experienced of 2016, until amphipod abundance increased above bivalves an abundance increase during the summer months (fig. 2, during autumn 2016 and winter 2017. This seasonal pattern table 1). Bivalve abundance was relatively low throughout continued into 2018. The peaks in amphipods abundance sampling, with abundance never surpassing 200 individuals were both linked to changes in Grandidierella. However, per 0.05 m2 (individuals/0.05 m2); they were most abundant the autumn 2016 peak also corresponded with changes in M. during summer to autumn 2016 and summer 2017 before acherusicum and the winter 2018 peak was also linked to decreasing because of fluctuations inG. gemma and P. amu- changes in Sinocorophium alienense (Chapman 1988). rensis. Annelids were the most abundant taxon during every All taxa peaked in May 2017 and decreased in July 2016 month of sampling except November 2016, when bivalves and July 2017 in Coyote Creek at station SB04 (fig. 5, table 4). Results 5

Bivalves maintained a low abundance throughout sampling, amurensis. Annelids were the dominant taxon at station Upcoy except in August 2016, which had about 370 individuals/0.05 for all months sampled, except May 2016, January 2017, and m2. Annelid abundance peaked in summer/autumn 2016 and January 2018. S. benedicti and Oligochaetes were the larg- summer/winter 2017 and had little similarity to amphipod est contributors to these patterns. Amphipods peaked during abundance. The summer 2016 and winter 2017 annelid peaks winter and late summer throughout the sampling period. These coincided with amphipod decreases in abundance, whereas peaks were related to separate species. In summer 2016, A. the fall 2016 and summer 2017 annelid peaks coincided with spinicorne was the dominant amphipod species, whereas in amphipod peaks in abundance. Most annelid fluctuations were winter 2017 and 2018, G. japonica was the dominant amphi- related to changes in S. benedicti and Oligochaete abundance; pod. Cumaceans remained at a low abundance until after the however, Boccardiella ligerica (Ferronnière 1898) abundance March 2017 decrease, when they slowly began to increase in also influenced the spring 2017 abundance peak. Amphipods abundance. A slight peak in summer 2017 was followed by a had substantial peaks (greater than [>] 1,550 individuals/0.05 larger peak in January 2018 of about 620 individuals/0.05 m2. m2) and decreases (3–240 individuals/0.05 m2) in abundance during 2016. In spring 2017, amphipods were not as abundant as 2016, and decreased for the rest of the year. In March 2018 Spatial Trends in Community Composition there was small increase in amphipod abundance. Overall, amphipods peaked during spring and autumn of 2016 and Total abundance across all stations was highest from May spring of 2017 and 2018. A. spinicorne was the main contribu- 2016 to March 2017, with taxa across stations experiencing tor to the spring 2016 and 2017 abundance peaks, whereas larger peaks in abundance than observed following March Si. alienense was the largest contributor to the relatively high 2017 (figs. 8–14, at back of report). Annelids, amphipods, and abundance from autumn 2016 to winter 2017. bivalves were the dominant taxonomic groups throughout the Total abundance changed substantially (plus or minus study and were responsible for most changes in total abun- [±] 1,000 individuals/0.05 m2) in almost every month until dance observed at the different stations. Annelids peaked dur- September 2017 at station SB13 in Artesian Slough (fig. 6, ing summer and autumn but were in relatively high abundance table 5). Station SB13 was highly abundant compared to the throughout sampling. Amphipods exhibited high variability other stations, with a maximum total abundance (about 8,500 across stations through time, with abundance peaking during individuals/0.05 m2 in January 2017) quadruple that of the spring and winter. In contrast, bivalves peaked in abundance maxima of most other stations. The exception to this was the during summer and autumn, and maintained relatively low ostracod boom in December 2017 at station SB15. Despite this abundance across all stations. high abundance, cumaceans, isopods, ostracods, and bivalves Annelids were dominant in Artesian Slough and promi- were negligible contributors to the total abundance at station nent in Coyote Creek and Alviso Slough during 2016 and SB13. Bivalves reached their highest abundance in Septem- became the most dominant taxon starting January 2017 when ber 2016 (89 individuals/0.05 m2) because of P. amurensis, S. benedicti became highly abundant in southern San Fran- before decreasing to abundances less than 30 individuals/0.05 cisco Bay as well as in the sloughs (figs. 8–13).S. benedicti, m2 starting in November 2016. Annelids were the second along with Heteromastus filiformis Claparède 1864 in the most abundant taxon at station SB13, and three of their four western stations (SB03, Alviso, and Mud stations) and B. peaks opposed amphipod abundance. Annelids peaked dur- ligerica in the eastern stations (SB04, SB13, SB14, SB15 and ing summer and autumn 2016, as well as spring and sum- Upcoy) maintained high abundance from January 2017 until mer 2017. Overall, abundance gradually decreased from its sampling concluded in March 2018. Streblospio benedicti maximum abundance in autumn 2016. The autumn 2016 peak is an opportunistic pioneer species that was present in high and gradual decrease of annelids was due to a surge and then abundance across all stations because of its ability to tolerate a decrease in S. benedicti and Oligochaetes, and B. ligerica. The wide range of temperature, salinity, and disturbance (Lee and highest peak in amphipod abundance was January 2017 (more others, 2003). than 8,000 individuals/0.05 m2), with July 2016 (about 4,900 Amphipods were primarily dominant in Coyote Creek individuals/0.05 m2) and May 2017 (about 3,400 individu- and Artesian Slough during May to July 2016 and Novem- als/0.05 m2) representing the previously mentioned summer ber 2016 to May 2017 before being surpassed in abundance and spring peaks. During their peaks, amphipods were also the by annelids in July 2017 (figs. 8–9 and 12–16). Amphipod most abundant taxon at SB13. Fluctuations in amphipod abun- abundance fluctuated greatly in Artesian Slough, with changes dance were due to changes in A. spinicorne, and to a lesser of plus or minus thousands at station SB13 every month extent, G. japonica. sampled. These changes were concurrent with large shifts in All taxa decreased in abundance at station Upcoy in M. acherusicum in southern San Francisco Bay and Coyote Artesian Slough between November 2016 and March 2017, Creek, with A. spinicorne in the sloughs, and with abundance when total abundance decreased from almost 1,400 to 90 changes in G. japonica across all stations. These species are individuals/0.05 m2 (fig. 7, table 6). Bivalves maintained low all suspension feeders that consume phytoplankton and brood abundance for most of the study but peaked at about 300 indi- their young; however, M. acherusicum prefers a saline envi- viduals/0.05 m2 in November 2016 related to an increase in P. ronment and cool waters, whereas A. spinicorne often occurs 6 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California in areas of low to moderate salinity. G. japonica is prevalent at pattern that is observed in the greater southern San Francisco all stations and tends to fluctuate withM. acherusicum and A. Bay. The amphipods were present all year but responded spinicorne but can tolerate a wider range of temperature and quickly to the changes in bivalve presence. The change in salinity (Bousfield and Hoover, 1997). amphipod abundance may have been due to relocating or Bivalves were dominant in Alviso Slough and Coyote being preyed upon, but they were still the most abundant Creek until November 2016 when bivalve abundance began group in at least one station in the sloughs from September to decrease, and annelid abundance began to increase (figs. 2016 to May 2017. Changes in prominent species involved 8–12). From January 2017 until sampling concluded in March species that occupied the same ecological niche, as most of the 2018, bivalves were only the dominant taxa on two occasions: prominent amphipods were brooders and deposit or suspen- splitting abundance with annelids at station SB03 in May 2017 sion feeders. Species composition changed spatially based on and at station Alviso in September 2017 (figs. 15 and 17). The salinity, with species preferring saline environments occurring increase and decrease of bivalves is attributed to changes in in southern San Francisco Bay and Coyote Creek and species the abundance of P. amurensis, a spawning suspension feeder, preferring fresher environments occurring in the neighboring and G. gemma, a brooding suspension/filter feeder. sloughs to the east. Despite these relationships, most of the prominent amphipod species present across stations can live in a wide range of salinities. Artesian Slough Stations SB14 and SB15 Two stations in Artesian Slough, SB14 and SB15, were Conclusions sampled quarterly. These stations are unique because they rep- resent the only locations sampled where the ostracod, Cypr- Throughout sampling, species composition changed ideis sp., accounts for a substantial percentage of total abun- spatially in relation to the nearby freshwater inputs. West- dance (figs. 17–20). At station SB14,Cyprideis sp. peaked ern stations in southern San Francisco Bay are more saline, in September 2017. Bivalve abundance remained negligible whereas the eastern stations in the neighboring sloughs experi- until December 2017 when P. amurensis abundance increased. ence freshwater inputs from the wastewater treatment facility. Annelid abundance at station SB14 decreased slightly in Although all prevalent species occurring at stations throughout autumn 2017 following a loss of B. ligerica and Laonome the study can survive in relatively wide ranges of salinity calida Capa 2007 before recovering. A sharp increase in G. when necessary, the most abundant species present indicate japonica at station SB14 in December 2017 caused amphipod this west-east salinity gradient based on the areas they occur; abundance to peak (fig. 21 and table 7, at back of report). the species present in southern San Francisco Bay prefer more Cyprideis sp. exhibited extremely high abundance at saline conditions over fresher conditions, whereas the oppo- station SB15 and were subsequently heavily dominant, as site is true of species occurring in the nearby sloughs. This ostracods were essentially the only taxon present. More than underlying salinity gradient coupled with the rapid influx of 1,000 ostracods/0.05 m2 were present each month sampled freshwater associated with the heavy rains in water year 2017 from June 2017 to March 2018, with an estimate of more (the 12-month period from October 1, 2016, through Septem- than 15,000 individuals/0.05 m2 observed in December 2017. ber 30, 2017) coincides with drastic changes in the community Annelids were also present with about 1,400 individuals/0.05 composition and overall abundance throughout the southern m2 in March 2017 before greatly decreasing. Amphipod and San Francisco Bay and adjacent sloughs; water year is the bivalve abundance were negligible throughout sampling at sta- 12-month period from October 1 through September 30 and is tion SB15 (fig. 22, table 8). designated by the calendar year in which it ends. Bivalves declined starting in late 2016, which coincides with the onset of water year 2017. With fewer bivalves in Transitions in Benthic Community Function—As the environment to heavily consume phytoplankton (notably Consumers, as Prey, as Geochemical Enhancers Potamocorbula amurensis and Gemma gemma), other taxa had room to thrive. Filter feeders are effective at moving carbon from the Annelids, ever adaptable and sturdy, became dominant water column to the benthos as food and as feces, so their across the sampled areas starting in January 2017 during the presence can speed up the geochemical processing of organic heavy rain. Annelid abundance increased above bivalve and matter. For the entire sampling period, filter feeders were amphipod abundance following the influx of freshwater and the dominant feeding type present at the sampling stations. subsequent changes in salinity throughout the study area. Annelids were highly abundant spatially and temporally, and Streblospio benedicti, an opportunistic, tube-dwelling pioneer thus may serve as a food source for predators of the benthos. species with a wide salinity tolerance, flourished throughout The main species present throughout the study area were tube- the southern San Francisco Bay and the neighboring sloughs. dwellers or burrowers. Interestingly, another tube-dwelling annelid, Boccardiella Bivalves are an integral part of the phytoplankton growth ligerica, became a prevalent species in the eastern sloughs; dynamics. The decreased abundance of bivalves in the spring but unlike S. benedicti, B. ligerica prefers low salinity waters followed with increasing numbers by summer is a seasonal while tolerating brackish conditions. References Cited 7

Amphipod abundance closely followed the salinity California Department of Water Resources, 2017, Water gradient, with more saline species observed in the southern Year 2017—What a difference a year makes: Sacramento, San Francisco Bay and fresh or brackish species observed in California, California Department of Water Resources, 12 the eastern sloughs. For example, Monocorophium acherusi- p. Also available at https://water.ca.gov/-/media/DWR- cum, a marine amphipod, occurred most in the southern San Website/Web-Pages/Programs/Groundwater-Management/ Francisco Bay and Coyote Creek stations; in contrast, Ameri- Data-and-Tools/Files/Statewide-Reports/Water-Year-2017--- corophium spinicorne prefers more fresh water and occurred What-a-Difference-a-Year-Makes.pdf. in higher abundance in the eastern sloughs. All the amphipod Carlton, J.T., Thompson, J.K., Schemel, L.E., and Nichols, species that were prevalent in this study consume phytoplank- F.H., 1990, The remarkable invasion of San Francisco ton, and the increase in amphipod abundance also coincides Bay, California (USA) by the Asian clam Potamocorbula with an increase in freshwater and a decrease in bivalve amurensis (Mollusca: Bivalvia): Marine Ecology Progress abundance. Series, v. 66, no. 1 2, p. 81–94. Although the decline in bivalve abundance was met with an increase in abundance of other taxa, this increase does not Cloern, J.E., 2001, Our evolving conceptual model of the necessarily translate into equivalent prey sources for preda- coastal eutrophication problem: Marine Ecology Progress tors. The increase of annelids was related to rising numbers of Series, v. 210, p. 223–253. [Also available at https://doi. S. benedicti and B. ligerica, both of which are tube-dwellers org/10.3354/meps210223.] that are hard to access and therefore unlikely to be fed upon by Cloern, J.E., Jassby, A.D., Thompson, J.K., and Hieb, K., either fish or birds. The increase in amphipods was related to 2007, A cold phase of the east Pacific triggers new phy- the rising numbers of M. acherusicum in southern San Fran- toplankton blooms in San Francisco Bay: Proceedings of cisco Bay and Coyote Creek and A. spinicorne in the neigh- the National Academy of Sciences of the United States of boring sloughs, both of which also burrow into the benthos out America, v. 104, no. 47, p. 18561–18565. [Also available at of reach of predators and are mobile enough to escape. The ]https://doi.org/10.1073/pnas.0706151104. increased abundance of annelids and amphipods to match the decline in bivalves does not correlate to stable, available prey Feyrer, F., Herbold, B., Matern, S.A., Moyle, P.B., 2003, sources for birds and demersal fish. Dietary shifts in a stressed fish assemblage: Consequences Freshwater influxes tend to cause short-term changes of a bivalve invasion in the San Francisco Estuary, Environ- to benthic community composition. Given the tremendous mental Biology of Fishes, v. 67, no. 277 [Also available at amount of freshwater deposited into the San Francisco Bay- https://doi.org/10.1023/A:1025839132274.] Sacramento Delta system in water year 2017, the duration and Hornberger, M., Luoma, S., Cain, D., Parchaso, F., Brown, magnitude of such a shift in salinity and potential phytoplank- C., Bouse, R., Wellise, C., and Thompson, J., 2000, Link- ton and food web dynamics is not yet known. age of bioaccumulation and biological effects to changes in pollutant loads in South San Francisco Bay: Environmental Science & Technology, v. 34, no. 12, p. 2401–2409. [Also References Cited available at https://doi.org/10.1021/es991185g.] Jassby, A.D., Cloern, J.E., and Powell, T.M., 1993, Organic Alpine, A.E., and Cloern, J.E., 1992, Trophic interactions and carbon sources and sinks in San Francisco Bay; variability direct physical effects control phytoplankton biomass and induced by river flow: Marine Ecology Progress Series, v. production in an estuary: Limnology and Oceanography, 95, p. 39–54. [Also available at https://doi.org/10.3354/ v. 37, no. 5, p. 946–955. [Also available at, https://doi. meps095039.] org/10.4319/lo.1992.37.5.0946.] Jones, N.L., Thompson, J.K., Arrigo, K.R., and Monismith, S.G., 2009, Hydrodynamic control of phytoplankton Bousfield, E.L. and Hoover, P.W., 1997, The amphipod super- loss to the benthos in an estuarine environment: Limnol- family Corophioidea on the Pacific coast of North America: ogy and Oceanography, v. 54, no. 3, p. 952–969. [Also 5. Family Corophiidae: Corophiinae, new subfamily: sys- available at [Also available at https://doi.org/10.4319/ tematics and distributional ecology, Amphipacifica, v. 2, no. lo.2009.54.3.0952.] 3, p. 67–139. Kimmerer, W.J., Gartside, E., and Orsi, J.J., 1994, Predation Caffrey, J.M., 1995, Spatial and seasonal patterns in sediment by an introduced clam as the likely cause of substantial nitrogen remineralization and ammonium concentrations in declines in zooplankton in San Francisco Bay: Marine San Francisco Bay, California: Estuaries, v. 18, no. 1, Part Ecology Progress Series, v. 113, p. 81–93. [Also available at B, p. 219-233. https://doi.org/10.3354/meps113081.] 8 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California

