Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding

Elizabeth A Andruszkiewicz; Hilary A Starks; Francisco P Chavez; Lauren M Sassoubre; Barbara A Block; Alexandria B Boehm

doi:10.1371/journal.pone.0176343

Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding

PLoS One. 2017 Apr 25;12(4):e0176343. doi: 10.1371/journal.pone.0176343. eCollection 2017.

Authors

Elizabeth A Andruszkiewicz¹, Hilary A Starks², Francisco P Chavez³, Lauren M Sassoubre¹, Barbara A Block⁴, Alexandria B Boehm¹

Affiliations

¹ Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America.
² Center for Ocean Solutions, Stanford University, Stanford, CA, United States of America.
³ Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States of America.
⁴ Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, United States of America.

Abstract

Molecular analysis of environmental DNA (eDNA) can be used to assess vertebrate biodiversity in aquatic systems, but limited work has applied eDNA technologies to marine waters. Further, there is limited understanding of the spatial distribution of vertebrate eDNA in marine waters. Here, we use an eDNA metabarcoding approach to target and amplify a hypervariable region of the mitochondrial 12S rRNA gene to characterize vertebrate communities at 10 oceanographic stations spanning 45 km within the Monterey Bay National Marine Sanctuary (MBNMS). In this study, we collected three biological replicates of small volume water samples (1 L) at 2 depths at each of the 10 stations. We amplified fish mitochondrial DNA using a universal primer set. We obtained 5,644,299 high quality Illumina sequence reads from the environmental samples. The sequence reads were annotated to the lowest taxonomic assignment using a bioinformatics pipeline. The eDNA survey identified, to the lowest taxonomic rank, 7 families, 3 subfamilies, 10 genera, and 72 species of vertebrates at the study sites. These 92 distinct taxa come from 33 unique marine vertebrate families. We observed significantly different vertebrate community composition between sampling depths (0 m and 20/40 m deep) across all stations and significantly different communities at stations located on the continental shelf (<200 m bottom depth) versus in the deeper waters of the canyons of Monterey Bay (>200 m bottom depth). All but 1 family identified using eDNA metabarcoding is known to occur in MBNMS. The study informs the implementation of eDNA metabarcoding for vertebrate biomonitoring.

MeSH terms

Animals
Bays*
Biodiversity
California
DNA Barcoding, Taxonomic*
Ecosystem*
Environmental Monitoring / methods*
Fishes / genetics
Vertebrates / genetics*

Grants and funding

This work was supported by a gift from the Seaver Institute to Woods Institute for the Environment at Stanford University and was partially supported by NASA grant NNX14AP62A ‘National Marine Sanctuaries as Sentinel Sites for a Demonstration Marine Biodiversity Observation Network (MBON)’ funded under the National Ocean Partnership Program (NOPP RFP NOAA-NOS-IOOS-2014-2003803 in partnership between NOAA, BOEM, and NASA), and the U.S. Integrated Ocean Observing System (IOOS) Program Office. This publication was developed under STAR Fellowship Assistance Agreement no. F15E211913419 awarded by the U.S. Environmental Protection Agency (EPA). It has not been formally reviewed by EPA. The views expressed in this publication are solely those of Elizabeth Andruszkiewicz and co-authors, and EPA does not endorse any products or commercial services mentioned in this publication. The CANON cruise was supported by the David and Lucile Packard Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.