SFEWS Vol. 20, Issue 2 | June 2022
Climate Change Impacts on San Francisco Estuary Aquatic Ecosystems: A Review
Climate change is intensifying the effects of multiple interacting stressors on aquatic ecosystems, particularly in estuaries. In the San Francisco Estuary, signals of climate change are apparent in the long-term monitoring record. Here we synthesize current and potential future climate change effects on three main ecosystems (floodplain, tidal marsh, and open water) in the upper estuary and two representative native fishes that commonly occur in these ecosystems (anadromous Chinook Salmon, Oncorhynchus tshawytscha and estuarine resident Sacramento Splittail, Pogonichthys macrolepidotus).
Considerations for the Development of a Juvenile Production Estimate for Central Valley Spring-Run Chinook Salmon
Effective species management depends on accurate estimates of population size. There are, however, no estimates of annual juvenile production for Central Valley spring-run Chinook Salmon (“spring run”), a highly imperiled species in California, making it difficult to evaluate population status and effectively manage key issues such as entrainment of this species at water diversions. In recognition of this critical information gap, we initiated an effort to develop a juvenile production estimate (JPE) for spring run, defined here as an annual forecast of the number of juvenile Central Valley spring-run Chinook Salmon that enter the Sacramento–San Joaquin Delta (“Delta”) from the Sacramento Valley.
Machine Learning Forecasts to Reduce Risk of Entrainment Loss of Endangered Salmonids at Large-Scale Water Diversions in the Sacramento–San Joaquin Delta, California
Incidental entrainment of fishes at large-scale state and federal water diversion facilities in the Sacramento-San Joaquin Delta, California, can trigger protective management actions when limits imposed by environmental regulations are approached or exceeded. These actions can result in substantial economic costs, and likewise they can affect the status of vulnerable species. Here, we examine data relevant to water management actions during January–June; the period when juvenile salmonids are present in the Delta.
Gill Net Selectivity for Fifteen Fish Species of the Upper San Francisco Estuary
Gill-net size selectivity for 15 fish species occurring in the upper San Francisco Estuary was estimated from a data set compiled from multiple studies which together contained 7,096 individual fish observations from 882 gill net sets. The gill nets considered in this study closely resembled the American Fisheries Society’s recommended standardized experimental gill nets for sampling inland waters. Relationships between gill-net mesh sizes and the sizes for each fish species retained in them were estimated indirectly using generalized linear modeling and maximum likelihood.
Nutrient and Trace Element Contributions from Drained Islands in the Sacramento–San Joaquin Delta, California
Inventorying nutrient and trace element sources in the Sacramento-San Joaquin Delta (the Delta) is critical to understanding how changes—including alterations to point source inputs such as upgrades to the Sacramento Regional Wastewater Treatment Plant (SRWTP) and landscape-scale changes related to wetland restoration—may alter the Delta’s water quality. While island drains are a ubiquitous feature of the Delta, limited data exist to evaluate island drainage mass fluxes in this system. To better constrain inputs from island drains, we measured monthly discharge along with nutrient and trace element concentrations in island drainage on three Delta islands and surrounding rivers from June 2017 to September 2018.
Volume 16, Issue 2, 2018
[Abstracts are not presented for essays. -The SFEWS Editors.]
The salt marsh harvest mouse (SMHM, Reithrodontomys raviventris) is an endangered species, endemic to the San Francisco Estuary. Despite being protected for almost half a century and being included in a large number of recovery, restoration, and management plans, significant data gaps hinder conservation and management of the species, a challenge further complicated by developing threats such as climate change. In this review, we present the current state of knowledge; highlight research gaps on habitat requirements and distribution, taxonomic status and genetic structure, physiology, reproduction and demographics, population dynamics, and behavior and community interactions; and present an overview of threats to the species. Our review indicates that substantial data gaps exist; although some aspects of SMHM ecology, such as habitat use, have been addressed extensively, others, such as the effects of environmental contamination, are largely unaddressed. We suggest that conservation and restoration-planning processes consider experimental approaches within restoration designs to address these deficiencies. Continued investment in basic and applied SMHM ecology to collect baseline and long-term data will also be beneficial. Additionally, further coordination among managers and researchers can facilitate more effective responses to uncertainties and emerging threats, especially climate change, which threatens the SMHM and its habitat throughout its range.
