Science activities

The Diet and Condition study has provided information on the food habits of pelagic fishes in the estuary since 2005. We focus on the temporal and spatial differences in diet composition and feeding success of Delta Smelt, Striped Bass, Threadfin Shad, Longfin Smelt, Mississippi Silversides, and American Shad. Need Data from this project has been used to inform the Fall Low Salinity Habitat Program (FLaSH), Directed Outflow Project (DOP), and Management, Analysis and Synthesis Team reports, as well as life history models used for the conservation of fish and their habitats. Understanding what prey are utilized for food in the context of available prey, with the associated body-condition of fish, helps clarify the existence and timing of food limitation for young pelagic fish in the estuary. This work began as part of the Pelagic Organism Decline investigations and continued as a contributor to FLaSH investigations during which we in collaborated with the Fish Health Monitoring Project. Recently staff completed Longfin Smelt diet investigations as part element #296 (Longfin Smelt Investigations - in response to a litigation agreement) that will also contribute to the Longfin Smelt Conceptual Model and Synthesis effort (element #320). Finally, we will process Delta Smelt diets from investigations prompted by the Delta Smelt Resilience Strategy, and as part of the DOP. Objectives 1. What are the diets of pelagic fishes (especially Delta Smelt and Longfin Smelt) in the estuary and do they vary regionally or temporally? 2. Is there evidence of reduced feeding success spatially or temporally in the estuary? 3. Is feeding success associated with changes in relative weight or condition of fish? 4. Is there seasonal and regional overlap of diets between species (with a focus on age-0 Delta Smelt, Longfin Smelt, Striped Bass, Prickly Sculpin, Pacific Herring, and Threadfin Shad)?

California Department of Fish and Wildlife (CDFW) conducts the 20-mm Survey annually to monitor the distribution and relative abundance of larval and juvenile Delta Smelt (Hypomesus transpacificus) in the upper San Francisco Bay Estuary. The survey began in 1995 and supplies near real-time catch data to water and fisheries managers as part of an adaptive management strategy to limit the risk of Delta Smelt entrainment during water exports Data collected: temperature, electro-conductivity, water transparency, turbidity, water volume, tidal stage, fish, and zooplankton.

The San Francisco Bay Study (Bay Study) was established in 1980 to determine the effects of freshwater outflow on the abundance and distribution of fish and mobile crustaceans in the San Francisco Estuary, primarily downstream of the Sacramento-San Joaquin Delta. Sampling ranges from south of the Dumbarton Bridge in South San Francisco Bay, to just west of Alcatraz Island in Central San Francisco Bay, throughout San Pablo and Suisun bays, north to the confluence Steamboat and Cache sloughs on the Sacramento River, and east to Old River Flats on the San Joaquin River. The open water or boat survey samples 52 stations monthly: 35 original stations, 7 stations added in 1988, 4 stations added in 1991, and 6 stations added in 1994. The study included a beach seine survey, discontinued in 1987, and a shore-based ringnet survey for crabs, discontinued in 1994. The Bay Study uses a 42-foot stern trawler to sample with 2 trawl nets at each open water station. The otter trawl, which samples demersal fishes, shrimp, and crabs, is towed against the current at a standard engine rpm for 5 minutes then retrieved. The midwater trawl, which samples pelagic fishes, is towed with the current at a standard engine rpm for 12 minutes and retrieved obliquely such that all depths are sampled equally. The open water survey included a plankton net that sampled larval fish and crustaceans, but this was discontinued in 1989. Fish, caridean shrimp, and brachyuran crabs are identified, measured, and counted. Shrimp and crabs are also sexed. Sampling effort is quantified (i.e. distance towed, volume of water filtered) and salinity, water temperature, Secchi depth, and station depth are measured;wave height, tide, cloud cover, and tow direction are categorized. The length, catch, and effort data is used to calculate catch-per-unit-effort (CPUE) by species and age class. The CPUE data is used to calculate monthly and annual abundance indices, which are used to track seasonal and annual population trends. Important factors that control or regulate abundance and distribution of fish and mobile crustaceans in the estuary include salinity, temperature, freshwater outflow, ocean temperature, upwelling, and surface currents, primary and secondary productivity, and introduced species. We are interested in how species respond to changes in the physical environment on several temporal scales - seasonal, annual, decadal, and longer. We produce several annual Status and Trends reports that summarize recent changes for the most commonly collected species. These reports are published in the Spring issue of the IEP Newsletter, which can be found at IEP Newsletter. 

