SFEWS: Volume 19, Issue 3
In our September issue new research and commentary provide insights on several topics: how to integrate zooplankton science to inform estuary management; how simulated fishing can avoid missed fish and detect gear bias in the water; why juvenile Chinook Salmon length-at-date criteria don't match genetic run assignments; whether declines in breeding waterfowl population relate to wetland habitat and salinity; and what kinds of food web support can be achieved by use of a managed flow pulse.
Photo: Forster’s Terns at Crown Beach, public domain. Attribution: © Ingrid Taylar, Creative Commons 2.0 Generic license.
Catch as Catch Can
"Catchability" refers to the relationship between catch rate and the true population. Ecological monitoring programs use catch per unit of effort (CPUE) to standardize catch and monitor changes in fish populations; however, CPUE is proportional to the portion of the population that is vulnerable to the type of gear used in sampling, which is not necessarily the entire population. Tobais' simulation combines a module for sampling conditions with a module for individual fish behavior to estimate the proportion of available fish that would escape from the sample. The method is applied to the case study of the well monitored fish species Delta Smelt (Hypomesus transpacificus) in the San Francisco Estuary, where it has been hypothesized that changing water clarity may affect catchability for long-term monitoring studies.
Waterfowl Reproductive Success Depends on High Water, Low Salt
Availability of wetlands with low salinities during the breeding season can influence waterfowl reproductive success and population recruitment. Salinities as low as 2 ppt (3.6 mS/cm) can impair duckling growth and influence behavior, with mortality occurring above 9 ppt (14.8 mS/cm). Schacter et al. used satellite imagery to quantify the amount of available water, and sampled surface water salinity at Grizzly Island, in the brackish Suisun Marsh, at three time-periods during waterfowl breeding (April, May, July) over 4 years (2016–2019). Among their findings was during peak duckling production in May, 81%–95% of available water had salinity above 2 ppt, and 5%–21% was above 9 ppt. Local waterfowl populations would benefit from management practices that provide fresher water during peak duckling production in May and retain more water through July.
Deep Dives Among Waterbird Populations in South SF Bay
In south San Francisco Bay, former salt ponds now managed as wildlife habitat support large populations of breeding waterbirds. In 2006, the South Bay Salt Pond Restoration Project began the process of converting 50% to 90% of these managed pond habitats into tidal marsh. Hartman et al. compared waterbird populations in south San Francisco Bay before (2001) and after (2019) approximately 1,300 ha of managed ponds were breached to tidal action to begin tidal marsh restoration. Study results showed average annual nest abundance declined during 2017–2019 by 53%, 71%, and 36%, for American Avocets, Back-necked Stilts, and Forster’s Terns, respectively. All three species established nesting colonies on newly constructed islands within remaining managed ponds; however, these new colonies did not make up for the steep declines observed at other historical nesting sites. For future wetland restoration, retaining more managed ponds that contain islands suitable for nesting may help to limit further declines in breeding waterbird populations.
Managed Pulse Flows as Food Web Support
While freshwater inflow has been a major focus of resource management in estuaries, including the upper San Francisco Estuary, there is a growing interest in using focused flow actions to maximize benefits for specific regions, habitats, and species. To test this concept, in summer 2016, Frantzich et al. used a managed flow pulse to target an ecologically important region: a freshwater tidal slough called the Cache Slough Complex. Their goal was to improve estuarine habitat by increasing net flows through CSC to enhance downstream transport of lower trophic-level resources, an important driver for fishes such as the endangered Delta Smelt. Simulations using a 3-D hydrodynamic model (UnTRIM) indicated that the managed flow pulse had a large effect on the net flow of water through Yolo Bypass, and between the CSC and further downstream. The managed flow pulse resulted in increased densities of zooplankton (copepods, cladocerans) demonstrating potential advection from upper floodplain channels into the target CSC and Sacramento River regions. Though conducted during a single year, this study may provide an instructive example of how a relatively modest change in net flows can generate measurable changes in ecologically relevant metrics, and how an adaptive management action can help inform resource management.
