SFEWS Vol. 20, Issue 1 | March 2021
#CentralValley #ChinookSalmon #otolithchemistry #Steelhead #monitoring #surveys #catchability #detectionefficiency #DeltaSmelt #supplementation #Ich #pathogens #organiccarbon #stablecarbon #nitrogen #inputs #YubaRiver #watersheds
Variation in Juvenile Salmon Growth Opportunities Across a Shifting Habitat Mosaic
Coleman et al. 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). 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.
Counting the Parts to Understand the Whole: Rethinking Monitoring of Steelhead in California’s Central Valley
Eschenroeder et al. argue that a reallocation of monitoring resources to better understand the interaction between resident and anadromous Steelhead would provide better data to estimate the vital rates needed to evaluate the effects of recovery actions.
Relative Bias in Catch Among Long-Term Fish Monitoring Surveys Within the San Francisco Estuary
Huntsman et al. assessed relative catchability differences among four long-term fish monitoring surveys from the San Francisco Estuary. Their 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.
Investigation of Molecular Pathogen Screening Assays for Use in Delta Smelt
Gille et al. conducted 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. Although disease is not an overt cause of population decline of Delta Smelt in the San Francisco Estuary, comprehensive pathogen presence and prevalence data are lacking, and unintended transmission of pathogens can have devastating effects on populations already at-risk or on the natural ecosystem at large. Their results corroborate previous work that cultured Delta Smelt do not appear to present a high risk for pathogen transmission during population supplementation or reintroduction.
Multi-Biomarker Analysis for Identifying Organic Matter Sources in Small Mountainous River Watersheds: A Case Study of the Yuba River Watershed
Pondell and Canuel's study focused on identifying the composition of watershed-derived organic matter (OM). To better understand inputs to inland waters and improve distinguish between terrigenous and aquatic sources in downstream systems, such as estuaries and coasts, they surveyed OM sources from the Yuba River watershed in northern California to identify specific biomarkers that represent aquatic and terrigenous OM sources. Results 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.
Volume 16, Issue 1, 2018
Improving Multi-Objective Ecological Flow Management with Flexible Priorities and Turn-Taking: A Case Study from the Sacramento River and Sacramento–San Joaquin Delta
Management of the Sacramento River and Sacramento–San Joaquin Delta (SRD) is one of California’s greatest challenges, requiring trade-offs between valued components that serve a multiplicity of conflicting purposes. Trade-offs do not signal a failure to create clever enough models, or scenarios that find a single optimal solution. Rather, an optimal solution that meets multiple objectives does not exist. We demonstrate an improved method for multiple-objective allocation of water: “turn-taking” optimization (TTO) within a multi-model cloud computing framework. We apply TTO to an array of physical hydrologic models that are linked with the Ecological Flows Tool (EFT): a multi-species decision support framework to evaluate how specific components of the flow regime promote and balance favorable habitat conditions for 15 representative species and 31 indicators within the SRD. Applying the TTO approach incorporates the existing modelled representation of socio-economic water management criteria, priorities, and constraints — and optimizes water-release patterns each water year using a dynamically shifting set of EFT indicators. Rather than attempting to optimize conditions for all ecological indicators every year, TTO creates flexibility and opportunities for different indicators to be successful in different years, informed by the frequency with which each species’ ecological needs should be met. As an individual EFT indicator is successful in a particular year, its priority in one or more subsequent years is reduced (and vice versa). Comparing TTO to a Reference Case scenario based on current management practices, 12 EFT indicators are improved, 14 show no change, and 5 show a reduction in suitability. When grouped into nine species and life-history groups, performance improved in four (late-fall-run Chinook, winter-run Chinook, spring-run Chinook, and Fremont cottonwood), did not change in four (fall-run Chinook Salmon, Delta Smelt, Splittail, and Longfin Smelt), and was worse in one group (Steelhead).
Although brackish marsh has been the subject of decades of research, tidal freshwater regions are still poorly understood. To provide insight into spatial and temporal dynamics of nutrients, physical conditions, and the plankton community in freshwater tidal habitat, we investigated from 2011 to 2014 a remnant freshwater tidal slough complex located in the Sacramento–San Joaquin Delta region of the San Francisco Estuary. Our results suggest that the tidal slough complex showed different seasonal nutrient, physical, and biological conditions when compared to a relatively homogenous adjacent large river channel, the Sacramento River. The tidal slough complex also showed substantial spatial variability in habitat conditions compared to nearby main river channels. Nutrient dynamics in the tidal slough complex appear to be driven by a complex suite of factors, including inflow from upstream tributaries and tidal flows from the downstream reach of the Sacramento River. Chlorophyll a in the tidal sloughs responded more strongly to upstream flow pulses than other environmental variables. The tidal slough complex generated significantly higher levels of chlorophyll a than other freshwater regions of the Delta. The 2011 and 2012 results were especially notable because unusually large flow pulses through the tidal slough complex appear to have contributed to rare phytoplankton blooms in downstream areas of the Delta during the fall months. Moreover, the 2012 flow pulse stimulated higher trophic levels, because significantly higher levels of zooplankton were in the tidal slough complex after the flow event. These results have important implications for our understanding of the functioning of freshwater tidal habitat, and for the design of potential restoration projects in these regions.
Central Valley Spring-Run Chinook Salmon and Ocean Fisheries: Data Availability and Management Possibilities
Central Valley spring-run Chinook Salmon (CVSC) are designated threatened by state and federal authorities. Although CVSC are caught in ocean fisheries, their harvest is not actively managed, because it is assumed that measures currently in place to protect endangered Sacramento River winter-run Chinook Salmon (SWRC) will also sufficiently protect CVSC. Recoveries of tags and genetically-identified CVSC suggest these fish have a more northerly distribution than SRWC. Further, escapement data and cohort reconstructions suggest that CVSC mature later than SRWC. Thus, regulations (time/area restrictions and minimum size limits) crafted to protect SRWC alone may not adequately protect CVSC; on the other hand, regulations to constrain impacts on Klamath River and California coastal Chinook Salmon populations may also reduce impacts on CVSC. Trends in CVSC escapement were deemed acceptable in recent status updates, but concerns remain because of the negative effects caused by recent drought and ocean conditions. Should more active management of CVC be desired, current options are limited. The most promising approach is based on estimating age-specific ocean fishing mortality rates by using cohort reconstructions applied to tagged Chinook Salmon that originate from the Feather River Hatchery. At a minimum, ocean fishing mortality rates could be monitored and compared to proxy thresholds. If reference harvest rates were established, harvest models could be developed to predict how CVSC would be affected by fishing regulations, similar to the way fall-run Chinook Salmon fisheries are evaluated. Abundance forecasts would require improved juvenile production data (e.g., from genetic sampling of juvenile emigrants), since sibling-based forecasts commonly used for fall-run Chinook Salmon would not be available in time for pre-season planning. It is unclear if ocean fishing mortality rate estimates derived from hatchery proxies for natural-origin fish are truly representative, but existing data do not demonstrate obvious differences in ocean distribution or size-at-age fish. Substantial new investments in tagging or sampling would be needed to directly estimate ocean fishing mortality rates for natural-origin CVSC. Establishing specific harvest targets or limits for CVSC requires an improved understanding of production throughout their life cycle through juvenile production estimates and long-term information on spawner age structure.