Spatial distribution of environmental DNA in a nearshore marine habitat
In the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA o...
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| Format: | Article |
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PeerJ Inc.
2017-02-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/3044.pdf |
| _version_ | 1827606613186314240 |
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| author | James L. O’Donnell Ryan P. Kelly Andrew Olaf Shelton Jameal F. Samhouri Natalie C. Lowell Gregory D. Williams |
| author_facet | James L. O’Donnell Ryan P. Kelly Andrew Olaf Shelton Jameal F. Samhouri Natalie C. Lowell Gregory D. Williams |
| author_sort | James L. O’Donnell |
| collection | DOAJ |
| description | In the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA or eDNA); however, eDNA techniques have not yet seen widespread adoption as a routine method for biological surveillance primarily due to gaps in our understanding of the dynamics of eDNA in space and time. In order to identify the effective spatial scale of this approach in a dynamic marine environment, we collected marine surface water samples from transects ranging from the intertidal zone to four kilometers from shore. Using PCR primers that target a diverse assemblage of metazoans, we amplified a region of mitochondrial 16S rDNA from the samples and sequenced the products on an Illumina platform in order to detect communities and quantify their spatial patterns using a variety of statistical tools. We find evidence for multiple, discrete eDNA communities in this habitat, and show that these communities decrease in similarity as they become further apart. Offshore communities tend to be richer but less even than those inshore, though diversity was not spatially autocorrelated. Taxon-specific relative abundance coincided with our expectations of spatial distribution in taxa lacking a microscopic, pelagic life-history stage, though most of the taxa detected do not meet these criteria. Finally, we use carefully replicated laboratory procedures to show that laboratory treatments were remarkably similar in most cases, while allowing us to detect a faulty replicate, emphasizing the importance of replication to metabarcoding studies. While there is much work to be done before eDNA techniques can be confidently deployed as a standard method for ecological monitoring, this study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and confirms the promise of eDNA in dynamic environments. |
| first_indexed | 2024-03-09T06:40:23Z |
| format | Article |
| id | doaj.art-9374e1d13fc94df5b20e95a64bae8edd |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:40:23Z |
| publishDate | 2017-02-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-9374e1d13fc94df5b20e95a64bae8edd2023-12-03T10:51:45ZengPeerJ Inc.PeerJ2167-83592017-02-015e304410.7717/peerj.3044Spatial distribution of environmental DNA in a nearshore marine habitatJames L. O’Donnell0Ryan P. Kelly1Andrew Olaf Shelton2Jameal F. Samhouri3Natalie C. Lowell4Gregory D. Williams5School of Marine and Environmental Affairs, University of Washington, Seattle, WA, United States of AmericaSchool of Marine and Environmental Affairs, University of Washington, Seattle, WA, United States of AmericaEarth Resource Technology, Inc., Under Contract to the Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, United States of AmericaConservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, United States of AmericaSchool of Marine and Environmental Affairs, University of Washington, Seattle, WA, United States of AmericaPacific States Marine Fisheries Commission, Under Contract to the Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, United States of AmericaIn the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA or eDNA); however, eDNA techniques have not yet seen widespread adoption as a routine method for biological surveillance primarily due to gaps in our understanding of the dynamics of eDNA in space and time. In order to identify the effective spatial scale of this approach in a dynamic marine environment, we collected marine surface water samples from transects ranging from the intertidal zone to four kilometers from shore. Using PCR primers that target a diverse assemblage of metazoans, we amplified a region of mitochondrial 16S rDNA from the samples and sequenced the products on an Illumina platform in order to detect communities and quantify their spatial patterns using a variety of statistical tools. We find evidence for multiple, discrete eDNA communities in this habitat, and show that these communities decrease in similarity as they become further apart. Offshore communities tend to be richer but less even than those inshore, though diversity was not spatially autocorrelated. Taxon-specific relative abundance coincided with our expectations of spatial distribution in taxa lacking a microscopic, pelagic life-history stage, though most of the taxa detected do not meet these criteria. Finally, we use carefully replicated laboratory procedures to show that laboratory treatments were remarkably similar in most cases, while allowing us to detect a faulty replicate, emphasizing the importance of replication to metabarcoding studies. While there is much work to be done before eDNA techniques can be confidently deployed as a standard method for ecological monitoring, this study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and confirms the promise of eDNA in dynamic environments.https://peerj.com/articles/3044.pdfMarineMetabarcodingMetagenomicsEstuarineMolecular ecologyEnvironmental monitoring |
| spellingShingle | James L. O’Donnell Ryan P. Kelly Andrew Olaf Shelton Jameal F. Samhouri Natalie C. Lowell Gregory D. Williams Spatial distribution of environmental DNA in a nearshore marine habitat PeerJ Marine Metabarcoding Metagenomics Estuarine Molecular ecology Environmental monitoring |
| title | Spatial distribution of environmental DNA in a nearshore marine habitat |
| title_full | Spatial distribution of environmental DNA in a nearshore marine habitat |
| title_fullStr | Spatial distribution of environmental DNA in a nearshore marine habitat |
| title_full_unstemmed | Spatial distribution of environmental DNA in a nearshore marine habitat |
| title_short | Spatial distribution of environmental DNA in a nearshore marine habitat |
| title_sort | spatial distribution of environmental dna in a nearshore marine habitat |
| topic | Marine Metabarcoding Metagenomics Estuarine Molecular ecology Environmental monitoring |
| url | https://peerj.com/articles/3044.pdf |
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