Investigating Patterns of Larval Fish Community Dynamics Over the Past Two Decades Using a Novel Application of Environmental DNA Metabarcoding

Zachary Gold, University of California Los Angeles, Ecology and Evolutionary Biology, Los Angeles, CA, United States, Dovi Kacev, Scripps Institute of Oceanography, La Jolla, CA, United States, Paul H Barber, University of Los Angeles, Ecology and Evolutionary Biology, Los Angeles, CA, United States, Kelly D. Goodwin, NOAA Miami, Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, Miami, United States, Luke Thompson, Atlantic Oceanographic and Meteorological Laboratory, Miami, United States and Andrew Thompson, NOAA SWFSC, La Jolla, CA, United States
Abstract:
Plankton samples track stock biomass and ecosystem dynamics worldwide and are a critical component for monitoring and managing U.S. fisheries and marine ecosystems. Ichthyoplankton collected by the California Cooperative Oceanic Fisheries Investigations (CalCOFI) program helps inform rockfish and clupeoids stock assessments and fish ecosystem status within the California Current Ecosystem. However, traditional methods for identifying plankton are time and labor intensive, resulting in a backlog of samples that need to be processed. A promising new technique for efficiently quantifying species from plankton samples is high throughput sequencing of dissociated DNA from the ethanol-preservation buffer. This cost-effective and non-destructive technique utilizes DNA shed from plankton into the preservation buffer, thus allowing researchers to extract, amplify, sequence, identify, and potentially quantify DNA abundance of species without damaging archived samples. We use novel environmental DNA (eDNA) techniques to identify larval fish and zooplankton species from ethanol-preserved plankton samples collected by the CalCOFI program at 4 stations likely exposed to different oceanographic water masses between 1996 and 2019. Our aims are to 1) evaluate the efficacy of eDNA to accurately identify larval fishes by comparing genetic and morphologically identified samples; and 2) investigate the long-term dynamics of Southern California ichthyoplankton and zooplankton communities in response to climate forcing. We successfully amplified DNA from all stations and time points in triplicate using 4 metabarcodes targeting fish (12S), Sebastes (CytB), and zooplankton (CO1 and 16S). We test how fish and zooplankton biodiversity and assemblage structure respond to oceanographic dynamics including the 1997-98 El Niño and record-warm 2014-2016 marine heatwave. This project has the potential to greatly augment traditional ichthyoplankton processing and provide critical information on key ecosystem component dynamics in near real-time.
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