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

Occurrence
Latest version published by United States Geological Survey on Jun 6, 2023 United States Geological Survey
Publication date:
6 June 2023
License:
CC0 1.0

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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.

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 6,868 records.

1 extension data tables also exist. An extension record supplies extra information about a core record. The number of records in each extension data table is illustrated below.

Occurrence (core)
6868
dnaDerivedData 
13736

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

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

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is United States Geological Survey. To the extent possible under law, the publisher has waived all rights to these data and has dedicated them to the Public Domain (CC0 1.0). Users may copy, modify, distribute and use the work, including for commercial purposes, without restriction.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 46488f96-b51e-4c06-9a02-8c4c900f7f78.  United States Geological Survey publishes this resource, and is itself registered in GBIF as a data publisher endorsed by U.S. Geological Survey.

Keywords

FISH (UUID: ea855d4c-f132-44f9-b31c-447e1101684d); TRAWL (UUID: c386fdd8-5a49-46c6-9be6-b56a9428f30d); NERITIC ZONE (UUID: eb958dfb-5e38-401f-8b42-5f1273c75a4a); ATLANTIC OCEAN (UUID: cf249a36-2e82-4d32-84cd-23a4f40bb393); NEW JERSEY (UUID: 699b0e5a-6dbd-47aa-b0ca-c4502f044e35); marine biome (ENVO:00000447); coastal water (ENVO:00001250); waterborne particulate matter (ENVO:01000436); marine biota (ENVO: 06105013); Environmental DNA (NCIT:C169196); Fish (NCIT:C14207); Occurrence

Contacts

Mark Stoeckle
  • Metadata Provider
  • Author
  • Originator
  • Point Of Contact
Senior Research Associate
Rockefeller University
Jason Adolf
  • Author
  • Originator
Professor
Monmouth University
Zachary Charlop-Powers
  • Author
  • Originator
Rockefeller University
Keith J. Dunton
  • Author
  • Originator
Associate Professor
Monmouth University
Gregory Hinks
  • Author
  • Originator
  • Point Of Contact
Fisheries Biologist
Bureau of Marine Fisheries, New Jersey Department of Environmental Protection
Stacy M. VanMorter
  • Author
  • Originator
Research Technician
Bureau of Marine Fisheries, New Jersey Department of Environmental Protection
Stephen K. Formel
  • Metadata Provider
  • Processor
Biologist
U.S. Geological Surevy

Geographic Coverage

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.

Bounding Coordinates South West [38.658, -74.969], North East [40.468, -73.862]

Taxonomic Coverage

Marine Fish

Class Teleostei, Elasmobranchii, Chondrostei, Petromyzonti

Temporal Coverage

Start Date / End Date 2019-01-11 / 2019-11-10

Project Data

No Description available

Title Monmouth University—Rockefeller University Marine Science Policy Initiative

The personnel involved in the project:

Mark Stoeckle

Sampling Methods

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.

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.
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 step description:

  1. 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).

Bibliographic Citations

  1. 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
  2. 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
  3. 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

Additional Metadata

Purpose Evaluate performance of eDNA for monitoring marine fish populations by comparing bottom trawl catches to eDNA from concurrent water samples.
Alternative Identifiers https://www.sciencebase.gov/catalog/item/640a18afd34e0e602b90ff45
46488f96-b51e-4c06-9a02-8c4c900f7f78
https://obis.org/dataset/fe2ed263-2b21-47d7-a79f-f9b911132398
https://ipt-obis.gbif.us/resource?r=rockefeller_njtrawl_edna_assessment