San Francisco Estuary and Watershed Science

Historically, Chinook Salmon in the California Central Valley reared in the vast wetlands of the Sacramento–San Joaquin Delta. However, more than 95% of floodplain, riparian, and wetland habitats in the Delta have become degraded because of anthropogenic factors such as pollution, introduced species, water diversions, and levees. Despite pronounced habitat loss, previous work using otolith reconstructions has revealed that some juvenile salmon continue to successfully rear for extended periods in the Delta. However, the extent to which the Delta functions to promote salmon growth relative to other habitats remains unknown. In this study, we integrated otolith microstructure (daily increment count and width) and strontium isotope (87Sr/86Sr) records to fill this critical knowledge gap by comparing the growth of natural-origin fall-run Chinook Salmon from the American River that reared in the Delta with those that remained in their natal stream. Using generalized additive models, we compared daily otolith growth rates among rearing habitats (Delta vs. American River) and years (2014 to 2018), encompassing a range of hydrologic conditions. We found that juvenile Chinook Salmon grew faster in the Delta in some years (2016), but slower in the Delta during drought conditions (2014 to 2015). The habitat that featured faster growth rates varied within and among years, suggesting the importance of maintaining a habitat mosaic for juvenile salmonids, particularly in a dynamic environment such as the California Central Valley. Linking otolith chemistry with daily growth increments provides a valuable approach to explore the mechanisms governing interannual variability in growth across habitat types, and a useful tool to quantify the effects of large-scale restoration efforts on native fishes.

Steelhead (Oncorhynchus mykiss expressing an anadromous life history) in the Sacramento and San Joaquin rivers and their tributaries in California’s Central Valley (CCV) belong to a Distinct Population Segment (DPS) that is listed as threatened under the US Endangered Species Act. Although contemporary management and recovery plans include numerous planned and ongoing efforts seeking to aid in DPS recovery—such as gravel augmentation, manipulation of spring flows, and restoration of rearing and spawning habitat—a paucity of data precludes the possibility of evaluating the effect of these actions on populations of Steelhead in CCV streams. Knowledge gaps relating to historic and current abundance, population-specific ratios of resident and anadromous life-history expression, and the influence of hatchery-reared fish remain largely unaddressed. This is partly a result of aspects of Steelhead biology that make them difficult to monitor, including the multitude of factors that contribute to the expression of anadromy, polymorphic populations, and migration periods that coincide with challenging field conditions. However, these gaps in understanding are also partly the result of an institutional focus on Chinook Salmon (Oncorhynchus tshawytscha) and a pervasive notion that actions benefiting Chinook populations will also benefit Steelhead populations. To evaluate these gaps and to suggest approaches for assessing DPS recovery actions, we review available data and existing monitoring efforts, and consider the actions necessary to inform the development of targeted O. mykiss monitoring programs. Current management and recovery goals focus on abundance estimates of Steelhead only, yet current monitoring is insufficient for reliable estimates. We argue that a reallocation of monitoring resources to better understand the interaction between resident O. mykiss and Steelhead would provide better data to estimate the vital rates needed to evaluate the effects of recovery actions.

