New Technique for Identifying Plankton by Color
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ESTUARY SCIENCE • RESTORATION • WATERSHED • POLITICS SPECIES BAY • WATERSHED SCIENCE • RESTORATION San Francisco Estuary Partnership Mokelumne’s Pitch for Wild River Flatlines Dry Times for Valley Refuges New Technique for Identifying Plankton by Color PCB Levels in Small Fish Surprise Scientists Alameda Creek Crawls Toward Fish-Friendly Future Delta Council Finetunes Habitat Protocols NE WS SEPTEMBER 2014 VOL. 23, NO. 3 Plankton Pigments ...... 3 Lavender Invader ....... 4 New Water Atlas ........ 4 Alameda Creek ......... 5 PCBs & Small Fish ...... 6 Valley Refuges .......... 8 Delta Habitats .......... 9 Suspense for Mokelumne 10 Pelican Movie .........11 2 SEPTEMBER 2014 3 ESTUARY NEWS SCIENCE NEW INTERACTIVE MAP Around the Bay DEBUTS FOR FLOODZONE Our Coast, Our Revealing BIRDS CROWD ROCK VISITORS Future (OCOF), & VICE VERSA — Managing a collabora- Alcatraz — once a federal prison, now tive project with Plankton Pigments part of the National Park system—is a many partners delicate balancing act. As an historic site, designed to help Keeping tabs on San Francisco Bay’s fucoxanthin (brown), its cultural resources come first. But planners and land wildlife involves counting plants. That while dinoflagellates the return of colonial seabirds since the use managers means tracking the relative numbers have a lock on peridinin prison closure adds another mandate. prepare for rising and types of the microscopic floating (brown-gold), and cya- Alcatraz hosts San Francisco Bay’s larg- sea levels and plants that feed the Bay. Known as nobacteria alone make est breeding colony of western gulls; its changes in storm phytoplankton, their number includes zeaxanthin (orange). only colonies of Brandt’s cormorants, pe- patterns, has just diatoms, dinoflagellates, cyanobacte- lagic cormorants, and pigeon guillemots; added San Fran- ria, and chromophytes, to name a few. To obtain samples and rookeries of black-crowned night cisco Bay data to for pigment analysis, herons and snowy egrets (see “Seeing its online resourc- “Some are like the kale of the sea, technicians capture Seabirds,” Estuary News, October 2010.) es (data.prbo. others are like french fries,” says phytoplankton in a given They’re all protected under the Migratory org/apps/ocof). Jim Cloern, a scientist who monitors volume of Bay water on Bird Treaty. Visitors, for their part, would This includes an Bay food webs for the U.S. Geological filter paper — the same like more access to areas now off-limits interactive map of Survey. Some can also produce toxins, process used for micro- because of nesting birds. They’ve com- potentially flooded while others cannot. For these reasons, scope analysis. Back plained about the aggressive gulls, the areas, a King Tide understanding which phytoplankton are at the lab, the plankton smell of the seabird colonies, and the scenario for the in the Bay can help scientists predict are broken up to release flies they attract, and have sometimes Bay, and a suite Source: OCOF and partners including Point Blue Conservation Science, booms and busts in fish populations, their pigments, and sus- flushed the skittish cormorants off nests. of 40 sea level the US Geological Survey’s Pacific Coastal & Marine Science Center, the forecast toxic algal blooms, and warn pended in solvent. The The gulls also interfere with reconstruc- and storm projec- National Estuarine Research Reserve System, the National Park Service, seafood eaters of potential danger. solution is then forced the Gulf of the Farallones National Marine Sanctuary, and the Bay Area through a high perfor- tion of the flower beds tended by prison- tions. Workshops Ecosystems Climate Change Consortium. “What phytoplankton species are in mance liquid chromatog- ers and guards’ families. In 2005, the and webinars have the Bay has a big economic impact on raphy, or HPLC column. Park Service, the Golden Gate Parks been scheduled for fisheries, travel, and tourism. For ex- The column separates Conservancy, and other stakeholders local users. Coincidentally, the National ample, you can’t allow people to collect REBRANDED RIDGWAY the pigments so that Pigment analysis (top) and microscope analysis (bottom) pro- developed a Bird Conservation and Management Oceanic and Atmospheric Administra- mussels during a toxic bloom,” says The California clapper rail, endangered each emerges at a differ- duce similar results, but pigment analysis is better at identifying Strategy to address those conflicts. In the tion (NOAA), an OCOF partner, recently Misty Peacock, a postdoctoral fellow at poster child of San Francisco Bay’s ent time. As each pigment small or rare component species of phytoplankton. spirit of adaptive management, they’ve listed San Francisco as one of the UC Santa Cruz. ten US cities experiencing increased tidal marshes, is no more. No, it hasn’t emerges, a device that Source: Kudela Lab (inset), Peacock et al., UCSC, USGS, SFEI. gone back to the table for a ten-year gone extinct: it’s just been rebranded. review. Watch for an