Length-at-Date Criteria and Genetic Run Assignments
Four distinct runs of Central Valley Chinook Salmon are named after their primary adult return times: fall, late-fall, winter, and spring run. Estimating the run-specific composition of juveniles entering and leaving the Sacramento–San Joaquin Delta is crucial for assessing population status and processes that affect juvenile survival through the Delta. Historically, the run of juvenile Chinook Salmon captured in the field has been determined using a length-at-date criteria (LDC); however, LDC run assignments may be inaccurate if there is high overlap in the run-specific timing and size of juveniles entering and leaving the Delta. In this study, Brandes et al. use genetic run assignments to assess the accuracy of LDC at two trawl locations in the Sacramento River (Delta entry) and at Chipps Island (Delta exit).Across years, there was extensive overlap among the distributions of run-specific fork lengths of genetically identified juveniles, indicating that run compositions based on LDC assignments would tend to underestimate fall-run and especially late-fall-run compositions at both trawl locations, and greatly overestimate spring-run compositions (both locations) and winter-run compositions (Chipps Island). We therefore strongly support ongoing efforts to include tissue sampling and genetic run identification of juvenile Chinook Salmon at key monitoring locations in the Sacramento–San Joaquin River system.
Pelagic fish in the San Francisco Estuary are harder to catch in recent decades. Over the past thirty years, Delta Smelt catch in the Fall Midwater Trawl Survey has declined by 99%, Longfin Smelt catch has declined by over 95%, and even the notoriously hardy Striped Bass have declined by over 75%. To manage the system and reverse these declines, we need a better understanding of the “bottom-up” processes that exert control on these populations—we need to study fish food. In other words, in addition to studying fish directly, we need to increase our understanding of what pelagic fish eat: zooplankton. In this essay, Hartman et al. break down not only what fish eat (zooplankton) and why they are important drivers of species abundance in higher trophic areas of the food web, but also how scientists and natural resources managers can communicate better to understand which zooplankton data can inform and develop management-relevant questions.
Volume 10, Issue 2, 2012
Special Issue, Part II: Tidal Wetlands in the San Francisco Bay National Estuarine Research Reserve
This two-part special issue reviews the basic ecology of tidal wetlands in the San Francisco Estuary. Several articles highlight the well-preserved tracts of historic tidal marsh found at China Camp State Park and Rush Ranch Open Space Preserve. These two protected areas serve as important reference sites for wetland restoration and conservation and also comprise San Francisco Bay National Estuarine Research Reserve (SF Bay NERR). SF Bay NERR is part of the National Oceanic and Atmospheric Administration’s nationwide network of 28 estuarine research reserves (http://www.nerrs.noaa.gov) that all share common goals: (1) conducting standardized long-term monitoring, (2) supporting applied environmental research, (3) providing stewardship of estuarine natural resources, and (4) linking science with decision making in pursuit of effective solutions to coastal management problems.
Part II, Conclusion: Ecology and Regional Context of Tidal Wetlands in the San Francisco Bay National Estuarine Research Reserve
China Camp State Park and Rush Ranch Open Space Preserve contain rare examples of historic tidal wetlands, undeveloped coastal hills and grasslands, and a variety of ecotones once common (but now rare) in the San Francisco Estuary. The San Francisco Bay National Estuarine Research Reserve was designated in 2003 to support coastal management through long-term monitoring and research at China Camp and Rush Ranch. This two-part Special Issue [9(3) and 10(2)] summarizes the current regional context of the marshes at China Camp and Rush Ranch and reviews key aspects of their ecology. Scientific activities at these sites are complemented by stewardship and education programs that offer unique opportunities to improve the conservation and restoration of tidal wetlands throughout the estuary.