Kimmerer, W.J., 2002, Physical, biological, and management Poulton, V.K., Lovvorn, J.R., and Takekawa, J.Y., 2002, responses to variable freshwater flow into the San Francisco Clam density and scaup feeding behavior in San Pablo estuary: Estuaries, v. 25, no. 6B, p. 1275-1290. Bay, California: The Condor, v. 104, no. 3, p. 518–527. Lee, Henry, III, Thompson, Bruce, and Lowe, Sarah, 2003, [Also available at https://doi.org/10.1650/0010- Estuarine and scalar patterns of invasion in the soft-bottom 5422(2002)104[0518:CDASFB]2.0.CO;2.] benthic communities of the San Francisco Estuary: Biologi- Poulton, V.K., Lovvorn, J.R., and Takekawa, J.Y., 2004, cal Invasions, v. 5, no. 1/2, p. 85–102. [Also available at Spatial and overwinter changes in clam populations of San https://doi.org/10.1023/A:1024038522256.] Pablo Bay, a semiarid estuary with highly variable freshwa- Lucas, L.V., Koseff, J.R., Monismith, S.G., and Thompson, ter inflow: Estuarine, Coastal and Shelf Science, v. 59, no. J.K., 2009, Shallow water processes govern system-wide 3, p. 459–473. [Also available at https://doi.org/10.1016/j. bloom dynamics—A modeling study: Journal of Marine ecss.2003.10.005.] Systems, v. 75, no. 1–2, p. 70–86. [Also available at https:// Richman, S.E., and Lovvorn, J.R., 2004, Relative foraging doi.org/10.1016/j.jmarsys.2008.07.011.] value to Lesser Scaup ducks of native and exotic clams Nichols, F.H., and Thompson, J.K., 1985a, Persistence of an from San Francisco Bay: Ecological Applications, v. introduced mudflat community in South San Francisco Bay, 14, no. 4, p. 1,217–1,231. [Also available at https://doi. California: Marine Ecology Progress Series, v. 24, p. 83–97. org/10.1890/03-5032.] [Also available at https://doi.org/10.3354/meps024083.] Stenzel, L. E.Huber, H. R. & Page, G. W., 1976, Feeding Nichols, F.H., and Thompson, J.K., 1985b, Time scales of behaviour and diet of the Long-bill Curlew and Willet, Wil- change in the San Francisco Bay benthos: Hydrobiologia, son Bulletin v. 88, p. 314–32. v. 129, no. 1, p. 121–138. [Also available at https://doi. org/10.1007/BF00048691.] Thompson, J.K., Koseff, J.R., Monismith, S.G., and Lucas, Nichols, F.H., Thompson, J. K., and Schemel, L.E., 1990, L.V., 2008, Shallow water processes govern system-wide The remarkable invasion of San Francisco Bay (California, phytoplankton bloom dynamics—A field study: Journal of USA) by the Asian clam Potamocorbula amurensis—II Marine Systems, v. 74, no. 1–2, p. 153–166. [Also available Displacement of a former community: Marine Ecology at https://doi.org/10.1016/j.jmarsys.2007.12.006.] Progress Series v. 66, no. 1 2, p. 95–101. Figures 10 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California

CALIFORNIA Alviso MUD SB03 SB04 San Francisco station station station station

Latitude Latitude Latitude Latitude 37.461708 37.465302 37.458981 37.460373 SAN FRANCISCO Longitude Longitude Longitude Longitude BA -122.02179 -121.989296 -122.050148 -121.974983

Map area Redwood City

PACIFIC OCEAN PACIFIC SB13 SB14 SB15 UPCO station station station station 0 5 MES Sunnyvale N San Jose Latitude Latitude Latitude Latitude 0 5 KOMETERS 37.46138 37.45037 37.44313 37.461349 nset from ational Map. Longitude Longitude Longitude Longitude EPAATIO -121.964615 -121.9681 -121.9607 -121.950966 Sample sites etland area

COOTE CREE Mud

Alviso Upcoy SB04 SB13 SB03

SB14 Artesian Slough

SB15 Alviso Slough Guadalupe Slough

N 0 1 ME

0 1 KOMETER Base map from Tableau

Figure 1. Benthic sampling station locations in southern San Francisco Bay and sampling area in relation to San Francisco Bay proper.

Figure 1 Figures 11

SB03 1,800 EPAATIO 1,600 Annelida Amphipoda Cumacea 1,400 Isopoda stracoda 1,200 Bivalvia

1,000

800

600

400 Figure 2. Time series graph

Abundance, in number per 0.05 square meter showing abundance of 200 major taxa at station SB03 in southern San Francisco Bay, May 2016–March 2018. 0

May 2016 Sept. 2016 Jan. 2017 May 2017 Sept. 2017 Jan. 2018 Alviso Slough 1,200 EPAATIO 1,100 Annelida

1,000 Amphipoda Cumacea 900 Isopoda stracoda 800 Bivalvia

700

600

500

400

300 Figure 3. Time series graph Abundance, in number per 0.05 square meter 200 showing abundance of major taxa at station Alviso in Alviso 100 Slough, May 2016–March 2018.

0

Figure 2 May 2016 Sept. 2016 Jan. 2017 May 2017 Sept. 2017 Jan. 2018

Figure 3 12 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California

Mud 500 EPAATIO Annelida 450 Amphipoda Cumacea 400 Isopoda stracoda 350 Bivalvia

300

250

200

150

100 Abundance, in number per 0.05 square meter Figure 4. Time series graph 50 showing abundance of major taxa at station Mud in Coyote 0 Creek, May 2016–March 2018.

May 2016 Sept. 2016 Jan. 2017 May 2017 Sept. 2017 Jan. 2018

SB04 1,800 EPAATIO 1,600 Annelida Amphipoda

1,400 Cumacea Isopoda stracoda 1,200 Bivalvia

1,000

800

600

400 Abundance, in number per 0.05 square meter Figure 5. Time series graph 200 showing abundance of major taxa at station SB04 in Coyote 0 Creek, May 2016–March 2018.

Figure 4 May 2016 Sept. 2016 Jan. 2017 May 2017 Sept. 2017 Jan. 2018

Figure 5 Figures 13

SB13 Artesian 9,000

8,000 EPAATIO Annelida 7,000 Amphipoda Cumacea 6,000 Isopoda stracoda 5,000 Bivalvia

4,000

3,000

2,000 Figure 6. Time series graph Abundance, in number per 0.05 square meter 1,000 showing abundance of major taxa at station SB13 in Artesian Slough, 0 May 2016–March 2018.

May 2016 Sept. 2016 Jan. 2017 May 2017 Sept. 2017 Jan. 2018

Upcoy 1,600 EPAATIO Annelida 1,400 Amphipoda Cumacea 1,200 Isopoda stracoda 1,000 Bivalvia

800

600

400

Abundance, in number per 0.05 square meter Figure 7. Time series graph 1200 showing abundance of major taxa at station Upcoy in Artesian 0 Slough, May 2016—March 2018.

May 2016 Sept. 2016 Jan. 2017 May 2017 Sept. 2017 Jan. 2018 Figure 6

Figure 7 14 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California

Abundance of benthic taxa, May 25, 2016 EPAATIO Benthic taxa present Amphipoda Annelida Bivalvia Cumacea Isopoda COOTE CREE n=408 stracoda n=1,426 Mud n=2,066 n=3,156 n=1,087 n=61 Alviso SB4 SB13 Upcoy SB03 Artesian Slough

N 0 1 ME Guadalupe Slough Alviso Slough 0 1 KOMETER Base map from Tableau

Figure 8. Abundance of major taxa at six benthic sampling stations, measured in May of 2016. Total fauna abundance (n=) is represented in total number of specimen recovered per 0.05 square meter. The proportional representation of taxa at each station is shown on the pie charts with taxa represented by different colors.

Abundance of benthic taxa, July 11, 2016 EPAATIO Benthic taxa present Amphipoda Annelida Bivalvia Cumacea COOTE CREE Isopoda n=493 stracoda n=337 Mud n=6,681 n=1,727 n=1,727 n=72 Alviso Upcoy SB04 SB13 SB03

Artesian Slough

Alviso Slough 0 1 ME N Guadalupe Slough 0 1 KOMETER Base map from Tableau Figure 9. Abundance of major taxa at six benthic sampling stations, measured in July of 2016. Total fauna abundance (n=) is represented in total number of specimen recovered per 0.05 square meter. The proportional representation of taxa at each station is shown via pie chart with taxa represented by different colors.

Figure 8

Figure 9 Figures 15

Abundance of benthic taxa, August 19, 2016 EPAATIO Benthic taxa present Amphipoda Annelida Bivalvia Cumacea COOTE CREE n=115 Isopoda n=1,157 stracoda n=118 Mud n=897 n=1,206 n=190 Upcoy Alviso SB13 SB03 SB04

Artesian Slough

Guadalupe Slough 0 Alviso Slough 1 ME N

0 1 KOMETER Base map from Tableau Figure 10. Abundance of major taxa at six benthic sampling stations, measured in August of 2016. Total fauna abundance (n=) is represented in total number of specimen recovered per 0.05 square meter. The proportional representation of taxa at each station is shown via pie chart with taxa represented by different colors.

Abundance of benthic taxa, September 22, 2016 EPAATIO Benthic taxa present Amphipoda Annelida Bivalvia Cumacea COOTE CREE Isopoda n=324 stracoda n=983 Mud n=463 n=4,873 n=1,504 n=224 Alviso SB04 SB13 Upcoy SB03

Artesian Slough

N 0 1 ME Alviso Slough Guadalupe Slough 0 1 KOMETER Base map from Tableau Figure 11. Abundance of major taxa at six benthic sampling stations, measured in September of 2016. Total fauna abundance (n=) is represented in total number of specimen recovered per 0.05 square meter. The proportional representation of taxa at each station is shown via pie chart with taxa represented by different colors. 16 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California

Abundance of benthic taxa, ovember 18, 2016 EPAATIO Benthic taxa present Amphipoda Annelida Bivalvia Cumacea Isopoda COOTE CREE stracoda n=587 n=137 n=7,078 n=2,053 Mud n=2,202 n=365 Upcoy Alviso SB13 SB03 SB04

Artesian Slough

0 1 ME N Guadalupe Slough Alviso Slough 0 1 KOMETER Base map from Tableau Figure 12. Abundance of major taxa at six benthic sampling stations, measured in November of 2016. Total fauna abundance (n=) is represented in total number of specimen recovered per 0.05 square meter. The proportional representation of taxa at each station is shown via pie chart with taxa represented by different colors.

Abundance of benthic taxa, January 5, 2017 EPAATIO Benthic taxa present Amphipoda Annelida Bivalvia Cumacea COOTE CREE Isopoda n=178 stracoda n=103 n=1,322 Mud n=680 n=8,449 n=563 Alviso Upcoy SB04 SB13 SB03

Artesian Slough 0 Alviso Slough 1 ME N Guadalupe Slough 0 1 KOMETER

Base map from Tableau Figure 13. Abundance of major taxa at six benthic sampling stations, measured in January of 2017. Total fauna abundance (n=) is represented in total number of specimen recovered per 0.05 square meter. The proportional representation of taxa at each station is shown via pie chart with taxa represented by different colors. Figures 17

Abundance of benthic taxa, March 20, 2017 EPAATIO Benthic taxa present Amphipoda COOTE CREE Annelida n=91 Bivalvia Cumacea n=61 Mud n=90 n=436 Isopoda n=171 Alviso SB04 SB13 Upcoy stracoda SB03

n=465 SB14

Guadalupe Slough n=1,534 Artesian Slough N 0 1 ME Alviso Slough SB15

0 1 KOMETER Base map from Tableau Figure 14. Abundance of major taxa at six benthic sampling stations, measured in March of 2017. Total fauna abundance (n=) is represented in total number of specimen recovered per 0.05 square meter. The proportional representation of taxa at each station is shown via pie chart with taxa represented by different colors.

Abundance of benthic taxa, May 11, 2017 EPAATIO Benthic taxa present Amphipoda Annelida Bivalvia Cumacea Isopoda COOTE CREE n=1,157 stracoda

n=71 Mud n=1,493 n=4,060 n=829 n=305 Alviso SB04 SB13 Upcoy SB03

Artesian Slough N 0 1 ME Alviso Slough Guadalupe Slough 0 1 KOMETER

Base map from Tableau Figure 15. Abundance of major taxa at six benthic sampling stations, measured in May of 2017. Total fauna abundance (n=) is represented in total number of specimen recovered per 0.05 square meter. The proportional representation of taxa at each station is shown via pie chart with taxa represented by different colors. 18 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California

Abundance of benthic taxa, July 17, 2017 EPAATIO Benthic taxa present Amphipoda Annelida Bivalvia Cumacea COOTE CREE n=339 Isopoda stracoda n=236 n=1,296 n=908 n=989 Mud n=127 Alviso Upcoy SB04 SB13 SB03

Artesian Slough

0 Alviso Slough 1 ME N Guadalupe Slough 0 1 KOMETER

Base map from Tableau Figure 16. Abundance of major taxa at six benthic sampling stations, measured in July of 2017. Total fauna abundance (n=) is represented in total number of specimen recovered per 0.05 square meter. The proportional representation of taxa at each station is shown via pie chart with taxa represented by different colors.

Abundance of benthic taxa, September 28, 2017 EPAATIO Benthic taxa present Amphipoda Annelida Bivalvia COOTE CREE SB04 Cumacea n=485 Isopoda

n=161 Mud n=193 n=449 n=369 stracoda n=295 Alviso SB13 Upcoy SB03

n=771 SB14 Guadalupe Slough Artesian Slough n=1,775 Alviso Slough SB15 N 0 1 ME

0 1 KOMETER Base map from Tableau Figure 17. Abundance of major taxa at six benthic sampling stations, measured in September of 2017. Total fauna abundance (n=) is represented in total number of specimen recovered per 0.05 square meter. The proportional representation of taxa at each station is shown via pie chart with taxa represented by different colors. Figures 19

Abundance of benthic taxa, June 30, 2017 EPAATIO Benthic taxa present Amphipoda Annelida n=250 Bivalvia SB14 Cumacea Isopoda stracoda Artesian Slough

n=2,174 SB15

0 1 ME N

0 1 KOMETER

Base map from Tableau Figure 18. Abundance of major taxa at stations SB14 and SB15. measured in June of 2017. Total fauna abundance (n=) is represented in total number of specimen recovered per 0.05 square meter. The proportional representation of taxa at each station is shown via pie chart with taxa represented by different colors.

