eDNA observations, concurrent with trawl survey, of marine fish in coastal New Jersey, USA 2019

Mark Stoeckle; Jason Adolf; Zachary Charlop-Powers; Keith J. Dunton; Gregory Hinks; Stacy M. VanMorter

doi:10.15468/zsrtyb

eDNA observations, concurrent with trawl survey, of marine fish in coastal New Jersey, USA 2019

Citation

Stoeckle M, Adolf J, Charlop-Powers Z, Dunton K J, Hinks G, VanMorter S M, Formel S K (2023). eDNA observations, concurrent with trawl survey, of marine fish in coastal New Jersey, USA 2019. Version 1.4. United States Geological Survey. Occurrence dataset. https://ipt-obis.gbif.us/resource?r=rockefeller_njtrawl_edna_assessment&v=1.4 https://doi.org/10.15468/zsrtyb accessed via GBIF.org on 2024-12-14.

Description

These data are amplicon sequence variant (ASV) counts of marine fish derived from environmental DNA (eDNA) sampling targeting the 12S rDNA, V5 region. DNA was extracted from filtered water samples taken off coastal New Jersey during the 2019 New Jersey Ocean Trawl Survey. Sampling corresponded to the New Jersey Ocean Trawl Survey efforts, but trawl data are not included here. The data were originally published as supplementary tables in support of Stoeckle et al. (https://doi.org/10.1093/icesjms/fsaa225). Observations from supplementary tables 8A - 8D were subsequently aligned to Darwin Core.

Purpose

Evaluate performance of eDNA for monitoring marine fish populations by comparing bottom trawl catches to eDNA from concurrent water samples.

Sampling Description

Study Extent

Sampling of eDNA from filtered seawater taken off the New Jersey coast in 2019 to compare eDNA results to traditional trawl results. Samples were taken for about one-fourth of the trawls conducted by the New Jersey Bureau of Marine Fisheries Ocean Trawl Survey (NJ OTS) during 2019. NJ OTS field sampling was conducted during ∼1-week periods in January, June, August, and November 2019. The target for each month was ten paired samples (one surface and one bottom sample per selected tow site) distributed across strata by depth and north-south location.

Sampling

Samples were taken in the neritic zone ocean from New York Harbor south to Delaware Bay, from shoreline out to 30 m depth contour. Prior to tows, a 1.2-l stainless steel, polypropylene-lined Kemmerer water sampler was deployed at surface and bottom, and collected water was transferred to 1-l polypropylene bottles. Once filled, collection bottle was placed inside a plastic bag and into a dedicated cooler kept in a protected cabin location. Samples were maintained on ice and transported to a −20°C freezer within 24 h of collection. Collection bottles were thawed for 24–48 h at 4°C and contents poured into a glass filter manifold attached to wall suction and filtered through a 0.45-μM pore size nitrocellulose filter (Millipore). DNA was extracted with PowerSoil kit (Qiagen) with modifications from the manufacturer’s protocol as previously described.

Quality Control

As negative controls for each monthly set, 1 l of laboratory tap water was filtered using the same equipment and procedures, and on the same day as for field samples.

Method steps

For more detail see Stoeckle et al., 2020 (https://doi.org/10.1093/icesjms/fsaa225), Stoeckle et al., 2018 (https://doi.org/10.1371/journal.pone.0198717) and Stoeckle et al., 2020 (https://doi.org/10.3389/fmars.2020.00226).

Taxonomic Coverages

Marine Fish

Teleostei
rank: class
Elasmobranchii
rank: class
Chondrostei
rank: class
Petromyzonti
rank: class

Geographic Coverages

New Jersey Bureau of Marine Fisheries Ocean Trawl Survey (NJ OTS) sites. The neritic zone ocean from New York Harbor south to Delaware Bay, from shoreline out to 30m depth contour.

Bibliographic Citations

Mark Y Stoeckle, Jason Adolf, Zachary Charlop-Powers, Keith J Dunton, Gregory Hinks, Stacy M VanMorter, Trawl and eDNA assessment of marine fish diversity, seasonality, and relative abundance in coastal New Jersey, USA , ICES Journal of Marine Science, Volume 78, Issue 1, January-February 2021, Pages 293–304, https://doi.org/10.1093/icesjms/fsaa225 - https://doi.org/10.1093/icesjms/fsaa225
Stoeckle M. Y. , Das Mishu M. , Charlop-Powers Z. 2020. Improved environmental DNA reference library identifies overlooked marine fishes in coastal New Jersey, U.S.A. Frontiers in Marine Science, 7: 226 - https://doi.org/10.3389/fmars.2020.00226
Stoeckle, M. Y., Ausubel, J. H., & Coogan, M. (2022). 12S gene metabarcoding with DNA standard quantifies marine bony fish environmental DNA, identifies threshold for reproducible detection, and overcomes distortion due to amplification of non-fish DNA. Environmental DNA, 00, 1– 11. https://doi.org/10.1002/edn3.376 - https://doi.org/10.1002/edn3.376

Contacts

Mark Stoeckle
originator
position: Senior Research Associate
Rockefeller University
email: mark.stoeckle@rockefeller.edu
userId: https://orcid.org/0000-0002-8280-4795

Jason Adolf
originator
position: Professor
Monmouth University
email: jadolf@monmouth.edu
userId: https://orcid.org/0000-0002-6962-9267

Zachary Charlop-Powers
originator
Rockefeller University
userId: https://orcid.org/0000-0001-8816-4680

Keith J. Dunton
originator
position: Associate Professor
Monmouth University
email: kdunton@monmouth.edu

Gregory Hinks
originator
position: Fisheries Biologist
Bureau of Marine Fisheries, New Jersey Department of Environmental Protection
email: gregory.hinks@dep.nj.gov

Stacy M. VanMorter
originator
position: Research Technician
Bureau of Marine Fisheries, New Jersey Department of Environmental Protection

Mark Stoeckle
metadata author
position: Senior Research Associate
Rockefeller University
email: mark.stoeckle@rockefeller.edu
userId: https://orcid.org/0000-0002-8280-4795

Stephen K. Formel
metadata author
position: Biologist
U.S. Geological Surevy
email: sformel@usgs.gov
userId: https://orcid.org/0000-0001-7418-1244

Mark Stoeckle
author
position: Senior Research Associate
Rockefeller University
email: mark.stoeckle@rockefeller.edu
userId: https://orcid.org/0000-0002-8280-4795

Jason Adolf
author
position: Professor
Monmouth University
email: jadolf@monmouth.edu
userId: https://orcid.org/0000-0002-6962-9267

Zachary Charlop-Powers
author
Rockefeller University
userId: https://orcid.org/0000-0001-8816-4680

Keith J. Dunton
author
position: Associate Professor
Monmouth University
email: kdunton@monmouth.edu

Gregory Hinks
author
position: Fisheries Biologist
Bureau of Marine Fisheries, New Jersey Department of Environmental Protection
email: gregory.hinks@dep.nj.gov

Stacy M. VanMorter
author
position: Research Technician
Bureau of Marine Fisheries, New Jersey Department of Environmental Protection

Stephen K. Formel
processor
position: Biologist
U.S. Geological Surevy
email: sformel@usgs.gov
userId: https://orcid.org/0000-0001-7418-1244

Mark Stoeckle
administrative point of contact
position: Senior Research Associate
Rockefeller University
email: mark.stoeckle@rockefeller.edu
userId: https://orcid.org/0000-0002-8280-4795

Gregory Hinks
administrative point of contact
position: Fisheries Biologist
Bureau of Marine Fisheries, New Jersey Department of Environmental Protection
email: gregory.hinks@dep.nj.gov