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 17, Issue 3, 2019
Research Article
Chemically Enhanced Treatment Wetland to Improve Water Quality and Mitigate Land Subsidence in the Sacramento‒San Joaquin Delta: Cost and Design Considerations
Water quality impairment and land surface subsidence threaten the viability of the Sacramento–San Joaquin Delta (Delta), a critical component of California’s water conveyance system. Current-day irrigation drainage through Delta island peat soils affects drinking water treatment and is linked to mercury transport, potentially posing both ecological and public health concerns. To cost-effectively treat agricultural drainage water from subsided Delta islands to reduce the export of drinking Water Quality Constituents of Concern and mitigate land subsidence through accretion, we studied hybrid coagulation-treatment wetland systems, termed Chemically Enhanced Treatment Wetlands (CETWs). We provide cost estimates and design recommendations to aid broader implementation of this technology. Over a 20-year horizon using a Total Annualized Cost analysis, we estimate treatment costs of $602 to $747 per acre-foot (ac‑ft) water treated, and $36 to $70 per kg dissolved organic carbon (DOC) removed, depending upon source water DOC concentrations for a small 3-acre CETW system. For larger CETW systems scaled for island sizes of 3,500 to 14,000 acres, costs decrease to $108 to $239 per ac-ft water treated, and $11 to $14 per kg DOC removed. We estimated the footprints of CETW systems to be approximately 3% of the area being treated for 4-day hydraulic retention time (HRT) systems, but they would decrease to less than 1% for 1-day HRT systems. CETWs ultimately address several of the Delta’s key internal issues while keeping water treatment costs competitive with other currently available treatment technologies at similar scales on a per-carbon-removed basis. CETWs offer a reliable system to reduce out-going DOC and mercury loads, and they provide the additional benefit of sediment accretion. System costs and treatment efficacy depend significantly on inflow source water conditions, land availability, and other practical matters. To keep costs low and removal efficacy high, wetland design features will need site-specific evaluation.
- 1 supplemental PDF
Effects of Drought and the Emergency Drought Barrier on the Ecosystem of the California Delta
In 2015, the fourth year of the recent drought, the California Department of Water Resources installed a rock barrier across False River west of Franks Tract to limit salt intrusion into the Delta at minimal cost in freshwater. This Barrier blocked flow in False River, greatly reducing landward salt transport by decreasing tidal dispersion in Franks Tract. We investigated some ecological consequences of the Barrier, examining its effects on water circulation and exchange, on distributions of submerged aquatic vegetation (SAV) and bivalves, and on phytoplankton and zooplankton. The Barrier allowed SAV to spread to areas of Franks Tract that previously had been clear. The distributions of bivalves (Potamocorbula and Corbicula) responded to the changes in salinity at time–scales of months for newly settled individuals, to 1 or more years for adults, but the Barrier’s effect was confounded with that of the drought. Nutrients, phytoplankton biomass, and a Microcystis abundance index showed little response to the Barrier. Transport of copepods — determined using output from a particle-tracking model — indicated some intermediate-scale reduction with the Barrier in place, but monitoring data did not show a larger-scale response in abundance. These studies were conducted separately and synthesized after the fact, and relied on reference conditions that were not always suitable for identifying the Barrier’s effects. If barriers are considered in the future, we rcommend a modest program of investigation to replicate study elements, and to ensure suitable reference conditions are available to allow barrier effects to be distinguished unambiguously from other sources of variability.