Abundance of benthic taxa, December 6, 2017 EPAATIO Benthic taxa present Amphipoda Annelida Bivalvia n=1,163 Cumacea SB15 Artesian Slough Isopoda stracoda

n=15,045

SB14

N 0 1 ME

0 1 KOMETER

Base map from Tableau Figure 19. Abundance of major taxa at stations SB14 and SB15, measured in December of 2017. Total fauna abundance (n=) is represented in total number of specimen recovered per 0.05 square meter. The proportional representation of taxa at each station is shown via pie chart with taxa represented by different colors. 20 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California

Abundance of benthic taxa, March 8, 2018 EPAATIO Benthic taxa present Amphipoda COOTE CREE Annelida n=362 Bivalvia Cumacea n=198 Mud n=1,152 n=1,469 n=353 n=71 Isopoda Alviso SB04 SB13 Upcoy stracoda SB03

n=1,232 SB14

Artesian Slough

Alviso Slough n=2,196 SB15 Guadalupe Slough N 0 1 ME

0 1 KOMETER

Base map from Tableau Figure 20. Abundance of major taxa at six benthic sampling stations, measured in March of 2018. Total fauna abundance (n=) is represented in total number of specimen recovered per 0.05 square meter. The proportional representation of taxa at each station is shown via pie chart with taxa represented by different colors.

SB14 900 EPAATIO 800 Annelida Amphipoda 700 Cumacea Isopoda 600 stracoda Bivalvia

500

400

300

200

Abundance, in number per 0.05 square meter Figure 21. Time series graph 100 showing abundance of major taxa at station SB14 in Artesian 0 Slough, May 2016–March 2018.

Jan. 2018 Mar. 2018 Mar. 2017 May 2017 July 2017 Sept. 2017 Nov. 2017

Figure 20 Figures 21

SB15 16,000 EPAATIO Annelida 14,000 Amphipoda Cumacea 12,000 Isopoda stracoda 10,000 Bivalvia

8,000

6,000

4,000

Abundance, in number per 0.05 square meter Figure 22. Time series graph 2,000 showing abundance of major taxa at station SB15 in Artesian Slough, May 2016 –March 2018. 0

Jan. 2018 Mar. 2018 Mar. 2017 May 2017 July 2017 Sept. 2017 Nov. 2017 22 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California

Page intentionally left blank Tables 24 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 07-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 05-11-17 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 14 24 01-05-17 0 0 0 0 0 0 5 0 0 0 0 0 0 0 23 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 11 10 09-22-16 0 0 0 4 0 0 0 0 0 0 0 0 0 0 18 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 49 78 07-11-16 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-25-16 (Moore (Moore 1906) (E. Blanchard (Castle 1900) (Linneaus . (Laubier 1967) Hand & Bushnell (Girard, 1850) Taxon unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., sp. A Species list and abundance at sampling station SB03, southern San Francisco Bay, California, May 2016–March 2018. Species list and abundance at sampling station SB03, southern San Francisco Bay,

1967 1758) 1849) 1901) PHYLUM CNIDARIA Class Anthozoa Actiniaria unid. spp Diadumene Flosmaris grandis PHYLUM PLATYHELMINTHES Class Turbellaria tigrine Girardia unid. spp. Turbellaria PHYLUM NEMATODA Nematoda unid. spp PHYLUM ANNELIDA Class Oligochaeta Naididae unid. spp. Oligochaeta unid. spp. unid. spp. Tubificidae Hirudinida Order Gloiobdella elongata Helobdella stagnalis Helobdella triserialis microstoma Mooreobdella Placobdella montifera Class Polychaeta Acmira catherinae Table 1. Table Species typically found in the southern San Francisco Bay are included this table, despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. Abbreviations: many species of the same genera; SF1, denotes separate genera] Tables 25 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 03-08-18 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 01-09-18 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 11-09-17 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 09-28-17 —Continued 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 07-17-17 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 05-11-17 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 2 6 0 0 0 0 0 13 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 1 0 0 0 0 0 10 11-18-16 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 2 1 2 0 0 0 0 0 09-22-16 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 08-19-16 0 0 6 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 3 0 0 13 16 07-11-16 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-25-16

Hartman (Linneaus (Mesnil 1897) (Schmarda Leidy 1855 Blacke 1996 Moore 1911 Reish 1959 Hartman 1936 (Frabricius 1780) (Moore 1906) Berkeley & (Leuckart 1847) Taxon Berkele 1927 (Berkeley & and Malmgren 1865

Hartman 1936 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., unid. spp. sp. A Species list and abundance at sampling station SB03, southern San Francisco Bay, California, May 2016–March 2018. ­­ Species list and abundance at sampling station SB03, southern San Francisco Bay, sp. SF1 sp. A

Berkeley 1956) 1898) complex 1936 1861) 1938 1767) Class Polychaeta ­ —Continued Acmira lopezi Alitta brandti Alitta succinea Amaeana Armandia brevis Boccardiella ligerica (Ferronnière, Capitella capitata Cirratulidae unid. spp. Cirriformia moorei Cossura Dipolydora brachycephala Dipolydora caulleryi Dipolydora socialis Dipolydora Eteone californica Eteone lighti Euchone limnicola Exogone lourei Glycera americana Glycinde armigera Glycinde picta Glycinde Harmothoe imbricata Table 1. Table Species typically found in the southern San Francisco Bay are included this table, despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. Abbreviations: many species of the same genera; SF1, denotes separate genera] 26 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 106 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 09-28-17 —Continued 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 93 07-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 33 05-11-17 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 03-20-17 Sampling date 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 01-05-17 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 09-22-16 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 08-19-16 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 07-11-16 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-25-16 - - - Hart (Petti (Baird Hartman Örsted (Claparède Sikoski & Leidy 1859 (Imajima (Montagu Moore 1911 Hartman 1938 A apa 2007 (Johnson 1903) (Johnson 1897)

(Johnson 18970 (Berkeley & Berke Taxon sp. Berkeley & unid. spp. Species list and abundance at sampling station SB03, southern San Francisco Bay, California, May 2016–March 2018. ­­ Species list and abundance at sampling station SB03, southern San Francisco Bay,

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1864) bone 1957) Bick 2004 1966) 1813) ley 1945) man 1936 1941 1842 1942 1863) Class Polychaeta ­ —Continued Hediste limnicola filiformis Heteromastus Laonome calida C Leitoscoloplos pugettensis Lumbrineris inflata Manayunkia speciosa neglecta Marenzelleria Megasyllis nipponica Marphysa sanguinea Neoamphitrite Nephtys caecoides Nephtys cornuta pelagica neonigripes Nereis Paleanotus bellis Pectinaria californiensis Pholoides aspera Phyllodoce groenlandica Pista pacifica bicanaliculata Platynereis Polycirrus Table 1. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 27 - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 178 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 189 11-09-17 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 103 09-28-17 —Continued 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 539 07-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 66 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 101 03-20-17 Sampling date 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 359 01-05-17 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 115 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 175 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 46 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1519 07-11-16 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 05-25-16 (Ehlers Hartman (Moore Southern Webster 1879 Webster (O.F. Muller (O.F. (Chamberlin (Verrill 1873) (Verrill

Bosc 1802 A A A

Taxon

Barkeley 1929

(Berkeley & Berkeley

sp. A A

sp. sp. . sp. sp Species list and abundance at sampling station SB03, southern San Francisco Bay, California, May 2016–March 2018. ­­ Species list and abundance at sampling station SB03, southern San Francisco Bay, sp. A

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1921 (Okuda 1937) 1906) 1901) 1806) 1945) 1966 1919) Class Polychaeta ­ —Continued Polydora cornuta Pseudopolydora kempi Pseudopolydora paucibranchiata Sabaco elongatus Schistomeringos annulate Schistomeringos longicornis Scolelepis squamata Scoletoma luti californiensis Sphaerosyllis Sphaerosyllis Spiophanes duplex benedicti Streblospio Tharyx parvus PHYLUM ARTHROPODA Class Crustacea SubClass Copepoda Cyclopid SubClass Ostracoda Candona Cyclocypris Cypricercus Cyprideis Table 1. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 28 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California 0 1 0 0 0 0 0 0 0 2 0 0 0 3 0 0 03-08-18 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 68 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 —Continued 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 07-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 53 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 08-19-16 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 12 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-25-16 (Li (W. (W. (Van (Van (Gamo (Cushman Ortmann 1908 Li 1964 Darwin 1854 Nakazawa 1910 Holmes 1896 Hart 1930 Hart 1930 Taxon

A unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., A

sp. spp. Species list and abundance at sampling station SB03, southern San Francisco Bay, California, May 2016–March 2018. ­­ Species list and abundance at sampling station SB03, southern San Francisco Bay, sp.

1906) Kaufmann 1900 1932) Tattersall 1936) 1967) Name 1940) SubClass Ostracoda —Continued Eucypris Eusarsiella zostericola Herpetocypris brevicaudata Isocypris SubClass Cirripedia Balanus improvisus SubClass Malacostraca Mysidacea Order Acanthomysis aspera Alienacanthomysis macropsis Hyperacanthomysis longirostris Neomysis japonica Neomysis kadiakensis Neomysis mercedis Cumacea Order Cumella vulgaris pacifica Eudorella Nippoleucon hinumensis Tanaidacea Order Sinelobus Isopoda Order insulare Gnorimosphaeroma Table 1. Table Species typically found in the southern San Francisco Bay are included this table, despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. Abbreviations: many species of the same genera; SF1, denotes separate genera] Tables 29 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 01-09-18 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-09-17 0 0 5 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 —Continued 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 92 21 07-17-17 0 0 2 0 0 2 3 0 0 0 0 0 0 0 0 0 0 1 0 05-11-17 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 03-20-17 Sampling date 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 9 0 01-05-17 0 2 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 11-18-16 0 2 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 09-22-16 1 8 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 10 10 08-19-16 0 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 12 07-11-16 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 26 05-25-16 - - - (Mills (Stimp (Dana (Stimp (Shoe Stephensen (Miers 1881) Bousfield Richardson (Stimpson Shoemaker (Bousfield 1969) (Mills 1964) Holmes 1908 Mayer 1903 Smith 1873 Templeton 1836 Templeton —Continued Taxon unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., unid. spp. Species list and abundance at sampling station SB03, southern San Francisco Bay, California, May 2016–March 2018. ­­ Species list and abundance at sampling station SB03, southern San Francisco Bay,

Dana 1853 1909 1962) son 1857) maker 1941) 1938 1963 son 1856) 1853) 1938 1856) Order Order Isopoda ­ oregonensis Gnorimosphaeroma Paranthura japonica Synidotea laevidorsalis Amphipoda Order Americhelidium shoemakeri spinicorne Americorophium stimpsoni Americorophium Ampelisca abdita Ampelisca lobate Ampithoe plumulosa Ampithoe valida mendax Caprella scaura Caprella Crangonyx floridanus Eogammarus confervicolus Eusiroidae Gammarus daiberi Gnathopleustes pugettensis japonica Grandidierella Grandifoxus grandis Table 1. Table Species typically found in the southern San Francisco Bay are included this table, despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. Abbreviations: many species of the same genera; SF1, denotes separate genera] 30 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 01-09-18 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-09-17 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 125 09-28-17 —Continued 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 73 07-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 01-05-17 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-18-16 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 92 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 44 07-11-16 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 26 05-25-16 - (Yu (Yu Costa (Craw (Bergh (Bergh Rathbun (Chapman Stimpson (Stephensen (Heller 1862) Dana 1852 Shoemaker 1942 Taxon sp. A Smith 1873 unid. spp. Species list and abundance at sampling station SB03, southern San Francisco Bay, California, May 2016–March 2018. ­­ Species list and abundance at sampling station SB03, southern San Francisco Bay,

sp. A

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1853 ford 1937) 1932) 1988) 1938) 1856 1902 1894) Order Amphipoda—Continued Order Hyalella Melita nitida acherusicum Monocorophium insidiosum Monocorophium uenoi Monocorophium Paradexamine Photis brevipes alienense Sinocorophium heteroceratum Sinocorophium Stenothoe valida Talitridae Decapoda Order Crangon franciscorum Decopoda unid. spp. Palaemon modestus Palaemon macrodactylus Class Insecta Family Chironomidae Chironomidae unid. spp. PHYLUM MOLLUSCA Class Gastropoda Melanochlamys diomedea Table 1. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 31 - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 09-28-17 —Continued 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 39 07-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 88 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 87 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 180 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 76 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-25-16 (Tryon (Tryon (Linnaeus 1825) (Tryon 1865) (Tryon (Rowell 1863) (Benson 1842) (Say 1822) (Say 1817) (O. F. Müller (O. F. (Say 1822) Suter 1909 (Gould 1841) (Linnaeus 1758) Dall & Bartsch

(Menke 1830) (Say Say 1822 A (Totten 1834) (Totten Taxon A unid. spp. Baba 1960

Species list and abundance at sampling station SB03, southern San Francisco Bay, California, May 2016–March 2018. ­­ Species list and abundance at sampling station SB03, southern San Francisco Bay,

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many sp. A 1767) 1866) 1909 1774) Class Gastropoda—Continued Nudibranchia Okenia plana Onchidoris bilamellata Philine auriformis SubClass Pulmonata Ferrissia californica Gyraulus circumstriatus Helisoma anceps humilis Lymnaea columella Lymnaea Menetus dilatatus Physa Radix auricularia SuperFamily Hydrobioidea Assiminea californica Boonea bisuturalis plana Crepidula Epitonium sp. Fluminicola sp. Nassarius obsoletus Odostomia fetella Class Bivalvia senhousia Arcuatula Corbicula fluminea Gemma gemma Table 1. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 32 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 1 0 0 0 0 2 0 0 0 0 0 03-08-18 1 0 0 0 0 8 0 0 0 0 0 01-09-18 7 0 0 0 0 2 0 0 0 0 0 11-09-17 0 0 0 0 0 0 0 0 0 0 24 09-28-17 —Continued 2 0 0 0 0 0 1 0 0 0 86 07-17-17 7 0 0 0 0 0 0 0 0 0 21 05-11-17 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 5 0 5 0 0 0 01-05-17 0 0 0 0 0 0 7 0 0 0 10 11-18-16 0 0 0 0 0 1 0 0 0 0 0 09-22-16 0 0 0 0 0 1 0 0 0 0 0 08-19-16 0 0 0 0 0 0 3 0 0 0 39 07-11-16 0 0 0 0 0 1 0 0 0 0 0 05-25-16 (Shrenck (A. Adams (Say 1829) (De Kay Prime 1852 (Poli 1791) (Valenciennes (Valenciennes Gould 1861 Taxon Linnaeus 1758 (Herdman 1881) Species list and abundance at sampling station SB03, southern San Francisco Bay, California, May 2016–March 2018. ­­ Species list and abundance at sampling station SB03, southern San Francisco Bay,

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1821) 1861) & Reeve 1850) 1843) Class Bivalvia—Continued Macoma petalum Musculium transversum Mya arenaria Pisidium casertanum Pisidium compressum Potamocorbula amurensis Theora lubrica philippinarum Venerupis PHYLUM CHORDATA Class Ascidacea Molgula manhattensis Styela clava PHYLUM ECHINODERMATA Class Ophiuroidea Amphiuridae unid. spp. Table 1. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 33 - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 127 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 114 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 144 07-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 41 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 36 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 11-18-16 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 09-22-16 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 08-19-16 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 116 07-11-16 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 48 05-25-16 (Moore (Moore 1906) (E. Blanchard (Castle 1900) (Linneaus . (Laubier 1967) Hand & Bushnell (Girard, 1850) Taxon (Berkeley & and sp. A Species list and abundance at sampling station Alviso, Alviso Slough, California, May 2016–March 2018.

