Longfin Smelt and Zooplankton in the San Francisco Longfin Smelt and Zooplankton in the San Francisco
20 September 2021

Longfin Smelt and Zooplankton in the San Francisco Estuary

Written by: Joseph Miller

                Zooplankton are an important part of the San Francisco Estuary food web. Zooplankton are small (often crustaceous) organisms that feed on phytoplankton (algae) in the water. Phytoplankton derive their energy from the sun. Zooplankton filter the water and feed on the phytoplankton. These larger zooplankton are much more readily available as a food item to fish in the estuary compared to phytoplankton due to their larger size and greater nutritional value.

                The food web in the estuary is not the same as it historically was. The overbite clam (an invasive species) was accidentally introduced to the estuary in the late 1980’s, and this has a dramatic impact on the food web in the estuary. The overbite clams are more efficient filter feeders than most zooplankton and can devour a significant portion of the nutritious phytoplankton before the native zooplankton can. Additionally, the introduction of non-native zooplankton like Limnothoina tetraspina has also had significant impacts on the food web in the estuary. These non-native species can out compete some zooplankton for phytoplankton, and addidtionally by decreasing the total amount of phytoplankton can affect water clarity and chemistry creating other trophic cascades.

                Ultimately the introduction of these invasive species into the estuary led to substantial community shifts. Historically dominant taxa have become much less common in the estuary and have been replaced by species such as limnothoina teraspina.

                Recent studies have come out documenting the diet of longfin smelt. The historically dominant copepod Eurytemora affinis and mysids make up the overwhelming majority of their diets as larvae. Both of these taxa have seen substantial declines in abundance since the introduction of the overbite clam.

                Using historical zooplankton data from the Environmental Monitoring Program (EMP) I have assembled a dataset of abundances of these important dietary taxa. Converting catch per unit effort (CPUE) of Eurytemora affinis to carbon mass using a mean estimate of carbon weight for the zooplankter I have been able to calculate carbon mass per cubic meter of water. Similarly, I have summarized CPUE of Mysids. These summaries look at abundances of these taxa for every month of sampling for seven different stations for each year.

                The aim of this dataset is to understand if there are mismatches of when these zooplankton are abundant, and when longfin smelt larvae hatch. If these zooplankton are at peak abundances before or after longfin larvae hatch they would be unavailable to the fish for feeding, leading to low survival and poor recruitment into adulthood. Similarly, there could be a spatial mismatch where longfin larvae are hatching where these zooplankton are most abundant.

                Examining the spatial and temporal trends of critical zooplankton may help us inform our understanding of the recent poor spawning, survival, and recruitment of longfin smelt in the estuary.


Photo Credit: Steve Culberson, USFWS

Agency: U.S. Fish and Wildlife Service

Program: US Fish & Wildlife Service - DFP

Location: San Francisco Bay National Wildlife Refuge Complex

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