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California’s salmonids are at the southern limits of their individual species’ ranges, and display a wide diversity of strategies to survive in California’s highly variable climate. Land use changes after statehood in 1850 eliminated important habitats, or blocked access to them, and reduced the abundance, productivity, and distribution of California’s salmon. Habitat simplification, fishing, hatchery impacts, and other stressors led to the loss of genetic and phenotypic (life history, morphological, behavioral, and physiological) diversity in salmonids. Limited diversity and habitat loss left California salmon with reduced capacity to cope with a variable and changing climate. Since 1976, California has experienced frequent droughts, as were common in the paleo-climatological record, but rare in the peak dam-building era of 1936–1976. Increasing temperatures and decreasing snowpacks have produced harsher conditions for California’s salmon in their current habitats than they experienced historically. The most likely way to promote salmon productivity and persistence in California is to restore habitat diversity, reconnect migratory corridors to spawning and rearing habitats, and refocus management to replenish the genetic and phenotypic diversity of these southernmost populations.
While our knowledge of the range of survival that outmigrating juvenile Chinook Salmon experience in different routes of the Sacramento–San Joaquin Delta has increased in recent years, few studies have focused on their survival during outmigration in the Yolo Bypass, the Delta’s primary floodplain. The Yolo Bypass floodplain provides valuable rearing habitat and growth benefits to juvenile fish in flood years, and efforts are underway to improve access to the Yolo Bypass and the Toe Drain, its perennial navigation channel, under a broader range of flows and river stages than is currently possible. We compared variation in transit time, and estimated survival between different release groups of fish outmigrating through the Yolo Bypass or through migratory routes in the lower Sacramento River. Tagged late-fall-run juvenile Chinook Salmon were released in both systems in 2012 and 2013. There was no significant difference between the estimated cumulative probability of survival in the Yolo Bypass system and combined routes of the lower Sacramento River in either year (0.312–0.629 vs. 0.342–0.599, 95% credible interval in 2012; and 0.111–0.408 vs. 0.240–0.407, 95% credible interval in 2013, respectively). The Yolo Bypass had a higher coefficient of variation (CV) in travel time relative to the lower Sacramento River routes in both years (0.34 vs. 0.29 in 2012, and 0.44 vs. 0.34 in 2013). This work suggests that in relatively low water years, the estimated survival of outmigrating juvenile Chinook Salmon in the Toe Drain is directly comparable to routes in the lower Sacramento River, and that metrics of behavioral diversity in movement behavior can and should be incorporated into future telemetry studies.
The Effect of Submersed Aquatic Vegetation on Invertebrates Important in Diets of Juvenile Largemouth Bass Micropterus salmoides
A suite of submersed aquatic vegetation (SAV) species, and especially Brazilian Waterweed (Egeria densa), has proliferated rapidly in California’s Sacramento–San Joaquin Delta. This expansion is concurrent with population declines in native fish species and increases in many non-native fish species, including Largemouth Bass Micropterus salmoides. In this study, we investigated the effect of SAV species composition and E. densa specifically on macroinvertebrate communities and juvenile Largemouth Bass diets. Invertebrate communities differed across sites in the Delta, driven primarily by changes in abundance of the amphipod Hyalella sp., oligochaetes, ostracods, and insect larvae of the family Chironomidae. Juvenile Largemouth Bass consistently consumed SAV-associated invertebrates, and preferentially consumed larger taxa, when available. Gut fullness of juvenile Largemouth Bass was lowest in sites dominated by E. densa, although there was no clear mechanism for this difference. However, SAV species composition had little effect on abundance of Hyalella sp., chironomid larvae, or damselfly naiads, prey items commonly consumed by juvenile Largemouth Bass. Our results suggest that E. densa does not provide a qualitative increase in macroinvertebrate food for fishes compared to other SAV species.
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Evaluation of the Delta Simulation Model-2 in Computing Tidally Driven Flows in the Sacramento-San Joaquin Delta
We investigate the fidelity of the Delta Simulation Model-2 (DSM2), a one-dimensional branched network hydrodynamics solver, which is used to model water quality and ecology in the Sacramento–San Joaquin Delta estuary. We find that while DSM2 reproduces the total flows well, it does not accurately represent the harmonic components of the tides and tidal modulation of subtidal flow. The inaccurate representation of tidal dynamics affects prediction of subtidal flows, flow splits at key junctions, and salinity. These deviations are the result of coarse spatial and temporal representation of tides as well as unrepresented estuarine physical processes. We propose and evaluate two types of schemes intended to improve fidelity: modifying the model domain and specifying fine grid and boundary conditions, and incorporating and parameterizing more complex physical processes into the 1-D model. We also develop a comprehensive protocol to evaluate the model in which we assess the fidelity of model results. In this protocol, we also include a decomposition of the model error into a systematic component because of model representation, and an unsystematic component, which includes errors from both unmodeled physical processes and data precision. Our analysis reveals that these recommendations would be effective provided they can be incorporated with model recalibration. Both our proposed schemes and the model evaluation process will be useful in analyzing models of networked surface water systems such as the Delta in which the distribution of observations is spatially inhomogeneous.
- 1 supplemental PDF