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1967 1758) 1849) 1901) Berkeley 1956) PHYLUM CNIDARIA Class Anthozoa Actiniaria unid. spp Diadumene Flosmaris grandis PHYLUM PLATYHELMINTHES Class Turbellaria tigrine Girardia unid. spp. Turbellaria PHYLUM NEMATODA Nematoda unid. spp PHYLUM ANNELIDA Class Oligochaeta Naididae unid. spp. Oligochaeta unid. spp. unid. spp. Tubificidae Hirudinida Order Gloiobdella elongata Helobdella stagnalis Helobdella triserialis microstoma Mooreobdella Placobdella montifera Class Polychaeta Acmira catherinae Acmira lopezi Table 2. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 34 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 07-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-11-17 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 01-05-17 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-18-16 0 4 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 09-22-16 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 08-19-16 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 07-11-16 0 3 0 0 0 0 2 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 05-25-16

Hartman (Linneaus (Mesnil 1897) (Ferronnière, (Schmarda Leidy 1855 Blacke 1996 Moore 1911 Reish 1959 Hartman 1936 (Frabricius 1780) (Moore 1906) Berkeley & (Leuckart 1847) Berkele 1927 Taxon Malmgren 1865

Hartman 1936 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many unid. spp. sp. A Species list and abundance at sampling station Alviso, Alviso Slough, California, May 2016–March 2018.—Continued sp. SF1 sp. A

1898) complex 1936 1861) 1938 1767) Class Polychaeta—Continued Alitta brandti Alitta succinea Amaeana Armandia brevis ligerica Boccardiella Capitella capitata Cirratulidae unid. spp. Cirriformia moorei Cossura Dipolydora brachycephala Dipolydora caulleryi Dipolydora socialis Dipolydora Eteone californica Eteone lighti Euchone limnicola Exogone lourei Glycera americana Glycinde armigera Glycinde picta Glycinde Harmothoe imbricata Table 2. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. Abbreviations: species of the same genera; SF1, denotes separate genera] Tables 35 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-09-17 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 07-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-05-17 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 07-11-16 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-25-16 - - - Hart (Petti (Baird Hartman Örsted (Claparède Sikoski & Leidy 1859 (Imajima (Montagu Moore 1911 Hartman 1938 A apa 2007 (Johnson 1903) (Johnson 1897)

(Johnson 18970 (Berkeley & Berke Taxon sp. Berkeley & unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many Species list and abundance at sampling station Alviso, Alviso Slough, California, May 2016–March 2018.—Continued

1864) bone 1957) Bick 2004 1813) 1966) ley 1945) man 1936 1941 1842 1942 1863) Class Polychaeta—Continued Hediste limnicola filiformis Heteromastus Laonome calida C Leitoscoloplos pugettensis Lumbrineris inflata Manayunkia speciosa neglecta Marenzelleria Marphysa sanguinea Megasyllis nipponica Neoamphitrite Nephtys caecoides Nephtys cornuta pelagica neonigripes Nereis Paleanotus bellis Pectinaria californiensis Pholoides aspera Phyllodoce groenlandica Pista pacifica bicanaliculata Platynereis Table 2. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. Abbreviations: species of the same genera; SF1, denotes separate genera] 36 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 82 01-09-18 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 120 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 07-17-17 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 07-11-16 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 38 05-25-16 (Ehlers Hartman (Moore Southern Webster 1879 Webster (O.F. Muller (O.F. (Chamberlin (Verrill 1873) (Verrill

Bosc 1802 A A A

Taxon Barkeley 1929

(Berkeley & Berkeley

sp. A unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many sp. sp. . unid. spp. sp Species list and abundance at sampling station Alviso, Alviso Slough, California, May 2016–March 2018.—Continued sp. A

1921 (Okuda 1937) 1906) 1901) 1806) 1945) 1966 1919) Class Polychaeta—Continued Polycirrus Polydora cornuta Pseudopolydora kempi Pseudopolydora paucibranchiata Sabaco elongatus Schistomeringos annulate Schistomeringos longicornis Scolelepis squamata Scoletoma luti californiensis Sphaerosyllis Sphaerosyllis Spiophanes duplex benedicti Streblospio Tharyx parvus PHYLUM ARTHROPODA Class Crustacea SubClass Copepoda Cyclopid SubClass Ostracoda Candona Cyclocypris Cypricercus Table 2. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. Abbreviations: species of the same genera; SF1, denotes separate genera] Tables 37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 03-08-18 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 29 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 07-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11-18-16 0 0 8 0 0 0 0 0 0 0 0 0 0 0 2 0 0 09-22-16 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 08-19-16 0 0 3 0 0 0 0 0 0 0 0 0 0 0 5 0 0 07-11-16 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 17 05-25-16 (Li (W. (W. (Van (Van (Gamo (Cushman Ortmann 1908 Li 1964 Darwin 1854 Nakazawa 1910 Holmes 1896 Hart 1930 Hart 1930

Taxon

A A

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many A

sp. sp. spp. Species list and abundance at sampling station Alviso, Alviso Slough, California, May 2016–March 2018.—Continued sp.

1906) Kaufmann 1900 1932) Tattersall 1936) 1967) Name 1940) SubClass Ostracoda—Continued Cyprideis Eucypris Eusarsiella zostericola Herpetocypris brevicaudata Isocypris SubClass Cirripedia Balanus improvisus SubClass Malacostraca Mysidacea Order Acanthomysis aspera Alienacanthomysis macropsis Hyperacanthomysis longirostris Neomysis japonica Neomysis kadiakensis Neomysis mercedis Cumacea Order Cumella vulgaris pacifica Eudorella Nippoleucon hinumensis Tanaidacea Order Sinelobus Isopoda Order insulare Gnorimosphaeroma Table 2. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. Abbreviations: species of the same genera; SF1, denotes separate genera] 38 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-09-17 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 07-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-11-17 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-05-17 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-18-16 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 20 09-22-16 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 1 0 0 08-19-16 0 0 0 0 1 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 07-11-16 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 22 41 156 05-25-16 - - - (Mills (Stimp (Dana (Stimp (Shoe Stephensen (Miers 1881) Bousfield Richardson (Stimpson Shoemaker (Bousfield 1969) (Mills 1964) Holmes 1908 Mayer 1903 Smith 1873 Templeton 1836 Templeton Taxon unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many unid. Spp. Species list and abundance at sampling station Alviso, Alviso Slough, California, May 2016–March 2018.—Continued sp. A

Dana 1853 1909 1962) son 1857) maker 1941) 1938 1963 son 1856) 1853) 1938 1856) Order Isopoda—Continued Order oregonensis Gnorimosphaeroma Paranthura japonica Synidotea laevidorsalis Amphipoda Order Americhelidium shoemakeri spinicorne Americorophium stimpsoni Americorophium Ampelisca abdita Ampelisca lobate Ampithoe plumulosa Ampithoe valida mendax Caprella scaura Caprella Crangonyx floridanus Eogammarus confervicolus Eusiroidae Gammarus daiberi Gnathopleustes pugettensis japonica Grandidierella Grandifoxus grandis Hyalella Table 2. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. Abbreviations: species of the same genera; SF1, denotes separate genera] Tables 39 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 01-09-18 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 07-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-11-17 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 01-05-17 0 0 0 0 0 0 8 0 0 0 0 0 0 0 0 0 0 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-22-16 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 07-11-16 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 68 05-25-16 - (Yu (Yu Costa (Craw (Bergh (Bergh Rathbun (Chapman Stimpson (Stephensen (Heller 1862) Dana 1852 Shoemaker 1942 Taxon sp. A unid. spp. Smith 1873

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many unid. spp. Species list and abundance at sampling station Alviso, Alviso Slough, California, May 2016–March 2018.—Continued

1853 ford 1937) 1932) 1988) 1938) 1856 1902 1894) Order Amphipoda—Continued Order Melita nitida acherusicum Monocorophium insidiosum Monocorophium uenoi Monocorophium Paradexamine Photis brevipes alienense Sinocorophium heteroceratum Sinocorophium Stenothoe valida Talitridae Decapoda Order Crangon franciscorum Palaemon modestus Palaemon macrodactylus Decopoda unid. spp. Class Insecta Family Chironomidae Chironomidae unid. spp. PHYLUM MOLLUSCA Class Gastropoda Melanochlamys diomedea Nudibranchia Table 2. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. Abbreviations: species of the same genera; SF1, denotes separate genera] 40 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 07-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 793 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 63 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 166 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 3 0 903 05-25-16 (Tryon (Tryon (Linnaeus 1825) (Tryon 1865) (Tryon (Rowell 1863) (Benson 1842) (Say 1822) (Say 1817) (O. F. Müller (O. F. (Say 1822) Suter 1909 (Gould 1841) (Linnaeus 1758) Dall & Bartsch

(Menke 1830) (Say Say 1822 A (Totten 1834) (Totten Taxon A Baba 1960 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many Species list and abundance at sampling station Alviso, Alviso Slough, California, May 2016–March 2018.—Continued

sp. A 1767) 1866) 1909 1774) Class Gastropoda—Continued Okenia plana Onchidoris bilamellata Philine auriformis SubClass Pulmonata Ferrissia californica Gyraulus circumstriatus Helisoma anceps humilis Lymnaea columella Lymnaea Menetus dilatatus Physa Radix auricularia SuperFamily Hydrobioidea Assiminea californica Boonea bisuturalis plana Crepidula Epitonium sp. Fluminicola sp. Nassarius obsoletus Odostomia fetella Class Bivalvia senhousia Arcuatula Corbicula fluminea Gemma gemma Table 2. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. Abbreviations: species of the same genera; SF1, denotes separate genera] Tables 41 3 0 0 0 0 0 0 0 0 0 24 03-08-18 5 0 0 0 0 1 0 0 0 0 0 01-09-18 4 0 0 0 0 4 0 0 0 0 0 11-09-17 1 0 0 0 0 0 0 0 0 0 142 09-28-17 7 0 0 0 0 0 0 0 0 0 76 07-17-17 5 0 0 0 0 7 0 0 0 0 0 05-11-17 0 0 0 0 5 0 0 0 0 0 11 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 20 01-05-17 0 0 0 0 4 0 0 0 0 0 10 11-18-16 2 0 0 0 0 0 0 0 0 0 27 09-22-16 1 0 0 0 0 7 0 0 0 0 0 08-19-16 0 0 0 0 0 6 0 0 0 0 0 07-11-16 5 0 0 0 0 0 0 0 0 0 104 05-25-16 (Shrenck (A. Adams (Say 1829) (De Kay Prime 1852 (Poli 1791) (Valenciennes (Valenciennes Gould 1861 Taxon Linnaeus 1758 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many (Herdman 1881) Species list and abundance at sampling station Alviso, Alviso Slough, California, May 2016–March 2018.—Continued

1821) 1861) & Reeve 1850) 1843) Class Bivalvia—Continued Macoma petalum Musculium transversum Mya arenaria Pisidium casertanum Pisidium compressum Potamocorbula amurensis Theora lubrica philippinarum Venerupis PHYLUM CHORDATA Class Ascidacea Molgula manhattensis Styela clava PHYLUM ECHINODERMATA Class Ophiuroidea Amphiuridae unid. spp. Table 2. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. Abbreviations: species of the same genera; SF1, denotes separate genera] 42 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 67 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 42 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 165 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 42 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 130 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 197 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 10 03-20-17 Sampling date 1 0 0 0 0 0 0 0 0 0 0 0 0 63 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 74 143 11-18-16 0 0 0 0 0 0 0 3 0 0 0 0 0 0 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 47 08-19-16 0 0 0 0 0 0 0 7 0 0 0 0 0 0 07-11-16 2 0 0 0 0 0 0 0 0 0 0 0 0 102 05-25-16 (Moore (Moore (E. Blanchard (Castle 1900) (Linneaus . Hand & Bushnell (Girard, 1850) Taxon

sp. A Species list and abundance at sampling station Mud, Coyote Creek, California, May 2016–March 2018.

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1967 1758) 1849) 1901) 1906) PHYLUM CNIDARIA Class Anthozoa Actiniaria unid. spp Diadumene Flosmaris grandis PHYLUM PLATYHELMINTHES Class Turbellaria tigrine Girardia unid. spp. Turbellaria PHYLUM NEMATODA Nematoda unid. spp PHYLUM ANNELIDA Class Oligochaeta Naididae unid. spp. Oligochaeta unid. spp. unid. spp. Tubificidae Hirudinida Order Gloiobdella elongata Helobdella stagnalis Helobdella triserialis microstoma Mooreobdella Placobdella montifera Table 3. Table study. this in recorded being not despite table this in included are Bay San Francisco southern the found in typically Species meter. square 0.05 per per number shown in are data and abundance [Species viations: species of the same genera; SF1, denotes separate genera] Tables 43 - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 03-08-18 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 5 0 0 0 0 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 01-05-17 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 08-19-16 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 05-25-16

- Hartman (Mesnil 1897) (Ferronnière, (Schmarda Leidy 1855 Blacke 1996 Moore 1911 Reish 1959 (Laubier 1967) Hartman 1936 (Frabricius 1780) (Moore 1906) Berkeley & Berke Taxon (Leuckart 1847)

(Berkeley & and Malmgren 1865

Hartman 1936 unid. spp. sp. A Species list and abundance at sampling station Mud, Coyote Creek, California, May 2016–March 2018.—Continued sp. A

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many Berkeley 1956) 1898) complex 1936 1861) ley 1938 Class Polychaeta Alitta brandti Alitta succinea Amaeana Acmira catherinae Acmira lopezi Armandia brevis ligerica Boccardiella Capitella capitata Cirratulidae unid. spp. Cirriformia moorei Cossura Dipolydora brachycephala Dipolydora caulleryi Dipolydora socialis Dipolydora Eteone californica Eteone lighti Euchone limnicola Exogone lourei Glycera americana Glycinde armigera Table 3. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 44 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-09-17 0 0 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 0 0 0 0 1 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 81 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 11-18-16 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 09-22-16 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 08-19-16 0 0 0 1 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 07-11-16 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-25-16 - - - Hart (Petti Hartman Örsted (Claparède Sikoski & (Linneaus Leidy 1859 (Imajima (Montagu Moore 1911 Hartman 1938 A apa 2007 (Johnson 1903) (Johnson 1897)

(Johnson 18970 (Berkeley & Berke & (Berkeley Taxon Berkele 1927

sp. Berkeley & Species list and abundance at sampling station Mud, Coyote Creek, California, May 2016–March 2018.—Continued sp. SF1

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1767) 1864) bone 1957) Bick 2004 1813) 1966) ley 1945) man 1936 1941 1842 1942 Class Polychaeta—Continued Glycinde picta Glycinde Harmothoe imbricata Hediste limnicola filiformis Heteromastus Laonome calida C Leitoscoloplos pugettensis Lumbrineris inflata Manayunkia speciosa neglecta Marenzelleria Marphysa sanguinea Megasyllis nipponica Neoamphitrite Nephtys caecoides cornuta Nephtys pelagica neonigripes Nereis Paleanotus bellis Pectinaria californiensis Pholoides aspera Phyllodoce groenlandica Pista pacifica Table 3. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 45 - Abbre 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 172.0 03-08-18 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 340 01-09-18 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 242 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 11-18-16 0 0 1 0 0 0 0 0 0 0 0 0 0 8 0 0 0 0 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 117 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 104 05-25-16 - - (Ehlers Hart (Baird (Moore Southern Webster 1879 Webster (O.F. Muller (O.F. (Chamberlin (Verrill 1873) (Verrill

Bosc 1802 A A Taxon

Barkeley 1929

(Berkeley & Berke

sp. A sp. . unid. spp. sp Species list and abundance at sampling station Mud, Coyote Creek, California, May 2016–March 2018.—Continued sp. A

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1863) 1921 (Okuda 1937) 1906) 1901) 1806) ley 1945) man 1966 1919) Class Polychaeta—Continued bicanaliculata Platynereis Polycirrus Polydora cornuta Pseudopolydora kempi Pseudopolydora paucibranchiata Sabaco elongatus Schistomeringos annulate Schistomeringos longicornis Scolelepis squamata Scoletoma luti californiensis Sphaerosyllis Sphaerosyllis Spiophanes duplex benedicti Streblospio Tharyx parvus PHYLUM ARTHROPODA Class Crustacea SubClass Copepoda Cyclopid SubClass Ostracoda Candona Cypricercus Table 3. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 46 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 101.0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 88 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 75 09-28-17 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 70 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 437 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 72 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 59 01-05-17 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 11-18-16 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 05-25-16 (Li (W. (W. (Gamo (Cushman Ortmann Li 1964 Darwin 1854 Nakazawa 1910 Holmes 1896 Hart 1930 Hart 1930 A Taxon

A A

A

sp.

sp. sp. spp. Species list and abundance at sampling station Mud, Coyote Creek, California, May 2016–March 2018.—Continued sp.