- 2 supplemental PDFs
- 2 supplemental files
Chemical and Toxicological Effects on Cache Slough after Storm-Driven Contaminant Inputs
Chemical and toxicological testing in the Cache Slough complex (the slough) of the North Delta indicated the aquatic biota are exposed to a variety of wastewater-derived food additives, pharmaceuticals, and personal care products in highest concentration during dry periods, and many insecticides, herbicides and fungicides with peak concentrations after winter rains. The insecticide groups currently known to be of greatest toxicological concern are the pyrethroids and the fiproles (i.e., fipronil and its degradation products). After stormwater runoff enters the system via Ulatis Creek, both pesticide groups attained concentrations that posed a threat to aquatic life. When the commonly used testing species, Hyalella azteca, was placed in Cache Slough, toxicity — and, at times, near total mortality — was seen over at least an 8-km reach of Cache Slough that extended from the uppermost end almost to the junction with the Deep Water Ship Channel. Previous work over many years has shown similar results after other winter storms. However, when H. azteca that carried a mutation providing resistance to pyrethroid pesticides were also deployed in the slough, no ill effects were observed, which provided strong evidence that pyrethroids were responsible for toxicity to the non-resistant strain. Abundant resident H. azteca in Cache Slough carry any of four mutations that provide resistance to pyrethroids. They also carry a mutation that provides resistance to organophosphate pesticides, and likely carbamate pesticides as well. After many years of exposure, sensitive genotypes have been nearly eliminated from the system, and replaced by a population unaffected by many insecticides now in common use. We offer a variety of reasons why this shift to a population with mutant genotypes is of considerable concern, but also note that society has yet to fully consider the ecological and regulatory ramifications of the evolutionary attainment of pollutant resistance.
- 5 supplemental PDFs
Movement and Apparent Survival of Acoustically Tagged Juvenile Late-Fall Run Chinook Salmon Released Upstream of Shasta Reservoir, California
Stakeholder interests have spurred the reintroduction of the critically endangered populations of Chinook Salmon to tributaries upstream of Shasta Dam, in northern California. We released two groups of acoustically tagged, juvenile hatchery, late-fall Chinook Salmon to determine how juvenile salmon would distribute and survive. We measured travel times to Shasta Dam, and the number of fish that moved between locations within Shasta Reservoir. We used mark-recapture methods to determine detection and apparent survival probabilities of the tagged fish as they traveled through five reaches of the Sacramento River from the McCloud River to San Francisco Bay (~590 km) over the two 3-month observation periods. After our first (February) release of 262 tagged fish, 182 fish (70%) were detected at least once at the dam, 41 (16%) were detected at least once downstream of Shasta Dam, and 3 (1%) traveled as far as San Francisco Bay. After the second (November) release of 355 tagged fish, only 4 (1%) were detected at Shasta Dam. No fish were detected below Shasta Dam, so we could not estimate survival for this second release group. The first release of fish was fortuitously exposed to exceptionally high river flows and dam discharges, which may have contributed to the more distant downstream migration and detection of these fish — though other factors such as season, diploid versus triploid, and fish maturation and size may have also contributed to release differences. The reported fish travel times as well as detection and survival rates are the first estimates of juvenile salmon emigration from locations above Shasta Dam in more than 70 years. This information should help inform resource managers about how best to assess juvenile winter-run Chinook Salmon and assist in their reintroduction to watersheds upstream of Shasta Dam.
- 2 supplemental files
The Role of Seed Bank and Germination Dynamics in the Restoration of a Tidal Freshwater Marsh in the Sacramento–San Joaquin Delta
Liberty Island, California, is a historical freshwater tidal wetland that was converted to agricultural fields in the early 1900s. Liberty Island functioned as farmland until an accidental levee break flooded the area in 1997, inadvertently restoring tidal marsh hydrology. Since then, wetland vegetation has naturally recolonized part of the site. We conducted a seed bank assay at the site and found that despite a lack of germination or seedling recruitment at the site, the seed bank contained a diverse plant community, indicating that the site’s continuous flooding was likely suppressing germination. Additionally, the frequency of germinating seeds in the seed bank did not represent the dominant adult plant community. We conducted a cold stratification study to determine if this observed disparity could be explained by seed germination dynamics, and whether germination could be enhanced using a pre-germination cold exposure, particularly for species of concern for wetland restoration. The cold stratification study showed that longer durations of pre-germination cold enhanced germination in Schoenoplectus acutus, but reduced germination in Schoenoplectus californicus, and had no effect on Typha latifolia. Overall, germination of S. californicus and S. acutus was much lower than T. latifolia. Our findings suggest that seeding may not be an effective restoration technique for Schoenoplectus spp., and, to improve restoration techniques, further study is needed to more comprehensively understand the reproduction ecology of important marsh species.