Directed Outflow Project Lower Trophic Study

The upper San Francisco Bay Estuary and Sacramento San Joaquin Delta is critical habitat for the endemic Delta Smelt (Hypomesus transpacificus), an endangered planktivorous fish with an annual, semi-anadromous life cycle. Freshwater outflow actions during the fall season are hypothesized to improve Delta Smelt habitat and therefore Delta Smelt condition before the spawning life stage. As part of efforts to evaluate the effectiveness of such actions to benefit Delta Smelt populations, various studies were initiated by the U.S. Bureau of Reclamation under the Directed Outflow Project (DOP). One component of the DOP was to evaluate how the Fall X2 freshwater outflow action changed the lower trophic prey available to Delta Smelt. The action is hypothesized to change abiotic and biotic aspects that can benefit Delta Smelt habitat by using freshwater outflow to maintain the position of X2 (defined as the distance in kilometers from the Golden Gate Bridge to the tidally averaged 2 ppt salinity isohaline) at around 70 km during wet or above normal precipitation water years. This moves the low salinity zone (0.5 - 6 ppt) further seaward into Suisun Bay which increases the area of preferred Delta Smelt habitat. Field sampling began the September of 2017 and occurred bi-weekly through the end of November, paired with the U.S. Fish and Wildlife Service Enhanced Delta Smelt Monitoring program. Three random sites were sampled per target region (Suisun Bay, Suisun Marsh, the Lower Sacramento River, the Cache Slough Complex, and the Sacramento Deep Water Ship Channel) per week. Sites were chosen using a Generalized Random Tessellation Stratified design. During 2018, sampling was increased to weekly and in 2019-2020 sampling began in April and ended in November. Sampling occurs for three different habitat types: shoal, channel surface and channel deep at each site depending on the depth of the water column. The shoal habitat is less than 10 feet, channel habitat is greater than 10 feet and channel deep habitat is greater than 20 feet. Plankton nets are towed approximately 0.5-meters below the surface in shoal and channel habitats and targeting the lower half to lower third of the water column in channel deep habitats. Two size classes of zooplankton are targeted using a pair of nets with different mesh sizes: mesozooplankton (copepods and cladocerans) are targeted with a 150 micrometer mesh net and macrozooplankton (mysids and amphipods) are targeted with a 500 micrometer mesh net. Before each zooplankton tow water quality variables (temperature, dissolve oxygen, turbidity, specific conductivity, salinity, pH, and chlorophyll-a) are measured using a YSI EXO 2 sonde, 1 meter below the surface for channel surface and shoal habitats or at the target tow depth for channel deep habitats. Alongside zooplankton tows, phytoplankton samples are taken from a water sample and preserved in a Lugol's solution. In addition, whole water samples are filtered for nutrient (ammonium, nitrate, phosphate and dissolved organic carbon) and chlorophyll-a analysis. These samples are only taken at the channel surface and shoal habitats. This dataset has been used in numerous manuscripts, reports, and technical reports to examine the state of the lower trophic food web in the context of available food for Delta Smelt.