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1906) Kaufmann 1900 1932) Tattersall 1936) 1908 1967) SubClass Ostracoda—Continued Cyclocypris Cyprideis Eucypris Eusarsiella zostericola Herpetocypris brevicaudata Isocypris SubClass Cirripedia Balanus improvisus SubClass Malacostraca Mysidacea Order Acanthomysis aspera Alienacanthomysis macropsis Hyperacanthomysis longirostris Neomysis japonica Neomysis kadiakensis Neomysis mercedis Cumacea Order Cumella vulgaris pacifica Eudorella Nippoleucon hinumensis Tanaidacea Order Sinelobus Table 3. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 47 - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-09-17 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 13 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-05-17 0 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-18-16 0 6 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 08-19-16 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 10 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 05-25-16 - - - (Van (Van (Mills (Stimp (Dana (Stimp (Shoe (Miers Bousfield Richardson Shoemaker (Bousfield 1969) (Mills 1964) Holmes 1908 Mayer 1903 Smith 1873 Templeton 1836 Templeton Taxon

unid. Spp. Species list and abundance at sampling station Mud, Coyote Creek, California, May 2016–March 2018.—Continued

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many Name 1940) Dana 1853 1909 1881) 1962) son 1857) maker 1941) 1938 1963 son 1856) 1853) Order Isopoda Order insulare Gnorimosphaeroma oregonensis Gnorimosphaeroma Paranthura japonica Synidotea laevidorsalis Amphipoda Order Americhelidium shoemakeri spinicorne Americorophium stimpsoni Americorophium Ampelisca abdita Ampelisca lobate Ampithoe plumulosa Ampithoe valida mendax Caprella scaura Caprella Crangonyx floridanus Eogammarus confervicolus Eusiroidae Gammarus daiberi Gnathopleustes pugettensis Table 3. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 48 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 57 222 01-09-18 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 11-09-17 3 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 09-28-17 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 38 14 05-11-17 1 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 03-20-17 Sampling date 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 87 14 151 11-18-16 0 0 0 8 0 0 0 0 6 0 0 0 0 0 0 0 0 25 09-22-16 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 08-19-16 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 16 07-11-16 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-25-16 - (Yu (Yu Costa (Craw Rathbun (Chapman Stephensen Stimpson (Stephensen (Stimpson (Heller 1862) Dana 1852 Shoemaker 1942 Taxon

sp. A Smith 1873 unid. spp. Species list and abundance at sampling station Mud, Coyote Creek, California, May 2016–March 2018.—Continued

sp. A

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1938 1856) 1853 ford 1937) 1932) 1988) 1938) 1856 1902 Order Amphipoda—Continued Order japonica Grandidierella Grandifoxus grandis Hyalella Melita nitida acherusicum Monocorophium insidiosum Monocorophium uenoi Monocorophium Paradexamine Photis brevipes alienense Sinocorophium heteroceratum Sinocorophium Stenothoe valida Talitridae Decapoda Order Crangon franciscorum Decopoda unid. spp. Palaemon modestus Palaemon macrodactylus Class Insecta Family Chironomidae Chironomidae unid. spp. Table 3. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 49 - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-25-16 (Bergh (Bergh (Tryon (Tryon (Linnaeus 1825) (Tryon 1865) (Tryon (Rowell 1863) (Say 1822) (Say 1817) (Say 1822) Suter 1909 (Gould 1841) (Linnaeus 1758) Dall & Bartsch

(Menke 1830) (Say Say 1822 A Taxon

A unid. spp. Baba 1960

Species list and abundance at sampling station Mud, Coyote Creek, California, May 2016–March 2018.—Continued

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many sp. A 1767) 1894) 1866) 1909 PHYLUM MOLLUSCA Class Gastropoda Okenia plana Onchidoris bilamellata Melanochlamys diomedea Nudibranchia Philine auriformis SubClass Pulmonata Ferrissia californica Gyraulus circumstriatus Helisoma anceps humilis Lymnaea columella Lymnaea Menetus dilatatus Physa Radix auricularia SuperFamily Hydrobioidea Assiminea californica Boonea bisuturalis plana Crepidula Epitonium sp. Fluminicola sp. Nassarius obsoletus Odostomia fetella Table 3. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 50 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 10 03-08-18 0 0 0 2 0 0 0 0 0 0 0 0 0 38 01-09-18 0 0 0 4 0 0 0 0 0 0 0 0 0 0 11-09-17 0 0 0 5 0 0 0 0 0 0 0 0 0 99 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 19 90 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 33 314 05-11-17 0 0 0 0 0 0 0 3 0 0 0 0 0 0 03-20-17 Sampling date 0 0 1 3 0 0 0 0 3 0 0 0 0 0 01-05-17 0 1 0 0 0 0 0 0 0 0 0 11 18 49 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 13 231 09-22-16 0 0 7 0 0 0 0 0 0 0 0 0 27 26 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 15 306 07-11-16 1 0 7 0 0 0 0 0 0 0 0 0 57 101 05-25-16 (Shrenck (A. Adams (Say 1829) (De Kay Prime 1852 (Poli 1791) (Benson 1842) (O. F. Müller (O. F. (Valenciennes (Valenciennes (Totten 1834) (Totten Taxon Gould 1861

Linnaeus 1758 (Herdman 1881) Species list and abundance at sampling station Mud, Coyote Creek, California, May 2016–March 2018.—Continued

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1774) 1821) 1861) & Reeve 1850) 1843) Class Bivalvia senhousia Arcuatula Corbicula fluminea Gemma gemma Macoma petalum Musculium transversum Mya arenaria Pisidium casertanum Pisidium compressum Potamocorbula amurensis Theora lubrica philippinarum Venerupis PHYLUM CHORDATA Class Ascidacea Molgula manhattensis Styela clava PHYLUM ECHINODERMATA Class Ophiuroidea Amphiuridae unid. spp. Table 3. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 51 - Abbre 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 113 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 86 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 167 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 03-20-17 Sampling date 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 191 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 324 08-19-16 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 05-25-16 (Moore (Moore 1906) (E. Blanchard (Castle 1900) (Linneaus . Hand & Bushnell (Girard, 1850) (Leuckart 1847) TAXON

Malmgren 1865 sp. A sp. A Species list and abundance at sampling station SB04, Coyote Creek, California, May 2016–March 2018.

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1967 1758) 1849) 1901) PHYLUM CNIDARIA Class Anthozoa Actiniaria unid. spp Diadumene Flosmaris grandis PHYLUM PLATYHELMINTHES Class Turbellaria tigrine Girardia unid. spp. Turbellaria PHYLUM NEMATODA Nematoda unid. spp PHYLUM ANNELIDA Class Oligochaeta Naididae unid. spp. Oligochaeta unid. spp. unid. spp. Tubificidae Hirudinida Order Gloiobdella elongata Helobdella stagnalis Helobdella triserialis microstoma Mooreobdella Placobdella montifera Class Polychaeta Alitta brandti Alitta succinea Amaeana Table 4. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 52 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 48 03-08-18 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 15 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 65 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 235 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 46 11-18-16 0 0 0 7 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 09-22-16 0 0 0 3 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 3 08-19-16 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 07-11-16 0 0 0 0 0 0 0 0 0 0 9 0 0 2 0 1 0 0 0 0 0 3 2 05-25-16

Hartman (Claparède (Linneaus (Mesnil 1897) (Ferronnière, (Schmarda Leidy 1855 Blacke 1996 Moore 1911 Reish 1959 (Laubier 1967) Hartman 1936 (Frabricius 1780) (Johnson 1903) (Moore 1906) Berkeley & TAXON Berkele 1927

(Berkeley & and

Hartman 1936 unid. spp. Species list and abundance at sampling station SB04, Coyote Creek, California, May 2016–March 2018.—Continued sp. SF1 sp. A

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many Berkeley 1956) 1898) complex 1936 1861) 1938 1767) 1864) Class Polychaeta—Continued Acmira catherinae Acmira lopezi Armandia brevis ligerica Boccardiella Capitella capitata Cirratulidae unid. spp. Cirriformia moorei Cossura Dipolydora brachycephala Dipolydora caulleryi Dipolydora socialis Dipolydora Eteone californica Eteone lighti Euchone limnicola Exogone lourei Glycera americana Glycinde armigera Glycinde picta Glycinde Harmothoe imbricata Hediste limnicola filiformis Heteromastus Table 4. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 53 - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 09-28-17 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17-17-17 1 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 14 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 4 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 2 05-25-16 - - - Hart (Petti (Baird Hartman Örsted Sikoski & Southern Leidy 1859 (Imajima (Montagu Moore 1911 Hartman 1938 A apa 2007 (Johnson 1897)

(Johnson 18970 Bosc 1802 (Berkeley & Berke TAXON sp.

Berkeley & unid. spp. Species list and abundance at sampling station SB04, Coyote Creek, California, May 2016–March 2018.—Continued

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many bone 1957) Bick 2004 1813) 1966) ley 1945) man 1936 1941 1842 1942 1863) 1921 Class Polychaeta—Conitnued Laonome calida C Leitoscoloplos pugettensis Lumbrineris inflata Manayunkia speciosa neglecta Marenzelleria Marphysa sanguinea Megasyllis nipponica Neoamphitrite Nephtys caecoides Nephtys cornuta pelagica neonigripes Nereis Paleanotus bellis Pectinaria californiensis Pholoides aspera Phyllodoce groenlandica Pista pacifica bicanaliculata Platynereis Polycirrus Polydora cornuta Pseudopolydora kempi Table 4. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 54 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 436 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 32 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 276 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 169 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 247 05-25-16 (Ehlers Hartman (Moore (Cushman Webster 1879 Webster (O.F. Muller (O.F. (Chamberlin (Verrill 1873) (Verrill

A A A

TAXON

Barkeley 1929

(Berkeley & Berkeley

sp. A A

A sp. sp.

. sp. sp Species list and abundance at sampling station SB04, Coyote Creek, California, May 2016–March 2018.—Continued sp. A sp.

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many (Okuda 1937) 1906) 1901) 1806) 1945) 1966 1919) 1906) Class Polychaeta—Continued Pseudopolydora paucibranchiata Sabaco elongatus Schistomeringos annulate Schistomeringos longicornis Scolelepis squamata Scoletoma luti californiensis Sphaerosyllis Sphaerosyllis Spiophanes duplex benedicti Streblospio Tharyx parvus PHYLUM ARTHROPODA Class Crustacea SubClass Copepoda Cyclopid SubClass Ostracoda Cyclocypris Cypricercus Cyprideis Candona Eucypris Eusarsiella zostericola Table 4. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 55 - Abbre 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 82 10 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 223 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 0 0 0 0 0 0 0 0 0 0 5 0 0 1 0 0 17-17-17 0 0 0 0 0 1 0 1 0 0 0 1 0 4 0 48 251 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 01-05-17 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 6 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 6 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 3 05-25-16 (Li (W. (W. (Van (Van (Gamo (Miers 1881) Ortmann 1908 Li 1964 Richardson Darwin 1854 Nakazawa 1910 Holmes 1896 Hart 1930 Hart 1930 TAXON

A

sp. spp. Species list and abundance at sampling station SB04, Coyote Creek, California, May 2016–March 2018.—Continued

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many Kaufmann 1900 1932) Tattersall 1936) 1967) Name 1940) Dana 1853 1909 SubClass Ostracoda—Continued Herpetocypris brevicaudata Isocypris SubClass Cirripedia Balanus improvisus SubClass Malacostraca Mysidacea Order Acanthomysis aspera Alienacanthomysis macropsis Hyperacanthomysis longirostris Neomysis japonica Neomysis kadiakensis Neomysis mercedis Cumacea Order Cumella vulgaris pacifica Eudorella Nippoleucon hinumensis Tanaidacea Order Sinelobus Isopoda Order insulare Gnorimosphaeroma oregonensis Gnorimosphaeroma Paranthura japonica Synidotea laevidorsalis Table 4. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 56 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 204 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 577 157 05-11-17 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 28 338 03-20-17 Sampling date 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 56 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 269 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 122 1,455 05-25-16 - - - - Costa (Mills (Craw (Stimp (Dana (Stimp (Shoe Stephensen Bousfield (Stimpson Shoemaker (Bousfield 1969) (Mills 1964) Holmes 1908 Mayer 1903 Smith 1873 Templeton 1836 Templeton TAXON

Smith 1873 unid. Spp. Species list and abundance at sampling station SB04, Coyote Creek, California, May 2016–March 2018.—Continued sp. A

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1962) son 1857) maker 1941) 1938 1963 son 1856) 1853) 1938 1856) 1853 ford 1937) Order Amphipoda Order Americhelidium shoemakeri spinicorne Americorophium stimpsoni Americorophium Ampelisca abdita Ampelisca lobate Ampithoe plumulosa Ampithoe valida mendax Caprella scaura Caprella Crangonyx floridanus Eogammarus confervicolus Eusiroidae Gammarus daiberi Gnathopleustes pugettensis japonica Grandidierella Grandifoxus grandis Hyalella Melita nitida acherusicum Monocorophium insidiosum Monocorophium Table 4. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 57 - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 81 03-08-18 0 0 0 6 0 0 0 0 0 0 0 0 0 1 0 0 0 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17-17-17 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 558 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1,316 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 224 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-25-16 (Yu (Yu (Bergh (Bergh Rathbun (Chapman (Linnaeus Stimpson (Stephensen (Heller 1862) Suter 1909 Dana 1852 Shoemaker 1942 TAXON

sp. A unid. spp. Baba 1960

unid. spp. Species list and abundance at sampling station SB04, Coyote Creek, California, May 2016–March 2018.—Continued

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1932) 1988) 1938) 1856 1902 1894) 1767) Order Amphipoda—Continued Order uenoi Monocorophium Paradexamine Photis brevipes alienense Sinocorophium heteroceratum Sinocorophium Stenothoe valida Talitridae Decapoda Order Crangon franciscorum Decopoda unid. spp. Palaemon modestus Palaemon macrodactylus Class Insecta Family Chironomidae Chironomidae unid. spp. PHYLUM MOLLUSCA Class Gastropoda Melanochlamys diomedea Nudibranchia Okenia plana Onchidoris bilamellata Philine auriformis Table 4. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 58 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0 0 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 18 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 8 0 0 0 0 24 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 25 05-25-16 (Tryon (Tryon (Say 1829) Prime 1852 1825) (Tryon 1865) (Tryon (Poli 1791) (Rowell 1863) (Benson 1842) (Say 1822) (Say 1817) (O. F. Müller (O. F. (Say 1822) (Gould 1841) (Linnaeus 1758) Dall & Bartsch

(Valenciennes (Valenciennes (Menke 1830) (Say Say 1822 A (Totten 1834) (Totten TAXON

A Linnaeus 1758 Species list and abundance at sampling station SB04, Coyote Creek, California, May 2016–March 2018.—Continued

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many sp. A 1866) 1909 1774) 1821) SubClass Pulmonata Ferrissia californica Gyraulus circumstriatus Helisoma anceps humilis Lymnaea columella Lymnaea Menetus dilatatus Physa Radix auricularia SuperFamily Hydrobioidea Assiminea californica Boonea bisuturalis plana Crepidula Epitonium sp. Fluminicola sp. Nassarius obsoletus Odostomia fetella Class Bivalvia senhousia Arcuatula Corbicula fluminea Gemma gemma Macoma petalum Musculium transversum Mya arenaria Pisidium casertanum Pisidium compressum Table 4. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 59 - Abbre 8 0 0 0 0 0 03-08-18 1 0 0 0 0 0 01-09-18 0 0 0 0 0 0 11-09-17 1 0 0 0 0 0 09-28-17 0 0 0 0 0 24 17-17-17 0 0 0 0 0 28 05-11-17 0 0 0 0 0 15 03-20-17 Sampling date 0 0 0 0 0 11 01-05-17 0 0 0 0 0 54 11-18-16 0 0 0 0 0 143 09-22-16 0 0 0 0 0 332 08-19-16 0 0 0 0 0 44 07-11-16 0 0 0 0 0 130 05-25-16 (Shrenck (A. Adams (De Kay Gould 1861 TAXON

(Herdman 1881) Species list and abundance at sampling station SB04, Coyote Creek, California, May 2016–March 2018.—Continued

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1861) & Reeve 1850) 1843) Class Bivalvia—Continued Potamocorbula amurensis Theora lubrica philippinarum Venerupis PHYLUM CHORDATA Class Ascidacea Molgula manhattensis Styela clava PHYLUM ECHINODERMATA Class Ophiuroidea Amphiuridae unid. spp. Table 4. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 60 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 0 0 0 3 0 0 0 0 0 0 0 0 82 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 493 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 218 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 54 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 197 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 27 474 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 1,388 03-20-17 Sampling date 0 0 0 0 0 0 0 4 0 0 0 0 0 0 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 1,906 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 2,640 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 437 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 539 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 119 05-25-16 (Moore (Moore 1906) (E. Blanchard (Castle 1900) (Linneaus . Hand & Bushnell (Girard, 1850) Taxon

sp. A Species list and abundance at sampling station SB13, Artesian Slough, California, May 2016–March 2018.