We analyzed tidal wetland vegetation patterns in the San Francisco Bay–Delta estuary (Bay–Delta) and discuss their significance for future conservation. Our objective was to conduct a balanced, random sample of six historic “remnant” tidal wetlands along a salinity gradient that ranged from southern San Pablo Bay to the lower Delta. We also wanted to compare diversity among these sites at five different scales, ranging from small subplots to total species per site. We randomly established twenty 0.1-ha plots at each site, and sampled ten 7-m2 circular subplots (subplot scale) in each plot for species presence and cover. We calculated total species per plot (plot scale) and total species per site (site scale) based on these subplot data. We calculated importance values for each species found in subplots based on frequency of occurrence and proportion of total cover at each site. In addition, we recorded species found within the 0.1-ha plot but not sampled in subplots (plot_all scale), and calculated the total species for each site based on these plot_all data (site_all scale). Thus, richness at each site was evaluated at five different scales that ranged from 7 m2 to 20,000 m2. We conducted a one-way ANOVA that compared mean richness among three scales with continuous data: subplot, plot, and plot_all. At lower estuary (San Pablo Bay) sites, richness values at these three scales were significantly lower than upper estuary (Suisun–Delta) sites. In Suisun–Delta sites, significant differences in richness varied, depending on sampling scale. Rush Ranch, a brackish wetland, had the highest average number of species per plot, whereas Sand Mound Slough, a freshwater wetland, had the highest average number of species at the subplot scale and the most total species at the site_all scale. Sand Mound Slough also had the highest number of unique species (22) compared to the other sites. We found a strong negative correlation (r2 = 0.99) between total species number and salinity (the most in the Delta at the lowest salinity, and the least at China Camp with the greatest salinity). Our analysis suggests the following conservation recommendations: (1) restore habitat for freshwater plant species diversity in the Delta; (2) restore transitional brackish wetland habitat in salt marshes of the San Pablo Bay and San Francisco Bay; and (3) focus on control of pepperweed (Lepidium latifolium) in brackish marshes.
China Camp (Marin County, California) preserves extensive relict stands of salt marsh vegetation developed on a prehistoric salt marsh platform with a complex sinuous tidal creek network. The low salt marsh along tidal creeks supports extensive native stands of Pacific cordgrass (Spartina foliosa). The outer salt marsh accreted following hydraulic gold mining sedimentation. It consists of a wave-scarped pickleweed-dominated (Sarcocornia pacifica) high salt marsh terrace with a broad fringing low marsh dominated by S. foliosa, including intermittent, variable stands of alkali-bulrush (Bolboschoenus maritimus). Most of the extensive prehistoric salt marsh plains within the tidal creek network also support mixed assemblages of S. pacifica, but high marsh zones along tidal creek banks support nearly continuous linear stands of gumplant (Grindelia stricta) and saltgrass (Distichlis spicata) with more diverse salt marsh forb assemblages. Salt pans with submerged wigeongrass (Ruppia maritima) are scarce, local, and small. The landward edge of the tidal marsh forms rare examples of ecotones with adjacent terrestrial vegetation, including those of alluvial valleys (riparian scrub and woodland, freshwater marsh, sedge-rush meadows) and hillslope grassland and oak woodland vegetation. Narrow high tidal marsh ecotones bordering terrestrial grasslands are locally dominated by creeping wildrye (Elymus triticoides) and Baltic rush (Juncus balticus), mostly on south-facing slopes. Brackish tidal marsh ecotones above ordinary high tides are associated with freshwater discharges from groundwater and surface flows. Brackish marsh ecotones support large clonal stands of sedge, bulrush, and rush vegetation (Carex praegracilis, C. barbarae, Bolboschoenus maritimus, Juncus phaeocephalus, Schoenoplectus acutus), intergrading with terrestrial freshwater wetlands and salt marsh. The terrestrial ecotone assemblages at China Camp are comparable with those of other prehistoric tidal marshes in the San Francisco Estuary, but China Camp lacks most native clonal perennial Asteraceae and halophytic annual forbs of the region’s remnant high tidal marsh ecotones. Few globally rare salt marsh plant populations have been reported from China Camp within the National Estuarine Research Reserve and State Park boundaries, but some species regionally uncommon in San Francisco Bay tidal marshes occur. To date, non-native tidal marsh plant invasions have been relatively minor and localized within China Camp.