update once the plan nuisance flooding caused by sea level Since 1988, the U.S. Geologi- analyzes its color detects The American Ornithologists’ Union, resolution phytoplankton snapshot. Al- has been revised. JE rise. JE cal Survey has tracked the types of its presence and records this informa- the ultimate authority on the taxonomy phytoplankton in the Bay by taking tion as a graph. Each pigment forms though the technique has been around CONTACT Kelly Higgason, of North American birds, has decided a distinctively-shaped peak, and the since the 1990s, Peacock and the USGS [email protected] water samples at 36 locations from Rio that clapper rails on the Pacific Coast Vista to Alviso. They send two plankton larger the area under the peak, the are the first to apply it to long-term REDO FOR CCMP — San Francisco are genetically distinct from Atlantic samples from each cruise to a labora- more of the pigment is present. monitoring in San Francisco Bay. Estuary Partnership staff is leading an and Gulf Coast populations and should tory for microscopic analysis. Finding an accessory pigment is However, Peacock says, pigment effort to update the landmark Compre- be classified as a separate species, Ridgway’s rail. Research by James Though a tried and true technique, like locating a fingerprint at a crime analysis shouldn’t replace microscopy hensive Conservation and Management Plan. Maley and Robb Brumfield of Louisi- microscopic analysis is also expensive scene. “Even if we didn’t see that but rather should be used alongside it. First approved in 1993, the Plan has ana State University supports the split and time-consuming. Technicians must organism via microscopy but we Pigments alone can’t identify a phy- resulted in numerous projects and pro- (insert your own Abe Lincoln joke here.) be trained to identify phytoplankton see their diagnostic pigment in our toplankton species. That means the grams that have improved the health The new name honors artist/ornitholo- types by sight, and must painstakingly samples, we know they’re still in the technique cannot pinpoint the source of of the estuary (see Estuary News October gist Robert Ridgway, who described count hundreds of the tiny cells in water,” Peacock says. For this reason, harmful algal blooms, which can suf- 2013). Work now underway will create the local form in 1874. The species samples. pigment analysis is the method of focate fish and poison everything from an update that looks forward to 2050, also includes the (former) light-footed choice for finding relatively rare and pelicans to people. Over the past year, Peacock has takes into consideration new ideas and clapper rail of the Southern Califor- extremely tiny organisms. helped the USGS identify a faster and Yet the technique can guide Bay conditions, and emphasizes issues not nia coast, the Yuma clapper rail of the cheaper plankton-counting method. The total amount of cells in the sampling efforts. “If I saw an increase deeply addressed in past versions, such lower Colorado River’s marshes, and Known as pigment analysis, this sample is determined by analyzing the of cyanobacteria using pigment analy- as climate change and population in- three forms that occur only in Mexico. technique deduces which groups are amount of chlorophyll a present. The sis, I would know it was important to go crease. The new plan will also describe The three found in the United States re- present by identifying their unique pho- proportion of each class of phytoplank- out and sample more in the Bay. The how the Partnership will track progress tain their federal and state endangered tosynthetic pigments. Each pigment ton can be determined by the relative results can help us decide where the on priority actions, and be grounded status. With their disjunct ranges and in measures of estuary health laid out reflects different light wavelengths, amount of its accessory pigment. best places to monitor some of these sedentary natures, they’re unlikely to harmful species might be,” Peacock in the 2011 State of the Bay Report. Staff is making them different colors. share genes. Give them a few millennia Pigment analysis promises to says. This would allow scientists to stay currently setting committee sched- and who knows—they might qualify as While all phytoplankton produce revolutionize our ability to track what’s on top of an evolving bloom, and alert ules, drafting workplans, and starting species in their own right. JE chlorophyll a, each class also pro- in the Bay at any given time. Because health authorities accordingly. KW conversations with many organizations, duces at least one unique accessory the technique is so economical, the Black crowned night heron. agencies, and individuals about this pigment. For example, diatoms are agency can sample up to 15 samples CONTACT Misty Peacock Photo by Verne Nelson. critical work. the only phytoplankton that produce per cruise and obtain a much higher- [email protected] 4 SEPTEMBER 2014 5 ESTUARY NEWS CONSERVATION Now a project known as the New Cal- CREEKS where sediment collects on the ifornia Water Atlas seeks to make mold- bottom.