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 6, Issue 1, 2008
The biological productivity of river-dominated estuaries is affected strongly by variation in freshwater inflow, which affects nursery habitat quality. Previous research has shown this is generally true in the upper San Francisco Estuary, California, USA; however, one endemic species of high management importance, delta smelt (Hypomesus transpacificus), has shown ambiguous population responses to river inflow variation. We hypothesized that population-level associations with abiotic habitat metrics have not been apparent because the effects occur seasonally, and at spatial scales smaller than the entire upper San Francisco Estuary. We tested this hypothesis by applying regression techniques and principal components analysis (PCA) to a long-term data-set (1970–2004) of summertime fish catch, and concurrently measured water quality (specific conductance, Secchi disk depth, and water temperature). We found that all three water quality variables predicted delta smelt occurrence, and we identified three distinct geographic regions that had similar long-term trends in delta smelt capture probabilities. The primary habitat region was centered on the confluence of the Sacramento and San Joaquin rivers; delta smelt relative abundance was typically highest in the Confluence region throughout the study period. There were two marginal habitat regions—including one centered on Suisun Bay—where specific conductance was highest and delta smelt relative abundance varied with specific conductance. The second marginal habitat region was centered on the San Joaquin River and southern Sacramento-San Joaquin Delta. The San Joaquin region had the warmest water temperatures and the highest water clarity, which increased strongly in this region during 1970–2004. In the San Joaquin region, where delta smelt relative abundance was correlated with water clarity, catches declined rapidly to zero from 1970–1978 and remained consistently near zero thereafter. However, when we combined these regional results into estuary-wide means, there were no significant relationships between any of the water quality variables and delta smelt relative abundance. Our findings support the hypothesis that basic water quality parameters are predictors of delta smelt relative abundance, but only at regional spatial scales.
Phytoplankton in the Upper San Francisco Estuary: Recent Biomass Trends, Their Causes, and Their Trophic Significance
Several pelagic fish populations in the upper San Francisco Estuary have recently declined to historically low abundances, prompting an interest in the status of their food supply. Previous studies have indicated that the primary food supply for metazoans in the Delta is phytoplankton productivity, and the long-term decrease in phytoplankton over the last few decades may very well play a role in the long-term decline of pelagic fish abundance. Regional phytoplankton biomass trends during 1996–2005, however, are positive in the Delta and neutral in Suisun Bay, the two major sub-regions of the upper estuary. The trend in Delta primary productivity is also positive. Changes in phytoplankton biomass and production during the last decade are therefore unlikely to be the cause of these more recent metazoan declines. The main source of interannual phytoplankton variability in the Delta during 1996–2005, including the upward trend, appears to have been freshwater flow variability and its effect on particle residence time. This conclusion is supported by trend analyses; the concurrence of these time trends at widely-separated stations; empirical models at the annual and monthly time scales; particle residence time estimates; and experience from other estuaries. A significant temperature increase was also noticed, at least partially independent of flow changes, but its net effect on the phytoplankton community is unknown because of differential effects on growth and loss processes. Phytoplankton biomass in Suisun Bay, in contrast to the Delta, did not increase during 1996–2005. Consistent with this observation, Suisun Bay phytoplankton exhibited relatively low responsiveness to flow variability. This behavior differs from earlier chlorophyll-flow relationships reported in the literature. The reason appears to be the invasion of Suisun Bay by a clam—Corbula amurensis—in 1986, which has since maintained the phytoplankton community mostly at low levels by vigorous filter-feeding. In the past, flows into Suisun Bay generally diluted the higher phytoplankton concentrations within the bay; now they bring in higher phytoplankton concentrations from upstream. The supply of phytoplankton carbon to Suisun Bay has always been dominated by allochthonous sources, at least for mean flow conditions. Now this dominance must be even more pronounced.
Principal Hydrologic Responses to Climatic and Geologic Variability in the Sierra Nevada, California
Sierra Nevada snowpack is a critical water source for California’s growing population and agricultural industry. However, because mountain winters and springs are warming, on average, precipitation as snowfall relative to rain is decreasing, and snowmelt is earlier. The changes are stronger at mid-elevations than at higher elevations. The result is that the water supply provided by snowpack is diminishing. In this paper, we describe principal hydrologic responses to climatic and spatial geologic variations as gleaned from a series of observations including snowpack, stream-flow, and bedrock geology. Our analysis focused on peak (maximum) and base (minimum) daily discharge of the annual snowmelt-driven hydrographs from 18 Sierra Nevada watersheds and 24 stream gage locations using standard correlation methods. Insights into the importance of the relative magnitudes of peak flow and soil water storage led us to develop a hydrologic classification of mountain watersheds based on runoff versus base flow as a percentage of peak flow. Our findings suggest that watersheds with a stronger base flow response store more soil water than watersheds with a stronger peak-flow response. Further, the influence of antecedent wet or dry years is greater in watersheds with high base flow, measured as a percentage of peak flow. The strong correlation between 1) the magnitude of peak flow, and 2) snow water equivalent can be used to predict peak flow weeks in advance. A weaker but similar correlation can be used to predict the magnitude of base flow months in advance. Most of the watersheds show a trend that peak flow is occurring earlier in the year.
Investigating Particle Transport and Fate in the Sacramento–San Joaquin Delta Using a Particle-Tracking Model
Movements of pelagic organisms in the tidal freshwater regions of estuaries are sensitive to the movements of water. In the Sacramento-San Joaquin Delta—the tidal freshwater reach of the San Francisco Estuary—such movements are key to losses of fish and other organisms to entrainment in large water-export facilities. We used the Delta Simulation Model-2 hydrodynamic model and its particle tracking model to examine the principal determinants of entrainment losses to the export facilities and how movement of fish through the Delta may be influenced by flow. We modeled 936 scenarios for 74 different conditions of flow, diversions, tides, and removable barriers to address seven questions regarding hydrodynamics and entrainment risk in the Delta. Tide had relatively small effects on fate and residence time of particles. Release location and hydrology interacted to control particle fate and residence time. The ratio of flow into the export facilities to freshwater flow into the Delta (export:inflow or EI ratio) was a useful predictor of entrainment probability if the model were allowed to run long enough to resolve particles’ ultimate fate. Agricultural diversions within the Delta increased total entrainment losses and altered local movement patterns. Removable barriers in channels of the southern Delta and gates in the Delta Cross Channel in the northern Delta had minor effects on particles released in the rivers above these channels. A simulation of losses of larval delta smelt showed substantial cumulative losses depending on both inflow and export flow. A simulation mimicking mark–recapture experiments on Chinook salmon smolts suggested that both inflow and export flow may be important factors determining survival of salmon in the upper estuary. To the extent that fish behave passively, this model is probably suitable for describing Delta-wide movement, but it is less suitable for smaller scales or alternative configurations of the Delta.