Description

Invasive submerged aquatic species (SAV) greatly impact habitat for endangered species in the Delta. In the past decade, we have seen a huge increase in SAV cover and an influx of new invasive species like ribbonweed. This study will build species distribution models (SDM) for SAV using predictors such as water speed, depth, salinity from the UnTRIM hydrodynamic model, turbidity derived from Sentinel-2 and temperature derived from ECOSTRESS satellite imagery. The SDMs will be used to study the effect of flow management actions and restoration activities on SAV distribution. SAV community data collected in the field (available on EDI) will be analyzed to study if the SAV community composition has changed from 2007-08 to present time. The same dataset will be used to explore if the SAV SDM can be refined based on species presence data to see if there are significant differences in SDMs of individual SAV species.

Need

Invasive aquatic vegetation has been identified as a major concern in the IEP Science Strategy document and a topic meriting more study. Assessing the effects of flow alteration management actions on the Delta is also a recommended key topic of research. This study furthers both these objectives. It complements ongoing projects such as the water primrose ecoengineering project (PEN #348), which is similarly building an SDM for Ludwigia spp., determining plant characteristics that enable Ludwigia invasion and mapping invasion risk for the remnant Delta marshes. The work also builds off the conclusions of the Sentinel project which mapped the temporal phenological signal of SAV in the Delta. The results of this study will help design restorations to be more resistant to invasion, plan for climate change impacts, and predict invasion risk in Delta regions that are being reconnected tidally to the Delta waterways network through current and future restoration projects.

Objectives

• Which environmental factors and habitat characteristics are associated with SAV?
• What is the SAV community structure and has it shifted since 2007?
• Is there sufficient data to determine SAV species-specific SDM within the SAV community SDM? How different are SDMs of individual species?
• How might climate change alter the distribution of SAV species and assemblages into the future?  Will future conditions constrain or expand SAV distribution? Can we simulate SAV distribution under other scenarios such as ecorestore projects?

The California Department of Parks and Recreation, Division of Boating and Waterways (DBW) operates a control program for both floating and submerged IAV. This project is an IEP Synthesis effort that will integrate a historical and ongoing dataset of the Delta IAV coverage and DBW IAV treatment records for the past 14 years. This study seeks to determine if treatment efficacy differs across space (e.g., different habitat types) and time. It will assess the impact of IAV control effort on the distribution, growth rate, spread and persistence, and species richness and community composition of the IAV communities. Gaining such understanding on the relationship between IAV treatment and IAV distribution, coverage, and species composition is an urgent management issue for the Delta, given the sharp rise in coverage of IAV from 9000 acres in 2004 to 12,500 acres in 2014 and its likely impact on the shallow-water habitat.

The objectives of this study are:

1.     What are the rates and patterns of spread for floating IAV? Do the rates of spread into water or marsh differ? Where do these floating IAV persist and what mechanisms can be linked to their ability of persistence? If there are specific locations that promote persistence, for example over-wintering nurseries, could they be targeted for removal?

2.     Has treatment for both water primrose and water hyacinth been successful in reducing species cover over the last 15 years? If so, was treatment effective in reducing density, reducing growth rates, slowing down expansion, and therefore changing distribution of target species? Does treatment efficacy change over different habitats and through time?

3.     Does herbicide control of target submerged IAV species reduce density, growth rates, slow down expansion and persistence, and change submerged community composition towards native species? Does treatment efficacy change over different habitats and through time? Does it change the patch size and distribution?