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1967 1758) 1849) 1901) PHYLUM CNIDARIA Class Anthozoa Actiniaria unid. spp Diadumene Flosmaris grandis PHYLUM PLATYHELMINTHES Class Turbellaria tigrine Girardia unid. spp. Turbellaria PHYLUM NEMATODA Nematoda unid. spp PHYLUM ANNELIDA Class Oligochaeta Naididae unid. spp. Oligochaeta unid. spp. unid. spp. Tubificidae Hirudinida Order Gloiobdella elongata Helobdella stagnalis Helobdella triserialis microstoma Mooreobdella Placobdella montifera Table 5. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 61 - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 598 03-08-18 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 298 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 885 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 187 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 1 0 0 0 0 0 0 246 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 6 0 0 0 0 0 0 176 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 4 0 0 0 0 0 0 265 08-19-16 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 182 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 0 0 130 05-25-16

Hartman (Mesnil 1897) (Schmarda Leidy 1855 Blacke 1996 Moore 1911 Reish 1959 (Laubier 1967) Hartman 1936 (Frabricius 1780) (Moore 1906) Berkeley & Taxon (Leuckart 1847) Berkele 1927

(Berkeley & and Malmgren 1865

Hartman 1936 unid. spp. sp. A Species list and abundance at sampling station SB13, Artesian Slough, California, May 2016–March 2018.—Continued sp. SF1 sp. A

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many Berkeley 1956) 1898) complex 1936 1861) 1938 Class Polychaeta Alitta brandti Alitta succinea Amaeana Acmira catherinae Acmira lopezi Armandia brevis Boccardiella ligerica (Ferronnière, Capitella capitata Cirratulidae unid. spp. Cirriformia moorei Cossura Dipolydora brachycephala Dipolydora caulleryi Dipolydora socialis Dipolydora Eteone californica Eteone lighti Euchone limnicola Exogone lourei Glycera americana Glycinde armigera Glycinde picta Glycinde Table 5. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 62 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 3 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 5 0 6 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 05-11-17 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-05-17 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-18-16 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-22-16 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 08-19-16 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 07-11-16 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-25-16 - - - Hart (Petti Hartman Örsted (Claparède Sikoski & (Linneaus Leidy 1859 (Imajima (Montagu Moore 1911 Hartman 1938 A apa 2007 (Johnson 1903) (Johnson 1897)

(Johnson 18970 (Berkeley & Berke Taxon

sp. Berkeley & Species list and abundance at sampling station SB13, Artesian Slough, California, May 2016–March 2018.—Continued

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1767) 1864) bone 1957) Bick 2004 1813) 1966) ley 1945) man 1936 1941 1842 1942 Class Polychaeta—Continued Harmothoe imbricata Hediste limnicola filiformis Heteromastus Laonome calida C Leitoscoloplos pugettensis Lumbrineris inflata Manayunkia speciosa neglecta Marenzelleria Marphysa sanguinea Megasyllis nipponica Neoamphitrite Nephtys caecoides Nephtys cornuta pelagica neonigripes Nereis Paleanotus bellis Pectinaria californiensis Pholoides aspera Phyllodoce groenlandica Pista pacifica Table 5. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 63 - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 130 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 03-20-17 Sampling date 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 64 33 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 733 11-18-16 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 10 1,555 09-22-16 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 445 08-19-16 0 0 4 9 0 0 0 0 0 0 0 0 0 0 0 0 845 07-11-16 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 375 05-25-16 (Ehlers Hartman (Baird (Moore Southern Webster 1879 Webster (O.F. Muller (O.F. (Chamberlin (Verrill 1873) (Verrill Bosc 1802 A Taxon

Barkeley 1929

(Berkeley & Berkeley

sp. A . unid. spp. sp Species list and abundance at sampling station SB13, Artesian Slough, California, May 2016–March 2018.—Continued sp. A

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1863) 1921 (Okuda 1937) 1906) 1901) 1806) 1945) 1966 1919) Class Polychaeta—Continued bicanaliculata Platynereis Polycirrus Polydora cornuta Pseudopolydora kempi Pseudopolydora paucibranchiata Sabaco elongatus Schistomeringos annulate Schistomeringos longicornis Scolelepis squamata Scoletoma luti californiensis Sphaerosyllis Sphaerosyllis Spiophanes duplex benedicti Streblospio Tharyx parvus PHYLUM ARTHROPODA Class Crustacea SubClass Copepoda Cyclopid SubClass Ostracoda Candona Table 5. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 64 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 133 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 186 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 177 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-25-16 (Li (W. (W. (Gamo (Cushman Ortmann 1908 Li 1964 Darwin 1854 Nakazawa 1910 Holmes 1896 Hart 1930

Hart 1930 A A Taxon

A A

A sp.

sp.

sp. sp. spp. Species list and abundance at sampling station SB13, Artesian Slough, California, May 2016–March 2018.—Continued sp.

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1906) Kaufmann 1900 1932) Tattersall 1936) 1967) SubClass Ostracoda—Continued Cyclocypris Cypricercus Cyprideis Eucypris Eusarsiella zostericola Herpetocypris brevicaudata Isocypris SubClass Cirripedia Balanus improvisus SubClass Malacostraca Mysidacea Order Acanthomysis aspera Alienacanthomysis macropsis Hyperacanthomysis longirostris Neomysis japonica Neomysis kadiakensis Neomysis mercedis Cumacea Order Cumella vulgaris pacifica Eudorella Nippoleucon hinumensis Tanaidacea Order Sinelobus Table 5. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 65 - Abbre 0 2 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 74 291 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 58 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 30 156 17-17-17 0 8 0 4 0 0 0 0 0 0 0 0 0 0 0 0 3 399 2,967 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 564 03-20-17 Sampling date 0 0 0 2 0 0 0 0 0 5 0 0 0 0 0 0 0 681 7,389 01-05-17 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 71 3,031 1,303 11-18-16 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 318 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 30 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98 114 331 136 4,391 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 10 32 104 2,349 05-25-16 - - - (Van (Van (Mills (Stimp (Dana (Stimp (Shoe Stephensen (Miers 1881) Bousfield Richardson Shoemaker (Bousfield 1969) (Mills 1964) Holmes 1908 Mayer 1903 Smith 1873 Templeton 1836 Templeton Taxon

unid. Spp. Species list and abundance at sampling station SB13, Artesian Slough, California, May 2016–March 2018.—Continued

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many Name 1940) Dana 1853 1909 1962) son 1857) maker 1941) 1938 1963 son 1856) 1853) 1938 Order Isopoda Order insulare Gnorimosphaeroma oregonensis Gnorimosphaeroma Paranthura japonica Synidotea laevidorsalis Amphipoda Order Americhelidium shoemakeri spinicorne Americorophium stimpsoni Americorophium Ampelisca abdita Ampelisca lobate Ampithoe plumulosa Ampithoe valida mendax Caprella scaura Caprella Crangonyx floridanus Eogammarus confervicolus Eusiroidae Gammarus daiberi Gnathopleustes pugettensis japonica Grandidierella Table 5. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 66 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 83 03-08-18 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 38 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17-17-17 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 74 05-11-17 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 5 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-18-16 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 11 09-22-16 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-25-16 - (Yu (Yu Costa (Craw Rathbun (Chapman Stimpson (Stephensen (Stimpson (Heller 1862) Dana 1852 Shoemaker 1942 Taxon

sp. A Smith 1873 unid. spp. Species list and abundance at sampling station SB13, Artesian Slough, California, May 2016–March 2018.—Continued

sp. A

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1856) 1853 ford 1937) 1932) 1988) 1938) 1856 1902 Order Amphipoda—Continued Order Grandifoxus grandis Hyalella Melita nitida acherusicum Monocorophium insidiosum Monocorophium uenoi Monocorophium Paradexamine Photis brevipes alienense Sinocorophium heteroceratum Sinocorophium Stenothoe valida Talitridae Decapoda Order Crangon franciscorum Decopoda unid. spp. Palaemon modestus Palaemon macrodactylus Class Insecta Family Chironomidae Chironomidae unid. spp. Table 5. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 67 - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-25-16 (Bergh (Bergh (Tryon (Tryon (Linnaeus 1825) (Tryon 1865) (Tryon (Rowell 1863) (Say 1822) (Say 1817) (Say 1822) Suter 1909 (Gould 1841) (Linnaeus 1758) Dall & Bartsch

(Menke 1830) (Say Say 1822 A Taxon

A unid. spp. Baba 1960

Species list and abundance at sampling station SB13, Artesian Slough, California, May 2016–March 2018.—Continued

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many sp. A 1767) 1894) 1866) 1909 PHYLUM MOLLUSCA Class Gastropoda Okenia plana Onchidoris bilamellata Melanochlamys diomedea Nudibranchia Philine auriformis SubClass Pulmonata Ferrissia californica Gyraulus circumstriatus Helisoma anceps humilis Lymnaea columella Lymnaea Menetus dilatatus Physa Radix auricularia SuperFamily Hydrobioidea Assiminea californica Boonea bisuturalis plana Crepidula Epitonium sp. Fluminicola sp. Nassarius obsoletus Odostomia fetella Table 5. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 68 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 0 0 0 0 0 0 0 9 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 32 01-09-18 0 0 0 2 0 0 0 0 0 0 0 0 0 0 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 0 0 2 0 0 0 0 8 0 0 0 0 0 17-17-17 0 0 0 0 0 0 0 0 6 0 0 0 0 0 05-11-17 0 0 0 6 0 0 0 0 1 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 14 01-05-17 0 0 0 3 0 0 0 0 0 0 0 0 0 23 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 45 89 09-22-16 0 0 0 4 0 0 0 0 8 0 0 0 0 0 08-19-16 0 0 0 4 0 0 0 0 0 0 0 0 0 24 07-11-16 0 0 0 5 0 0 0 0 0 0 0 0 0 13 05-25-16 (Shrenck (A. Adams (Say 1829) (De Kay Prime 1852 (Poli 1791) (Benson 1842) (O. F. Müller (O. F. (Valenciennes (Valenciennes (Totten 1834) (Totten Taxon Gould 1861

Linnaeus 1758 (Herdman 1881) Species list and abundance at sampling station SB13, Artesian Slough, California, May 2016–March 2018.—Continued

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1774) 1821) 1861) & Reeve 1850) 1843) Class Bivalvia senhousia Arcuatula Corbicula fluminea Gemma gemma Macoma petalum Musculium transversum Mya arenaria Pisidium casertanum Pisidium compressum Potamocorbula amurensis Theora lubrica philippinarum Venerupis PHYLUM CHORDATA Class Ascidacea Molgula manhattensis Styela clava PHYLUM ECHINODERMATA Class Ophiuroidea Amphiuridae unid. spp. Table 5. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 69 - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 361 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 319 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 194 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 267 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 535 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 591 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 195 01-05-17 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 733 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 491 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 555 08-19-16 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 394 07-11-16 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 159 05-25-16 (Moore (Moore 1906) (E. Blanchard (Castle 1900) (Linneaus . Hand & Bushnell (Girard, 1850) (Leuckart 1847) Taxon Malmgren 1865 sp. A sp. A Species list and abundance at sampling station Upcoy, Artesian Slough, California, May 2016–March 2018. Species list and abundance at sampling station Upcoy,

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1967 1758) 1849) 1901) PHYLUM CNIDARIA Class Anthozoa Actiniaria unid. spp Diadumene Flosmaris grandis PHYLUM PLATYHELMINTHES Class Turbellaria tigrine Girardia unid. spp. Turbellaria PHYLUM NEMATODA Nematoda unid. spp PHYLUM ANNELIDA Class Oligochaeta Naididae unid. spp. Oligochaeta unid. spp. unid. spp. Tubificidae Hirudinida Order Gloiobdella elongata Helobdella stagnalis Helobdella triserialis microstoma Mooreobdella Placobdella montifera Class Polychaeta Alitta brandti Alitta succinea Amaeana Table 6. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 70 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 25 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 33 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 76 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 35 05-11-17 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 7 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 01-05-17 0 0 0 2 0 0 0 0 0 3 0 0 2 0 0 0 0 0 0 0 0 1 31 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 66 09-22-16 0 0 0 0 0 0 0 0 0 1 0 0 9 0 0 0 0 0 0 0 0 1 12 08-19-16 0 0 0 0 0 0 0 0 0 3 0 0 9 0 0 0 0 0 0 0 0 2 16 07-11-16 0 0 0 0 0 0 0 0 0 1 1 0 3 0 0 0 0 0 0 0 0 1 20 05-25-16

Hartman (Claparède (Linneaus (Mesnil 1897) (Schmarda Leidy 1855 Blacke 1996 Moore 1911 Reish 1959 (Laubier 1967) Hartman 1936 (Frabricius 1780) (Johnson 1903) (Moore 1906) Berkeley & Berkele 1927 Taxon (Berkeley & and

Hartman 1936 unid. spp. Species list and abundance at sampling station Upcoy, Artesian Slough, California, May 2016–March 2018.—Continued Species list and abundance at sampling station Upcoy, sp. SF1 sp. A

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many Berkeley 1956) 1898) complex 1936 1861) 1938 1767) 1864) Class Polychaeta—Continued Acmira catherinae Acmira lopezi Armandia brevis Boccardiella ligerica (Ferronnière, Capitella capitata Cirratulidae unid. spp. Cirriformia moorei Cossura Dipolydora brachycephala Dipolydora caulleryi Dipolydora socialis Dipolydora Eteone californica Eteone lighti Euchone limnicola Exogone lourei Glycera americana Glycinde armigera Glycinde picta Glycinde Harmothoe imbricata Hediste limnicola filiformis Heteromastus Table 6. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 71 - Abbre 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 11-09-17 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 2 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-05-17 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 1 0 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 1 0 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 3 0 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 25 07-11-16 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 05-25-16 - - - Hart (Petti (Baird Hartman Örsted Sikoski & Southern Leidy 1859 (Imajima (Montagu Moore 1911 Hartman 1938 A apa 2007 (Johnson 1897)

(Johnson 18970 Bosc 1802 (Berkeley & Berke sp. Taxon Berkeley & unid. spp. Species list and abundance at sampling station Upcoy, Artesian Slough, California, May 2016–March 2018.—Continued Species list and abundance at sampling station Upcoy,

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many bone 1957) Bick 2004 1813) 1966) ley 1945) man 1936 1941 1842 1942 1863) 1921 (Okuda 1937) Class Polychaeta—Continued Laonome calida C Leitoscoloplos pugettensis Lumbrineris inflata Manayunkia speciosa neglecta Marenzelleria Marphysa sanguinea Megasyllis nipponica Neoamphitrite Nephtys caecoides Nephtys cornuta pelagica neonigripes Nereis Paleanotus bellis Pectinaria californiensis Pholoides aspera Phyllodoce groenlandica Pista pacifica bicanaliculata Platynereis Polycirrus Polydora cornuta Pseudopolydora kempi Pseudopolydora paucibranchiata Table 6. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 72 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 704 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 280 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 447 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 09-28-17 0 0 0 0 0 0 0 0 2 0 1 0 0 0 0 0 0 0 0 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-11-17 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 354 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 613 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 624 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 454 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 521 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 130 05-25-16 (Ehlers Hartman (Moore (Cushman Webster 1879 Webster (O.F. Muller (O.F. (Chamberlin (Verrill 1873) (Verrill

A A A

Barkeley 1929

Taxon (Berkeley & Berkeley

sp. A A A

A sp.

sp.

