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Environmental DNA from Seawater Samples Correlate with Trawl Catches of Subarctic, Deepwater Fishes

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      Abstract

      Remote polar and deepwater fish faunas are under pressure from ongoing climate change and increasing fishing effort. However, these fish communities are difficult to monitor for logistic and financial reasons. Currently, monitoring of marine fishes largely relies on invasive techniques such as bottom trawling, and on official reporting of global catches, which can be unreliable. Thus, there is need for alternative and non-invasive techniques for qualitative and quantitative oceanic fish surveys. Here we report environmental DNA (eDNA) metabarcoding of seawater samples from continental slope depths in Southwest Greenland. We collected seawater samples at depths of 188–918 m and compared seawater eDNA to catch data from trawling. We used Illumina sequencing of PCR products to demonstrate that eDNA reads show equivalence to fishing catch data obtained from trawling. Twenty-six families were found with both trawling and eDNA, while three families were found only with eDNA and two families were found only with trawling. Key commercial fish species for Greenland were the most abundant species in both eDNA reads and biomass catch, and interpolation of eDNA abundances between sampling sites showed good correspondence with catch sizes. Environmental DNA sequence reads from the fish assemblages correlated with biomass and abundance data obtained from trawling. Interestingly, the Greenland shark ( Somniosus microcephalus) showed high abundance of eDNA reads despite only a single specimen being caught, demonstrating the relevance of the eDNA approach for large species that can probably avoid bottom trawls in most cases. Quantitative detection of marine fish using eDNA remains to be tested further to ascertain whether this technique is able to yield credible results for routine application in fisheries. Nevertheless, our study demonstrates that eDNA reads can be used as a qualitative and quantitative proxy for marine fish assemblages in deepwater oceanic habitats. This relates directly to applied fisheries as well as to monitoring effects of ongoing climate change on marine biodiversity—especially in polar ecosystems.

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            Author and article information

            Affiliations
            [1 ]Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
            [2 ]Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
            [3 ]Technical University of Denmark, National Institute of Aquatic Resources, Charlottenlund, Denmark
            [4 ]Greenland Institute of Natural Resources, Nuuk, Greenland
            [5 ]Department of Zoology, University of Cambridge, Cambridge, United Kingdom
            [6 ]Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
            Central Michigan University, UNITED STATES
            Author notes

            Competing Interests: The authors have declared that no competing interests exist.

            • Conceptualization: PFT PRM OAJ EW.

            • Data curation: PFT PRM OAJ EES.

            • Formal analysis: PFT PRM OAJ EES SWK.

            • Funding acquisition: PFT PRM OAJ EW.

            • Investigation: PFT PRM OAJ.

            • Methodology: PFT PRM OAJ.

            • Project administration: PFT PRM OAJ EW.

            • Resources: PFT PRM OAJ EES SWK EW.

            • Software: PFT EES SWK.

            • Supervision: PFT PRM OAJ EW.

            • Validation: PFT PRM EES SWK.

            • Visualization: PFT PRM EES SWK.

            • Writing – original draft: PFT PRM OAJ.

            • Writing – review & editing: PFT PRM OAJ EW EES SWK.

            Contributors
            Role: Editor
            Journal
            PLoS One
            PLoS ONE
            plos
            plosone
            PLoS ONE
            Public Library of Science (San Francisco, CA USA )
            1932-6203
            16 November 2016
            2016
            : 11
            : 11
            27851757 5112899 10.1371/journal.pone.0165252 PONE-D-16-27987
            © 2016 Thomsen et al

            This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

            Counts
            Figures: 6, Tables: 1, Pages: 22
            Product
            Funding
            Danish National Research Foundation funded the work. Greenland Institute of Natural Resources, Greenland Self-government, Department for education and research funded the work. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
            Categories
            Research Article
            Biology and Life Sciences
            Organisms
            Animals
            Vertebrates
            Fishes
            Biology and Life Sciences
            Molecular Biology
            Molecular Biology Techniques
            Artificial Gene Amplification and Extension
            Polymerase Chain Reaction
            Research and Analysis Methods
            Molecular Biology Techniques
            Artificial Gene Amplification and Extension
            Polymerase Chain Reaction
            Biology and Life Sciences
            Organisms
            Animals
            Vertebrates
            Fishes
            Marine Fish
            Biology and Life Sciences
            Marine Biology
            Marine Fish
            Earth Sciences
            Marine and Aquatic Sciences
            Marine Biology
            Marine Fish
            Research and Analysis Methods
            Database and Informatics Methods
            Biological Databases
            Sequence Databases
            Biology and Life Sciences
            Molecular Biology
            Molecular Biology Techniques
            Sequencing Techniques
            Sequence Analysis
            Sequence Databases
            Research and Analysis Methods
            Molecular Biology Techniques
            Sequencing Techniques
            Sequence Analysis
            Sequence Databases
            Earth Sciences
            Hydrology
            Sea Water
            Biology and Life Sciences
            Taxonomy
            Computer and Information Sciences
            Data Management
            Taxonomy
            Biology and Life Sciences
            Organisms
            Animals
            Vertebrates
            Fishes
            Chondrichthyes
            Elasmobranchii
            Sharks
            Biology and Life Sciences
            Agriculture
            Fisheries
            Custom metadata
            Illumina MiSeq raw sequence data are available from the Dryad Digital Repository ( http://dx.doi.org/10.5061/dryad.ch576). Full sequences for reference Greenlandic fish species generated from tissue samples have been added to Genbank (NCBI Accession no. KX929879-KX929923).

            Uncategorized

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