San Francisco Estuary and Watershed Science

Abstracts are not associated with Notes. -- the SFEWS Editors

Ecosystems in the Sacramento–San Joaquin Delta are changing rapidly, as are ecosystems around the world. Extreme events are becoming more frequent and thresholds are likely to be crossed more often, creating greater uncertainty about future conditions. The accelerating speed of change means that ecological systems may not remain stable long enough for scientists to understand them, much less use their research findings to inform policy and management. Faced with these challenges, those involved in science, policy, and management must adapt and change and anticipate what the ecosystems may be like in the future. We highlight several ways of looking ahead—scenario analyses, horizon scanning, expert elicitation, and dynamic planning—and suggest that recent advances in distributional ecology, disturbance ecology, resilience thinking, and our increased understanding of coupled human–natural systems may provide fresh ways of thinking about more rapid change in the future. To accelerate forward-looking science, policy, and management in the Delta, we propose that the State of California create a Delta Science Visioning Process to fully and openly assess the challenges of more rapid change to science, policy, and management and propose appropriate solutions, through legislation, if needed.

Climate change-driven sea level rise and altered precipitation regimes are predicted to alter patterns of salt intrusion within the San Francisco Estuary. A central question is: Can we use existing knowledge and future projections to predict and manage the anticipated ecological impacts? This was the subject of a 2018 symposium entitled “Ecological and Physiological Impacts of Salinization of Aquatic Systems from Human Activities.” The symposium brought together an inter-disciplinary group of scientists and researchers, resource managers, and policy-makers. Here, we summarize and review the presentations and discussions that arose during the symposium. From a historical perspective, salt intrusion has changed substantially over the past 10,000 years as a result of changing climate patterns, with additional shifts from recent anthropogenic effects. Current salinity patterns in the San Francisco Estuary are driven by a suite of hydrodynamic processes within the given contexts of water management and geography. Based on climate projections for the coming century, significant changes are expected in the processes that determine the spatial and temporal patterns of salinity. Given that native species—including fishes such as the Delta Smelt and Sacramento Splittail—track favorable habitats, exhibit physiological acclimation, and can adaptively evolve, we present a framework for assessing their vulnerability to altered salinity in the San Francisco Estuary. We then present a range of regulatory and structural management tools that are available to control patterns of salinity within the San Francisco Estuary. Finally, we identify major research priorities that can help fill critical gaps in our knowledge about future salinity patterns and the consequences of climate change and sea level rise. These research projects will be most effective with strong linkages and communication between scientists and researchers, resource managers, and policy-makers.

The Fall Midwater Trawl Survey has provided data on aquatic organisms in the San Francisco Estuary for over 5 decades. In 2014–2015, a study was conducted to investigate and quantify the efficiency of this trawl for catching the endangered fish species Delta Smelt (Hypomesus transpacificus). In an analysis based on that study, we calculated retention probability—the probability that a Delta Smelt is retained in the cod end of the trawl—as a function of fish length, and fit a selectivity curve that reflected the relationship between size and retention. Here, we return to the same gear efficiency study and further utilize the data set by (1) fitting selectivity curves for three additional pelagic fish species: Threadfin Shad (Dorosoma petenense), American Shad (Alosa sapidissima), and Mississippi Silverside (Menidia beryllina); (2) refitting the selectivity curve for Delta Smelt to incorporate between-haul variability; and (3) calculating the lengths of 50% and 95% retention in order to characterize and compare the resulting selectivity curves. We also present retention data on age-0 Striped Bass (Morone saxatilis), all of which were retained in the cod end. We found that Threadfin Shad, American Shad, and Delta Smelt are 95% retained at 45-, 49-, and 61-mm fork length, respectively. Because data were limited for Mississippi Silverside, American Shad, and age-0 Striped Bass, we used body shape—in conjunction with retention data—to develop hypotheses about selectivity based on whether each species’ body shape resembles that of Threadfin Shad, which are more deep-bodied and laterally compressed, or Delta Smelt, which are more fusiform. We also found that retention-at-length was more variable for Delta Smelt than for Threadfin Shad, potentially because length is a good predictor of retention in deep-bodied, laterally compressed fish, whereas maximum girth is a better predictor of retention in fusiform fish.

Survival of juvenile salmonids in the Sacramento–San Joaquin Delta (Delta) varies by migration route, and thus the proportion of fish that use each route affects overall survival through the Delta. Understanding factors that drive routing at channel junctions along the Sacramento River is therefore critical to devising management strategies that maximize survival. Here, we examine entrainment of acoustically tagged juvenile Chinook Salmon into Sutter and Steamboat sloughs from the Sacramento River. Because these sloughs divert fish away from the downstream entrances of the Delta Cross Channel and Georgiana Slough (where fish access the low-survival region of the interior Delta), management actions to increase fish entrainment into Sutter and Steamboat sloughs are being investigated to increase through-Delta survival. Previous studies suggest that fish generally “go with the flow”—as net flow into a divergence increases, the proportion of fish that enter that divergence correspondingly increases. However, complex tidal hydrodynamics at sub-daily time-scales may be decoupled from net flow. Therefore, we modeled routing of acoustic tagged juvenile salmon as a function of tidally varying hydrodynamic data, which was collected using temporary gaging stations deployed between March and May of 2014. Our results indicate that discharge, the proportion of flow that entered the slough, and the rate of change of flow were good predictors of an individual’s probability of being entrained. In addition, interactions between discharge and the proportion of flow revealed a non-linear relationship between flow and entrainment probability. We found that the highest proportions of fish are likely to be entrained into Steamboat Slough and Sutter Slough on the ascending and descending limbs of the tidal cycle, when flow changes from positive to negative. Our findings characterize how patterns of entrainment vary with tidal flow fluctuations, providing information critical for understanding the potential effect of management actions (e.g., fish guidance structures) to modify routing probabilities at this location.

Resource managers often rely on long-term monitoring surveys to detect trends in biological data. However, no survey gear is 100% efficient, and many sources of bias can be responsible for detecting or not detecting biological trends. The SmeltCam is an imaging apparatus developed as a potential sampling alternative to long-term trawling gear surveys within the San Francisco Estuary, California, to reduce handling stress on sensitive species like the Delta Smelt (Hypomesus transpacificus). Although believed to be a reliable alternative to closed cod-end trawling surveys, no formal test of sampling efficiency has been implemented using the SmeltCam. We used a paired deployment of the SmeltCam and a conventional closed cod-end trawl within the Napa River and San Pablo Bay, a Bayesian binomial N-mixture model, and data simulations to determine the sampling efficiency of both deployed gear types to capture a Delta Smelt surrogate (Northern Anchovy, Engraulis mordax) and to test potential bias in our modeling framework. We found that retention efficiency—a component of detection efficiency that estimates the probability a fish is retained by the gear, conditional on gear contact—was slightly higher using the SmeltCam (mean = 0.58) than the conventional trawl (mean = 0.47, Probability SmeltCam retention efficiency > trawl retention efficiency = 94%). We also found turbidity did not affect the SmeltCam’s retention efficiency, although total fish density during an individual tow improved the trawl’s retention efficiency. Simulations also showed the binomial model was accurate when model assumptions were met. Collectively, our results suggest the SmeltCam to be a reliable alternative to sampling with conventional trawling gear, but future tests are needed to confirm whether the SmeltCam is as reliable when applied to taxa other than Northern Anchovy over a greater range of conditions.