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.
Zooplankton, Anyone?
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 4, Issue 2, 2006
Research Article
Variation in Spring Nearshore Resident Fish Species Composition and Life Histories in the Lower San Joaquin Watershed and Delta
Providing freshwater to human populations while protecting or rehabilitating ecosystem health is a significant challenge to water resource managers and requires accurate knowledge of aquatic resources. Previous studies of fish assemblages in the San Francisco Estuary and watershed have focused on specific habitat types, water bodies, or geographic subregions. In this study, we use seining data from two monitoring programs to provide an integrated view of spring nearshore resident fish species composition and life history characteristics in five regions: the San Joaquin River, the upper Sacramento River, the lower Sacramento River, the northern Sacramento-San Joaquin Delta (North Delta), and the Interior Delta. Data for the period March-May from 1994 to 2002, showed that spring species composition of the San Joaquin River was very different from the other four regions. Total catch in the San Joaquin River was dominated by small, short-lived batch spawning alien species (93%), particularly red shiner Cyprinella lutrensis (>75% of total catch). The upper and lower Sacramento River were very similar in species composition and life history characteristics and less dominated by alien fish (<45% of total catch). Ordination of species percentage abundances by non–metric multidimensional scaling confirmed that the major gradient was from assemblages dominated by native species to assemblages dominated by alien species. Two-way analysis of variance of ordination scores indicated that spatial variability was more important than annual variability in explaining patterns in species composition. The potential benefits of San Joaquin River native fish restoration appear high because there is so much potential for improvement; however, it is unclear how to best manipulate the system to achieve such restoration. Addressing such uncertainties is necessary if society desires the reservation and restoration of native biodiversity as human demands on water resources increase.
Hydrologic Variability of the Cosumnes River Floodplain
Natural floodplain ecosystems are adapted to highly variable hydrologic regimes, which include periodic droughts, infrequent large floods, and relatively frequent periods of inundation. To more effectively manage water resources and maintain ecosystem services provided by floodplains – and associated aquatic, riparian, and wetland habitats – requires an understanding of seasonal and inter-annual hydrologic variability of floodplains. The Cosumnes River, the largest river on the west-slope Sierra Nevada mountains without a major dam, provides a pertinent test case to develop a systematic classification of hydrologic variability. By examining the dynamics of its relatively natural flow regime, and a 98-year streamflow record (1908 – 2005), we identified 12 potential flood types. We identified four duration thresholds, defined as short (S), medium (M), long (L), and very long (V). We then intersected the flood duration division by three magnitude classes, defined as small-medium (1), large (2), and very large (3). Of the 12 possible flood types created by this classification matrix, the Cosumnes River streamflow record populated 10 such classes. To assess the robustness of our classification, we employed discriminant analysis to test class fidelity based on independent measures of flood capability, such as start date. Lastly, we used hierarchical divisive clustering to classify water years by flood type composition resulting in 8 water year types. The results of this work highlight the significant seasonal and inter-annual variability in natural flood regimes in Central Valley rivers. The construction of water impoundment and flood control structures has significantly altered all aspects of the flood pulse. Restoring floodplain ecosystem services will require re-establishing key elements of these historic flood regimes in order to achieve regional restoration goals and objectives.
Arsenic in Groundwater: A Review of Current Knowledge and Relation to the CALFED Solution Area with Recommendations for Needed Research
Ground water with arsenic concentrations greater than the U.S. Environmental Protection Agency drinking water standard exists throughout much of the CALFED solution area. These high concentrations are of con-cern from the standpoint of both existing water supply and development of conjunctive use projects. Much is known about arsenic mobility in ground water subject to different hydrologic and geochemical conditions. However, some important knowledge gaps exist that limit the ability to design water supply projects that could prevent arsenic mobilization or promote arsenic removal from ground water. A few well studied sys-tems could provide a much better understanding of methods for preventing or eliminating high arsenic problems. Within the context of the examination of a few detailed field studies, some important research needs include: 1.) Determining the significance of metal-bridging aqueous complexes involving inorgan-ic arsenic and natural organic matter, 2.) In the con-text of in situ remediation, determining whether of metal oxides. Little is known about the quantitative significance competition of inorganic arsenic with other inorganic aqueous species in natu-ral systems. Experiments should be conducted with actual aquifer materials, as the effects of aging on arsenic desorption in laboratory studies are quite sig-nificant. 3.) Devise methods to detect and quantify rates of oxidation/reduction reactions of arsenic that are carried out by microorganisms at ambient concen-trations of arsenic and under in situ conditions. The findings from detailed field studies have the potential for greatly reducing the cost of meeting the new drinking-water standard for arsenic. The research would benefit a broad constituency.
Policy and Program Analysis
Environmental Decision Analysis: Meeting the Challenges of Making Good Decisions at CALFED
We present a methodology to support decision making at CALFED based on the principles of decision analysis, an analytical approach to decision making designed to handle complex decisions involving both uncertainty and multiple dimensions of value. The impetus for such an approach is a recognized need to enhance communication between scientists and management and between program elements within CALFED. In addition, the environmental decision analysis framework supports both the explicit representation of uncertainty in the decision problem and communication about risk, important elements of most environmental management decisions. The decision analysis cycle consists of four phases: 1) formulate, 2) evaluate, 3) appraise, and 4) decide. In phase one, we identify the objectives and also the alternatives, or possible actions. To facilitate inter-comparison between proposed actions, we recommend formulation of a set of common metrics for CALFED. In our pilot study, we introduced common metrics for salinity, winter-run Chinook salmon survival, and habitat health. The second phase focuses on quantifying possible impacts on the set of metrics, drawing on existing data, model runs, and expert opinions. For the evaluation phase, we employ tools such as decision trees to assess the system-wide impacts of a given action. In the final phase, tools such as expected cost-benefit analysis, value contribution diagrams, and 3-D tradeoff plots aid communication between various stakeholders, scientists, and managers. While decision analysis provides a spectrum of decision support tools, we emphasize that it does not dictate a solution but rather enhances communication about tradeoffs associated with different actions.