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Abundance, Species Richness, and Reproductive Success of Tidal Marsh Birds at China Camp State Park, Marin County, California
Extensive habitat loss and degradation have resulted in decreases in populations of tidal marsh breeding birds in the San Francisco Estuary in the past 150 years. We conducted point count surveys and nest monitoring in tidal marsh habitat at China Camp State Park from 1996 through 2007 to assess bird abundance, species richness and reproductive success over time. We found overall species richness at China Camp to be significantly lower than that of other San Pablo Bay tidal marshes, but also to be increasing during the study period. We present relative density indices and confirm breeding for three focal species that are of conservation concern: San Pablo song sparrow (Melospiza melodia samuelis), California black rail (Laterallus jamaicensis coturniculus), and California clapper rail (Rallus longirostris obsoletus). Song sparrows were observed at higher densities at China Camp than at other San Pablo Bay sites. There was no apparent trend in song sparrow density during the study period at China Camp, in contrast with the rest of San Pablo Bay, which displayed a significant decline. We determined song sparrow nest survival probability using the method described by Mayfield (1975) and found that nest survival at China Camp varied markedly among years, from >30% in 1996 to 6% in 2006, with no discernible trend. The main causes of nest failure were predation and tidal flooding. Song sparrow nests were found predominantly in gumplant (Grindelia stricta) and pickleweed (Sarcocornia pacifica) and less commonly in saltgrass (Distichlis spicata). Clapper rails nested exclusively in pickleweed and black rail nests were found mainly in gumplant and less commonly in saltgrass. China Camp’s expansive ancient marsh supports endemic and bird species of conservation concern, while serving as a reference site for tidal marsh studies in San Francisco Bay. The long-term monitoring of tidal marsh bird breeding parameters at China Camp has the potential to provide early detection of declining population trends before local populations become imperiled.
China Camp State Park is primarily a forested area with a fringing saline marsh while the Rush Ranch Open Space Preserve has large brackish marshes backed by grass-covered hills. The emphasis of this chapter is on small mammals common to both areas, i.e. endangered salt marsh harvest mice and several rare shrews. Both China Camp and Rush Ranch contain significant stretches of intact marsh–upland ecotone that provide refuge for small mammals during periods of high water. This refuge habitat will become even more important as accelerating sea level rise increases marsh inundation and reduces other available cover. Future efforts to conserve populations of salt marsh harvest mice and shrews around San Francisco Bay should focus on protection and expansion of the marsh–upland ecotone.
Rush Ranch, with the largest contiguous area of fully-tidal marsh remaining in northern Suisun Bay, is critical habitat for a number of endemic bird species that breed in brackish tidal marsh. Despite the abundance of non-native invasive plants (particularly perennial pepperweed, Lepidium latifolium) and altered hydrology, it is the best remaining representative in Solano County of the tidal marsh that once covered more than 27,000 ha (67,000 acres) in Suisun Bay. This paper presents a synthesis of bird population studies conducted at Rush Ranch since the late 1970s, concentrating on California clapper rail (Rallus longirostris obsoletus), California black rail (Laterallus jamaicensis coturniculus), Suisun song sparrow (Melospiza melodia maxillaris), common yellowthroat (Geothlypis trichas), and marsh wren (Cistothorus palustris). These studies indicate declines in clapper rail abundance, when we compared the past 8 years to surveys conducted 10 to 25 years ago. However, black rails appear to be increasing at Rush Ranch, and overall in Suisun Bay. Nest monitoring of reproductive attempts by song sparrows conducted between 1996 and 2005 indicates low overall nest survival rates, mainly from high predation rates, but also great year-to-year variability. Low nest survival rates of tidal marsh song sparrows observed at Rush Ranch appear to be too low to sustain populations, and such low rates are consistent with the apparent population declines observed for this subspecies at Rush Ranch. Nest survival and other components of reproductive success of tidal marsh birds should be monitored in the future to provide information on ecosystem condition and population health, as well as the response of these species to management, including control of non-native plant species.