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Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems

Antarctic benthic ecosystems support high biodiversity but their characterization is limited to a few well-studied areas, due to the extreme environment and remoteness making access and sampling difficult. Our aim was to compare water and sediment as sources of environmental DNA (eDNA) to better cha...

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Autores principales: Clarke, Laurence J., Suter, Leonie, Deagle, Bruce E., Polanowski, Andrea M., Terauds, Aleks, Johnstone, Glenn J., Stark, Jonathan S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8601059/
https://www.ncbi.nlm.nih.gov/pubmed/34820189
http://dx.doi.org/10.7717/peerj.12458
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author Clarke, Laurence J.
Suter, Leonie
Deagle, Bruce E.
Polanowski, Andrea M.
Terauds, Aleks
Johnstone, Glenn J.
Stark, Jonathan S.
author_facet Clarke, Laurence J.
Suter, Leonie
Deagle, Bruce E.
Polanowski, Andrea M.
Terauds, Aleks
Johnstone, Glenn J.
Stark, Jonathan S.
author_sort Clarke, Laurence J.
collection PubMed
description Antarctic benthic ecosystems support high biodiversity but their characterization is limited to a few well-studied areas, due to the extreme environment and remoteness making access and sampling difficult. Our aim was to compare water and sediment as sources of environmental DNA (eDNA) to better characterise Antarctic benthic communities and further develop practical approaches for DNA-based biodiversity assessment in remote environments. We used a cytochrome c oxidase subunit I (COI) metabarcoding approach to characterise metazoan communities in 26 nearshore sites across 12 locations in the Vestfold Hills (East Antarctica) based on DNA extracted from either sediment cores or filtered seawater. We detected a total of 99 metazoan species from 12 phyla across 26 sites, with similar numbers of species detected in sediment and water eDNA samples. However, significantly different communities were detected in the two sample types at sites where both were collected (i.e., where paired samples were available). For example, nematodes and echinoderms were more likely to be detected exclusively in sediment and water eDNA samples, respectively. eDNA from water and sediment core samples are complementary sample types, with epifauna more likely to be detected in water column samples and infauna in sediment. More reference DNA sequences are needed for infauna/meiofauna to increase the proportion of sequences and number of taxa that can be identified. Developing a better understanding of the temporal and spatial dynamics of eDNA at low temperatures would also aid interpretation of eDNA signals from polar environments. Our results provide a preliminary scan of benthic metazoan communities in the Vestfold Hills, with additional markers required to provide a comprehensive biodiversity survey. However, our study demonstrates the choice of sample type for eDNA studies of benthic ecosystems (sediment, water or both) needs to be carefully considered in light of the research or monitoring question of interest.
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spelling pubmed-86010592021-11-23 Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems Clarke, Laurence J. Suter, Leonie Deagle, Bruce E. Polanowski, Andrea M. Terauds, Aleks Johnstone, Glenn J. Stark, Jonathan S. PeerJ Biodiversity Antarctic benthic ecosystems support high biodiversity but their characterization is limited to a few well-studied areas, due to the extreme environment and remoteness making access and sampling difficult. Our aim was to compare water and sediment as sources of environmental DNA (eDNA) to better characterise Antarctic benthic communities and further develop practical approaches for DNA-based biodiversity assessment in remote environments. We used a cytochrome c oxidase subunit I (COI) metabarcoding approach to characterise metazoan communities in 26 nearshore sites across 12 locations in the Vestfold Hills (East Antarctica) based on DNA extracted from either sediment cores or filtered seawater. We detected a total of 99 metazoan species from 12 phyla across 26 sites, with similar numbers of species detected in sediment and water eDNA samples. However, significantly different communities were detected in the two sample types at sites where both were collected (i.e., where paired samples were available). For example, nematodes and echinoderms were more likely to be detected exclusively in sediment and water eDNA samples, respectively. eDNA from water and sediment core samples are complementary sample types, with epifauna more likely to be detected in water column samples and infauna in sediment. More reference DNA sequences are needed for infauna/meiofauna to increase the proportion of sequences and number of taxa that can be identified. Developing a better understanding of the temporal and spatial dynamics of eDNA at low temperatures would also aid interpretation of eDNA signals from polar environments. Our results provide a preliminary scan of benthic metazoan communities in the Vestfold Hills, with additional markers required to provide a comprehensive biodiversity survey. However, our study demonstrates the choice of sample type for eDNA studies of benthic ecosystems (sediment, water or both) needs to be carefully considered in light of the research or monitoring question of interest. PeerJ Inc. 2021-11-15 /pmc/articles/PMC8601059/ /pubmed/34820189 http://dx.doi.org/10.7717/peerj.12458 Text en ©2021 Clarke et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Biodiversity
Clarke, Laurence J.
Suter, Leonie
Deagle, Bruce E.
Polanowski, Andrea M.
Terauds, Aleks
Johnstone, Glenn J.
Stark, Jonathan S.
Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems
title Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems
title_full Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems
title_fullStr Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems
title_full_unstemmed Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems
title_short Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems
title_sort environmental dna metabarcoding for monitoring metazoan biodiversity in antarctic nearshore ecosystems
topic Biodiversity
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8601059/
https://www.ncbi.nlm.nih.gov/pubmed/34820189
http://dx.doi.org/10.7717/peerj.12458
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