Fish monitoring gears rarely capture all available fish, an inherent bias in monitoring programs referred to as catchability. Catchability is a source of bias that can be affected by numerous aspects of gear deployment (e.g., deployment speed, mesh size, and avoidance behavior). Thus, care must be taken when multiple surveys—especially those using different sampling methods—are combined to answer spatio-temporal questions about population and community dynamics. We assessed relative catchability differences among four long-term fish monitoring surveys from the San Francisco Estuary: the Bay Study Otter Trawl (BSOT), the Bay Study Midwater Trawl (BSMT), the Fall Midwater Trawl (FMWT), and the Suisun Marsh Otter Trawl (SMOT). We used generalized additive models with a spatio-temporal smoother and survey as a fixed effect to predict gear-specific estimates of catch for 45 different fish species within large and small size classes. We used estimates of the fixed effect coefficients for each survey (e.g., BSOT) relative to the reference gear (FMWT) to develop relative measures of catchability among taxa, surveys, and fish-size classes, termed the catch-ratio. We found higher relative catchability of 27%, 22%, and 57% of fish species in large size classes from the FMWT than in the BSMT, BSOT, or SMOT, respectively. In the small size class, relative catchability was higher in the FMWT than the BSMT, BSOT, or SMOT for 50%, 18%, and 25% of fish species, respectively. As expected, relative catchability of demersal species was higher in the otter trawls (BSOT, SMOT) while relative catchability of pelagic species was higher in the midwater trawls (FMWT, BSMT). Our results demonstrate that catchability is a source of bias among monitoring efforts within the San Francisco Estuary, and assuming equal catchability among surveys, species, and size classes could result in significant bias when describing spatio-temporal patterns in catch if ignored.

Pathogen surveillance must be part of any population supplementation or reintroduction program for the conservation of threatened and endangered species. The unintended transmission of pathogens can have devastating effects on these already at-risk populations or the natural ecosystem at large. In the San Francisco Estuary (estuary), abundance of the endemic Delta Smelt (Hypomesus transpacificus) has declined to the point where regulatory managers are preparing to augment the wild population using fish propagated in a hatchery to prevent species extinction. Although disease is not an overt cause of population decline, comprehensive pathogen presence and prevalence data are lacking. Here, we performed a pilot study that applied molecular assays originally developed in salmonids to assess the presence of a wide variety of pathogens in the gill tissue of cultured and wild Delta Smelt—as well as cultured fish—deployed in enclosures in the estuary. We found the assays to be highly sensitive, and observed positive detections of a single pathogen, Ichthyophthirius multifiliis, in 13% of cultured Delta Smelt. We also detected ten other pathogens at very low levels in cultured, enclosure-deployed, and wild Delta Smelt that likely represent the ambient pathogen composition in the estuary (as opposed to actual infection). Our results corroborate previous work that cultured Delta Smelt do not appear to present a high risk for pathogen transmission during population supplementation or reintroduction. However, the molecular pathogen screening assays tested here have great utility as an early warning system indicator of when further diagnostic testing might be necessary to limit the extent and frequency of disease outbreaks; their utility will be further increased once they are customized for Delta Smelt.

Organic matter in soils and sediments derives from a mixture of biological origins, often making it difficult to determine inputs from individual sources. Complicating the determination of source inputs to soil and sedimentary organic matter (OM) is the fact that physical and microbial processes have likely modified the initial composition of these sources. This study focused on identifying the composition of watershed-derived OM to better understand inputs to inland waters and improve our ability to resolve between terrigenous and aquatic sources in downstream systems, such as estuaries and coasts. We surveyed OM sources from the Yuba River watershed in northern California to identify specific biomarkers that represent aquatic and terrigenous OM sources. Multiple classes of organic proxies—including sterols, fatty acids (FA), lignin phenols and stable carbon and nitrogen isotope values (δ¹³C, δ¹⁵N)—were measured in soils, vegetation, charcoal, and freshwater plankton to characterize representative source endmembers. Sterols—including 27-nor-24-cholesta-5,22-dien-3β-ol, cholesta-5,22-dien-3β-ol, 24-methylcholesta-5,22-dien-3β-ol and cholesta-5-en-3β-ol, and positive δ¹⁵N values—were associated with aquatic OM (plankton, suspended particulate OM), whereas lignin phenols, long chain FA, and diacids characterized terrigenous sources (soils, charcoal, vegetation). Trends in organic carbon and biomarker signatures in soil samples showed a response to environmental disturbance (i.e., mining, agriculture) through an inverse relationship between OM content and land use. Results from this study demonstrate the utility of multi-biomarker studies for distinguishing between OM from different sources and land uses, offering new insights for biogeochemical studies in aquatic systems.