. sp. sp sp. Species list and abundance at sampling station Upcoy, Artesian Slough, California, May 2016–March 2018.—Continued Species list and abundance at sampling station Upcoy, sp. A sp.

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many 1906) 1901) 1806) 1945) 1966 1919) 1906) Kaufmann 1900 Class Polychaeta—Continued Sabaco elongatus Schistomeringos annulate Schistomeringos longicornis Scolelepis squamata Scoletoma luti californiensis Sphaerosyllis Sphaerosyllis Spiophanes duplex benedicti Streblospio Tharyx parvus PHYLUM ARTHROPODA Class Crustacea SubClass Copepoda Cyclopid SubClass Ostracoda Candona Cypricercus Cyprideis Cyclocypris Eucypris Eusarsiella zostericola Herpetocypris brevicaudata Isocypris Table 6. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 73 - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 382 03-08-18 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 623 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 159 11-09-17 0 0 0 0 0 0 0 0 0 3 0 0 0 0 1 0 09-28-17 2 0 0 0 0 0 0 0 0 0 0 0 0 3 0 77 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 144 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 11-18-16 0 0 0 0 0 0 0 0 0 1 0 0 5 0 0 0 09-22-16 0 0 0 0 0 0 0 0 0 2 0 0 2 0 2 0 08-19-16 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 07-11-16 0 0 0 0 0 0 0 0 0 4 0 0 0 0 22 10 05-25-16 (Li (W. (W. (Van (Van (Mills (Gamo (Miers 1881) Ortmann 1908 Li 1964 Richardson Darwin 1854 Nakazawa 1910 Holmes 1896 Hart 1930 Hart 1930 Taxon spp. Species list and abundance at sampling station Upcoy, Artesian Slough, California, May 2016–March 2018.—Continued Species list and abundance at sampling station Upcoy,

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many Tattersall 1932) Tattersall 1936) 1967) Name 1940) Dana 1853 1909 1962) SubClass Cirripedia Balanus improvisus SubClass Malacostraca Mysidacea Order Acanthomysis aspera Alienacanthomysis macropsis Hyperacanthomysis longirostris Neomysis japonica Neomysis kadiakensis Neomysis mercedis Cumacea Order Cumella vulgaris pacifica Eudorella Nippoleucon hinumensis Tanaidacea Order Sinelobus Isopoda Order insulare Gnorimosphaeroma oregonensis Gnorimosphaeroma Paranthura japonica Synidotea laevidorsalis Amphipoda Order Americhelidium shoemakeri Table 6. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 74 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 03-08-18 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1,029 01-09-18 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 10 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 09-28-17 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 91 91 17-17-17 0 0 0 0 0 0 0 1 0 0 0 4 0 0 8 0 0 0 8 10 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 03-20-17 Sampling date 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 0 0 2 44 519 01-05-17 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 10 323 11-18-16 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 13 133 09-22-16 4 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 57 08-19-16 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 1 571 131 07-11-16 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 26 565 05-25-16 - - - (Yu (Yu Costa (Stimp (Dana (Stimp (Shoe (Chapman Stephensen Bousfield (Stimpson Shoemaker (Bousfield 1969) (Mills 1964) Holmes 1908 Mayer 1903 Smith 1873 Templeton 1836 Templeton Taxon Smith 1873 unid. Spp. Species list and abundance at sampling station Upcoy, Artesian Slough, California, May 2016–March 2018.—Continued Species list and abundance at sampling station Upcoy, sp. A

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many son 1857) maker 1941) 1938 1988) 1938) 1963 son 1856) 1853) 1938 1856) 1853 Order Amphipoda—Continued Order spinicorne Americorophium stimpsoni Americorophium Ampelisca abdita Ampelisca lobate Ampithoe plumulosa Ampithoe valida mendax Caprella scaura Caprella alienense Sinocorophium heteroceratum Sinocorophium Crangonyx floridanus Eogammarus confervicolus Eusiroidae Gammarus daiberi Gnathopleustes pugettensis japonica Grandidierella Grandifoxus grandis Hyalella Melita nitida acherusicum Monocorophium Table 6. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 75 - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 08-19-16 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 05-25-16 - (Craw (Bergh (Bergh Rathbun (Linnaeus Stimpson (Stephensen (Rowell 1863) (Heller 1862) Suter 1909 Dana 1852 Shoemaker 1942 Taxon sp. A unid. spp. Baba 1960

unid. spp. Species list and abundance at sampling station Upcoy, Artesian Slough, California, May 2016–March 2018.—Continued Species list and abundance at sampling station Upcoy,

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many ford 1937) 1932) 1856 1902 1767) 1894) Order Amphipoda—Continued Order insidiosum Monocorophium uenoi Monocorophium Paradexamine Photis brevipes Stenothoe valida Talitridae Decapoda Order Crangon franciscorum Palaemon modestus Palaemon macrodactylus Decopoda unid. spp. Class Insecta Family Chironomidae Chironomidae unid. spp. PHYLUM MOLLUSCA Class Gastropoda Okenia plana Onchidoris bilamellata Melanochlamys diomedea Nudibranchia Philine auriformis SubClass Pulmonata Ferrissia californica Table 6. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 76 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California - Abbre 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 75 01-09-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 3 11-09-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 9 09-28-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 19 17-17-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 7 05-11-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 6 03-20-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 2 0 0 0 0 48 131 01-05-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 5 0 0 0 0 63 217 11-18-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 9 0 0 0 0 12 127 09-22-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 3 8 0 0 0 0 25 08-19-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 9 0 0 0 0 14 15 07-11-16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 6 0 0 0 0 6 121 05-25-16 (Shrenck (Tryon (Tryon (Say 1829) Prime 1852 1825) (Tryon 1865) (Tryon (Poli 1791) (Benson 1842) (Say 1822) (Say 1817) (O. F. Müller (O. F. (Say 1822) (Gould 1841) (Linnaeus 1758) Dall & Bartsch

(Valenciennes (Valenciennes (Menke 1830) (Say Say 1822 A (Totten 1834) (Totten Taxon A Linnaeus 1758 Species list and abundance at sampling station Upcoy, Artesian Slough, California, May 2016–March 2018.—Continued Species list and abundance at sampling station Upcoy,

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many sp. A 1866) 1909 1774) 1821) 1861) SubClass Pulmonata—Continued Gyraulus circumstriatus Helisoma anceps humilis Lymnaea columella Lymnaea Menetus dilatatus Physa Radix auricularia SuperFamily Hydrobioidea Assiminea californica Boonea bisuturalis plana Crepidula Epitonium sp. Fluminicola sp. Nassarius obsoletus Odostomia fetella Class Bivalvia senhousia Arcuatula Corbicula fluminea Gemma gemma Macoma petalum Musculium transversum Mya arenaria Pisidium casertanum Pisidium compressum Potamocorbula amurensis Table 6. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] Tables 77 - Abbre 0 0 0 0 0 03-08-18 0 0 0 0 0 01-09-18 0 0 0 0 0 11-09-17 0 0 0 0 0 09-28-17 0 0 0 0 0 17-17-17 0 0 0 0 0 05-11-17 0 0 0 0 0 03-20-17 Sampling date 0 0 0 0 0 01-05-17 0 0 0 0 0 11-18-16 0 0 0 0 0 09-22-16 0 0 0 0 0 08-19-16 0 0 0 0 0 07-11-16 0 0 0 0 0 05-25-16 (A. Adams (De Kay Gould 1861 Taxon (Herdman 1881) Species list and abundance at sampling station Upcoy, Artesian Slough, California, May 2016–March 2018.—Continued Species list and abundance at sampling station Upcoy,

unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single genus level; spp., many & Reeve 1850) 1843) Class Bivalvia—Continued Theora lubrica philippinarum Venerupis PHYLUM CHORDATA Class Ascidacea Molgula manhattensis Styela clava PHYLUM ECHINODERMATA Class Ophiuroidea Amphiuridae unid. spp. Table 6. Table Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. viations: species of the same genera; SF1, denotes separate genera] 78 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 426 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 202 12-06-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 176 09-28-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 148 06-30-17 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 270 Abbreviations: 03-28-17 (Moore 1901) (Moore 1906) (E. Blanchard 1849) (Castle 1900) (Linneaus 1758) . (Laubier 1967) Hand & Bushnell 1967 Taxon (Girard, 1850) (Leuckart 1847) Malmgren 1865 sp. A sp. A Species list and abundance at sampling station SB14, Artesian Slough, California, May 2016–March 2018.

PHYLUM CNIDARIA Class Anthozoa Actiniaria unid. spp Diadumene Flosmaris grandis PHYLUM PLATYHELMINTHES Class Turbellaria tigrine Girardia unid. spp. Turbellaria PHYLUM NEMATODA Nematoda unid. spp PHYLUM ANNELIDA Class Oligochaeta Naididae unid. spp. Oligochaeta unid. spp. unid. spp. Tubificidae Hirudinida Order Gloiobdella elongata Helobdella stagnalis Helobdella triserialis microstoma Mooreobdella Placobdella montifera Class Polychaeta Alitta brandti Alitta succinea Amaeana Acmira catherinae Table 7. Table Cells Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. containing values greater than zero are highlighted red. species identified to the genus level; spp., denotes many of same genera; SF1, separate genera] Tables 79 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 19 03-08-18 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 6 0 0 19 12-06-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 09-28-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 86 06-30-17 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 2 0 0 84 Abbreviations: 03-28-17

Hartman 1936 (Pettibone (Claparède 1864) (Linneaus 1767) (Mesnil 1897) (Ferronnière, 1898) (Schmarda 1861) Moore 1911 Leidy 1855 Blacke 1996 Moore 1911 Reish 1959 Hartman 1936 (Frabricius 1780) apa 2007 (Johnson 1903) Taxon (Moore 1906) Berkeley & 1938 Berkele 1927 (Berkeley & and Berkeley

Hartman 1936 unid. spp. Species list and abundance at sampling station SB14, Artesian Slough, California, May 2016–March 2018.—Continued sp. SF1 sp. A

1956) complex 1957) Class Polychaeta—Continued Acmira lopezi Armandia brevis ligerica Boccardiella Capitella capitata Cirratulidae unid. spp. Cirriformia moorei Cossura Dipolydora brachycephala Dipolydora caulleryi Dipolydora socialis Dipolydora Eteone californica Eteone lighti Euchone limnicola Exogone lourei Glycera americana Glycinde armigera Glycinde picta Glycinde Harmothoe imbricata Hediste limnicola filiformis Heteromastus Laonome calida C Leitoscoloplos pugettensis Lumbrineris inflata Table 7. Table Cells Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. containing values greater than zero are highlighted red. species identified to the genus level; spp., denotes many of same genera; SF1, separate genera] 80 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 12-06-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 Sampling date 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 06-30-17 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Abbreviations: 03-28-17

(Okuda (Ehlers 1901) Hartman 1936 Hartman 1966 (Baird 1863) (Moore 1906) Hartman 1941 Örsted 1842 Sikoski & Bick Southern 1921 Leidy 1859 (Imajima 1966) (Montagu 1813) (O.F. Muller 1806) (O.F. (Chamberlin 1919) Hartman 1938 A (Verrill 1873) (Verrill Taxon (Johnson 1897)

(Johnson 18970 Bosc 1802 (Berkeley & Berkeley A sp. (Berkeley & Berkeley Berkeley & 1942 sp. unid. spp. Species list and abundance at sampling station SB14, Artesian Slough, California, May 2016–March 2018.—Continued

2004 1945) 1937) 1945) Class Polychaeta—Continued Manayunkia speciosa neglecta Marenzelleria Marphysa sanguinea Megasyllis nipponica Neoamphitrite Nephtys caecoides Nephtys cornuta pelagica neonigripes Nereis Paleanotus bellis Pectinaria californiensis Pholoides aspera Phyllodoce groenlandica Pista pacifica bicanaliculata Platynereis Polycirrus Polydora cornuta Pseudopolydora kempi Pseudopolydora paucibranchiata Sabaco elongatus Schistomeringos annulate Schistomeringos longicornis Scolelepis squamata Scoletoma luti californiensis Sphaerosyllis Sphaerosyllis Spiophanes duplex Table 7. Table Cells Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. containing values greater than zero are highlighted red. species identified to the genus level; spp., denotes many of same genera; SF1, separate genera] Tables 81 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 03-08-18 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 32 12-06-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 472 09-28-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 06-30-17 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 Abbreviations: 03-28-17 - (Li 1936) (W. Tat (W. Kaufmann (Cushman 1906) Ortmann 1908 Li 1964 Webster 1879 Webster Darwin 1854 Nakazawa 1910 Holmes 1896 Taxon

A A

Barkeley 1929

A A A

A sp.

sp.

. sp. sp sp. Species list and abundance at sampling station SB14, Artesian Slough, California, May 2016–March 2018 .—Continued sp. A sp.

1900 tersall 1932) Class Polychaeta—Continued benedicti Streblospio Tharyx parvus PHYLUM ARTHROPODA Class Crustacea SubClass Copepoda Cyclopid SubClass Ostracoda Cypricercus Cyclocypris Eucypris Herpetocypris brevicaudata Isocypris Eusarsiella zostericola Cyprideis Candona SubClass Cirripedia Balanus improvisus SubClass Malacostraca Mysidacea Order Acanthomysis aspera Alienacanthomysis macropsis Hyperacanthomysis longirostris Neomysis japonica Neomysis kadiakensis Neomysis mercedis Table 7. Table Cells Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. containing values greater than zero are highlighted red. species identified to the genus level; spp., denotes many of same genera; SF1, separate genera] 82 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California 0 0 1 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 574 102 03-08-18 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 47 13 12-06-17 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 62 09-28-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 06-30-17 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 106 Abbreviations: 03-28-17 Dana (Yu 1938) (Yu (Van Name (Van (Mills 1962) (Stimpson (Shoemaker (Chapman 1988) (Gamo 1967) (Miers 1881) Bousfield 1963 Richardson 1909 Shoemaker 1938 Hart 1930 Taxon (Mills 1964) Hart 1930 Holmes 1908 Mayer 1903 Smith 1873 Templeton 1836 Templeton spp. Species list and abundance at sampling station SB14, Artesian Slough, California, May 2016–March 2018.—Continued

1940) 1853 1857) 1941) Order Cumacea Order Cumella vulgaris pacifica Eudorella Nippoleucon hinumensis Tanaidacea Order Sinelobus Isopoda Order insulare Gnorimosphaeroma oregonensis Gnorimosphaeroma Paranthura japonica Synidotea laevidorsalis Amphipoda Order Americhelidium shoemakeri spinicorne Americorophium stimpsoni Americorophium Ampelisca abdita Ampelisca lobate Ampithoe plumulosa Ampithoe valida mendax Caprella scaura Caprella alienense Sinocorophium heteroceratum Sinocorophium Crangonyx floridanus Table 7. Table Cells Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. containing values greater than zero are highlighted red. species identified to the genus level; spp., denotes many of same genera; SF1, separate genera] Tables 83 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 86 03-08-18 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 790 12-06-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 09-28-17 Sampling date 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 06-30-17 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 Abbreviations: 03-28-17

Costa 1853 (Crawford (Dana 1853) (Stimpson Rathbun 1902 Stephensen 1938 Stimpson 1856 (Stephensen 1932) (Stimpson 1856) (Heller 1862) (Bousfield 1969) Taxon Dana 1852 Shoemaker 1942 sp. A Baba 1960 Smith 1873 unid. Spp. unid. spp. Species list and abundance at sampling station SB14, Artesian Slough, California, May 2016–March 2018.—Continued

sp. A

1856) 1937) Order Amphipoda—Continued Order Eogammarus confervicolus Eusiroidae Gammarus daiberi Gnathopleustes pugettensis japonica Grandidierella Grandifoxus grandis Hyalella Melita nitida acherusicum Monocorophium insidiosum Monocorophium uenoi Monocorophium Paradexamine Photis brevipes Stenothoe valida Talitridae Decapoda Order Crangon franciscorum Palaemon modestus Palaemon macrodactylus Decopoda unid. spp. Class Insecta Family Chironomidae Chironomidae unid. spp. PHYLUM MOLLUSCA Class Gastropoda Okenia plana Table 7. Table Cells Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. containing values greater than zero are highlighted red. species identified to the genus level; spp., denotes many of same genera; SF1, separate genera] 84 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12-06-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 09-28-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 06-30-17 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Abbreviations: 03-28-17 (Bergh 1894) (Bergh (Tryon 1866) (Tryon (Say 1829) (Linnaeus 1767) 1825) (Tryon 1865) (Tryon (Rowell 1863) (Benson 1842) (Say 1822) (Say 1817) (O. F. Müller 1774) (O. F. (Say 1822) Suter 1909 (Gould 1841) (Linnaeus 1758) Dall & Bartsch 1909

Taxon (Valenciennes 1821) (Valenciennes (Menke 1830) (Say Say 1822 A (Totten 1834) (Totten A Linnaeus 1758 unid. spp.

Species list and abundance at sampling station SB14, Artesian Slough, California, May 2016–March 2018.—Continued

sp. A Class Gastropoda—Continued Onchidoris bilamellata Melanochlamys diomedea Nudibranchia Philine auriformis SubClass Pulmonata Ferrissia californica Gyraulus circumstriatus Helisoma anceps humilis Lymnaea columella Lymnaea Menetus dilatatus Physa Radix auricularia SuperFamily Hydrobioidea Assiminea californica plana Crepidula Epitonium sp. Fluminicola sp. Nassarius obsoletus Boonea bisuturalis Odostomia fetella Class Bivalvia Corbicula fluminea Gemma gemma Macoma petalum Musculium transversum senhousia Arcuatula Mya arenaria Table 7. Table Cells Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. containing values greater than zero are highlighted red. species identified to the genus level; spp., denotes many of same genera; SF1, separate genera] Tables 85 0 0 4 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 45 12-06-17 0 0 1 0 0 0 0 0 09-28-17 Sampling date 0 0 0 0 0 0 0 0 06-30-17 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single 0 0 1 0 0 0 0 0 Abbreviations: 03-28-17 (Shrenck 1861) (A. Adams & (De Kay 1843) Prime 1852 (Poli 1791) Taxon Gould 1861 —Continued (Herdman 1881) Species list and abundance at sampling station SB14, Artesian Slough, California, May 2016–March 2018.—Continued

Reeve 1850) Class Bivalvia ­ Pisidium casertanum Pisidium compressum Potamocorbula amurensis Theora lubrica philippinarum Venerupis PHYLUM CHORDATA Class Ascidacea Molgula manhattensis Styela clava PHYLUM ECHINODERMATA Class Ophiuroidea Amphiuridae unid. spp. Table 7. Table Cells Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. containing values greater than zero are highlighted red. species identified to the genus level; spp., denotes many of same genera; SF1, separate genera] 86 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 155 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12-06-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 09-28-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 278 06-30-17 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 1,434 Abbreviations: 03-28-17 (Moore 1901) (Moore 1906) (E. Blanchard 1849) (Castle 1900) (Linneaus 1758) . (Laubier 1967) Hand & Bushnell 1967 Taxon (Girard, 1850) (Leuckart 1847) Malmgren 1865 sp. A sp. A Species list and abundance at sampling station SB15, Artesian Slough, California, May 2016–March 2018

PHYLUM CNIDARIA Class Anthozoa Actiniaria unid. spp Diadumene Flosmaris grandis PHYLUM PLATYHELMINTHES Class Turbellaria tigrine Girardia unid. spp. Turbellaria PHYLUM NEMATODA Nematoda unid. spp PHYLUM ANNELIDA Class Oligochaeta Naididae unid. spp. Oligochaeta unid. spp. unid. spp. Tubificidae Hirudinida Order Gloiobdella elongata Helobdella stagnalis Helobdella triserialis microstoma Mooreobdella Placobdella montifera Class Polychaeta Alitta brandti Alitta succinea Amaeana Acmira catherinae Table 8. Table Cells Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. containing values greater than zero are highlighted red. species identified to the genus level; spp., denotes many of same genera; SF1, separate genera] Tables 87 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12-06-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 Sampling date 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45 06-30-17 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 23 Abbreviations: 03-28-17

(Ehlers 1901) Hartman 1936 (Pettibone (Claparède 1864) (Linneaus 1767) (Mesnil 1897) (Schmarda 1861) Moore 1911 Leidy 1855 Blacke 1996 Moore 1911 Reish 1959 Hartman 1936 (Frabricius 1780) apa 2007 (Johnson 1903) Taxon (Moore 1906) Berkeley & 1938 Berkele 1927 (Berkeley & and Berkeley

Hartman 1936 unid. spp. Species list and abundance at sampling station SB15, Artesian Slough, California, May 2016–March 2018.—Continued sp. SF1 sp. A

1956) complex 1957) Class Polychaeta—Continued Acmira lopezi Armandia brevis Boccardiella ligerica (Ferronnière, 1898) Capitella capitata Cirratulidae unid. spp. Cirriformia moorei Cossura Dipolydora brachycephala Dipolydora caulleryi Dipolydora socialis Dipolydora Schistomeringos longicornis Eteone californica Eteone lighti Euchone limnicola Exogone lourei Glycera americana Glycinde armigera Glycinde picta Glycinde Harmothoe imbricata Hediste limnicola filiformis Heteromastus Laonome calida C Leitoscoloplos pugettensis Lumbrineris inflata Table 8. Table Cells Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. containing values greater than zero are highlighted red. species identified to the genus level; spp., denotes many of same genera; SF1, separate genera] 88 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12-06-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 06-30-17 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Abbreviations: 03-28-17

(Okuda Hartman 1936 Hartman 1966 (Baird 1863) (Moore 1906) Hartman 1941 Örsted 1842 Sikoski & Bick Southern 1921 Leidy 1859 Webster 1879 Webster (Montagu 1813) (O.F. Muller 1806) (O.F. (Chamberlin 1919) Hartman 1938 A (Verrill 1873) (Verrill (Johnson 1897)

(Johnson 18970 Taxon Bosc 1802 (Berkeley & Berkeley A sp. (Berkeley & Berkeley Berkeley & 1942 sp. unid. spp. Species list and abundance at sampling station SB15, Artesian Slough, California, May 2016–March 2018.—Continued

2004 1945) 1937) 1945) Class Polychaeta—Continued Manayunkia speciosa neglecta Marenzelleria Marphysa sanguinea Neoamphitrite Nephtys caecoides Nephtys cornuta pelagica neonigripes Nereis Paleanotus bellis Pectinaria californiensis Pholoides aspera Phyllodoce groenlandica Pista pacifica bicanaliculata Platynereis Polycirrus Polydora cornuta Pseudopolydora kempi Pseudopolydora paucibranchiata Sabaco elongatus Schistomeringos annulate Scolelepis squamata Scoletoma luti californiensis Sphaerosyllis Sphaerosyllis Spiophanes duplex benedicti Streblospio Table 8. Table Cells Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. containing values greater than zero are highlighted red. species identified to the genus level; spp., denotes many of same genera; SF1, separate genera] Tables 89 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1,351 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15,040 12-06-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1,758 09-28-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1,842 06-30-17 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 Abbreviations: 03-28-17 - (Li 1936) (W. Tat (W. Kaufmann (Cushman 1906) Ortmann 1908 (Imajima 1966) Li 1964 Darwin 1854 Nakazawa 1910 Holmes 1896

Taxon A A

Barkeley 1929

A A A

A sp.

sp.

. sp. sp sp. Species list and abundance at sampling station SB15, Artesian Slough, California, May 2016–March 2018.—Continued sp. A sp.

1900 tersall 1932) Class Polychaeta—Continued Tharyx parvus Megasyllis nipponica PHYLUM ARTHROPODA Class Crustacea SubClass Copepoda Cyclopid SubClass Ostracoda Cypricercus Cyclocypris Eucypris Herpetocypris brevicaudata Isocypris Eusarsiella zostericola Cyprideis Candona SubClass Cirripedia Balanus improvisus SubClass Malacostraca Mysidacea Order Acanthomysis aspera Alienacanthomysis macropsis Hyperacanthomysis longirostris Neomysis japonica Neomysis kadiakensis Neomysis mercedis Table 8. Table Cells Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. containing values greater than zero are highlighted red. species identified to the genus level; spp., denotes many of same genera; SF1, separate genera] 90 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 384 248 03-08-18 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 12-06-17 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 Sampling date 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 06-30-17 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 44 Abbreviations: 03-28-17 Dana (Yu 1938) (Yu (Van Name (Van (Mills 1962) (Stimpson (Stimpson (Shoemaker (Chapman 1988) (Gamo 1967) (Miers 1881) Bousfield 1963 Richardson 1909 Shoemaker 1938 Hart 1930 (Mills 1964) Hart 1930 Holmes 1908 Mayer 1903 Taxon Smith 1873 Templeton 1836 Templeton spp. Species list and abundance at sampling station SB15, Artesian Slough, California, May 2016–March 2018.—Continued

1940) 1853 1857) 1941) 1856) Order Cumacea Order Cumella vulgaris pacifica Eudorella Nippoleucon hinumensis Tanaidacea Order Sinelobus Isopoda Order insulare Gnorimosphaeroma oregonensis Gnorimosphaeroma Paranthura japonica Synidotea laevidorsalis Amphipoda Order Americhelidium shoemakeri spinicorne Americorophium stimpsoni Americorophium Ampelisca abdita Ampelisca lobate Ampithoe plumulosa Ampithoe valida mendax Caprella scaura Caprella alienense Sinocorophium heteroceratum Sinocorophium Crangonyx floridanus Eogammarus confervicolus Table 8. Table Cells Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. containing values greater than zero are highlighted red. species identified to the genus level; spp., denotes many of same genera; SF1, separate genera] Tables 91 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 25 20 03-08-18 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 12-06-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 09-28-17 Sampling date 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 06-30-17 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 Abbreviations: 03-28-17

Costa 1853 (Crawford (Dana 1853) (Bergh 1894) (Bergh Rathbun 1902 Stephensen 1938 (Linnaeus 1767) Stimpson 1856 (Stephensen 1932) (Stimpson 1856) (Heller 1862) —Continued (Bousfield 1969) Taxon Dana 1852 Shoemaker 1942 sp. A Baba 1960 Smith 1873 unid. Spp. unid. spp. Species list and abundance at sampling station SB15, Artesian Slough, California, May 2016–March 2018.—Continued

sp. A

1937) Order Order Amphipoda ­ Eusiroidae Gammarus daiberi Gnathopleustes pugettensis japonica Grandidierella Grandifoxus grandis Hyalella Melita nitida acherusicum Monocorophium insidiosum Monocorophium uenoi Monocorophium Paradexamine Photis brevipes Stenothoe valida Talitridae Decapoda Order Crangon franciscorum Palaemon modestus Palaemon macrodactylus Decopoda unid. spp. Class Insecta Family Chironomidae Chironomidae unid. spp. PHYLUM MOLLUSCA Class Gastropoda Okenia plana Onchidoris bilamellata Melanochlamys diomedea Table 8. Table Cells Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. containing values greater than zero are highlighted red. species identified to the genus level; spp., denotes many of same genera; SF1, separate genera] 92 Benthic Community Dynamics in Coyote Creek and Artesian Slough, Southern San Francisco Bay, California 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12-06-17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 09-28-17 Sampling date 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 06-30-17 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Abbreviations: 03-28-17 (Tryon 1866) (Tryon (Say 1829) 1825) (Tryon 1865) (Tryon (Poli 1791) (Rowell 1863) (Benson 1842) (Say 1822) (Say 1817) (O. F. Müller 1774) (O. F. (Say 1822) Suter 1909 (Gould 1841) (Linnaeus 1758) Dall & Bartsch 1909

(Valenciennes 1821) (Valenciennes (Menke 1830) Taxon (Say Say 1822 A (Totten 1834) (Totten A Linnaeus 1758 unid. spp.

Species list and abundance at sampling station SB15, Artesian Slough, California, May 2016–March 2018.—Continued

sp. A Class ­ —Continued Gastropoda Nudibranchia Philine auriformis SubClass Pulmonata Ferrissia californica Gyraulus circumstriatus Helisoma anceps humilis Lymnaea columella Lymnaea Menetus dilatatus Physa Radix auricularia SuperFamily Hydrobioidea Assiminea californica Boonea bisuturalis plana Crepidula Epitonium sp. Fluminicola sp. Nassarius obsoletus Odostomia fetella Class Bivalvia senhousia Arcuatula Corbicula fluminea Gemma gemma Macoma petalum Musculium transversum Mya arenaria Pisidium casertanum Table 8. Table Cells Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. containing values greater than zero are highlighted red. species identified to the genus level; spp., denotes many of same genera; SF1, separate genera] Tables 93 0 0 0 0 0 0 0 03-08-18 0 0 0 0 0 0 0 12-06-17 0 0 0 0 0 0 0 09-28-17 Sampling date 0 0 0 0 0 0 0 06-30-17 unid., denotes taxa that could not be identified to the species level but categorized a higher classification; sp., single 0 0 0 0 0 0 0 Abbreviations: 03-28-17 (Shrenck 1861) (A. Adams & (De Kay 1843) Prime 1852 Taxon Gould 1861 unid. spp. (Herdman 1881) Species list and abundance at sampling station SB15, Artesian Slough, California, May 2016–March 2018.—Continued

Reeve 1850) Class Bivalvia—Continued Pisidium compressum Potamocorbula amurensis Theora lubrica philippinarum Venerupis PHYLUM CHORDATA Class Ascidacea Molgula manhattensis Styela clava PHYLUM ECHINODERMATA Class Ophiuroidea Amphiuridae Table 8. Table Cells Species typically found in the southern San Francisco Bay are included this table despite not being recorded study. [Species and abundance data are shown in number per 0.05 square meter. containing values greater than zero are highlighted red. species identified to the genus level; spp., denotes many of same genera; SF1, separate genera] Menlo Park Publishing Service Center California Manuscript approved for publication May 14, 2019 Edited by John Buursma and Phil A. Frederick Layout and design by Kimber Petersen Shrader and others—Benthic Community Dynamics in Coyote Creek and Artesian Slough, South San Francisco Bay, California, May 2016 to March 2018— Open-File Report 2019–1057, July 2019 ISSN 2331-1258 (online)