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:	Laurence J. Clarke, Leonie Suter, Bruce E. Deagle, Andrea M. Polanowski, Aleks Terauds, Glenn J. Johnstone, Jonathan S. Stark
Formato:	article
Lenguaje:	EN
Publicado:	PeerJ Inc. 2021
Materias:	DNA metabarcoding Environmental DNA Benthos Sediment Cytochrome c oxidase subunit I (COI) Vestfold Hills Medicine R
Acceso en línea:	https://doaj.org/article/a58b92b679b648e694f20faea5c7c248
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spelling	oai:doaj.org-article:a58b92b679b648e694f20faea5c7c2482021-11-17T15:05:13ZEnvironmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems10.7717/peerj.124582167-8359https://doaj.org/article/a58b92b679b648e694f20faea5c7c2482021-11-01T00:00:00Zhttps://peerj.com/articles/12458.pdfhttps://peerj.com/articles/12458/https://doaj.org/toc/2167-8359Antarctic 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.Laurence J. ClarkeLeonie SuterBruce E. DeagleAndrea M. PolanowskiAleks TeraudsGlenn J. JohnstoneJonathan S. StarkPeerJ Inc.articleDNA metabarcodingEnvironmental DNABenthosSedimentCytochrome c oxidase subunit I (COI)Vestfold HillsMedicineRENPeerJ, Vol 9, p e12458 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	DNA metabarcoding Environmental DNA Benthos Sediment Cytochrome c oxidase subunit I (COI) Vestfold Hills Medicine R
spellingShingle	DNA metabarcoding Environmental DNA Benthos Sediment Cytochrome c oxidase subunit I (COI) Vestfold Hills Medicine R Laurence J. Clarke Leonie Suter Bruce E. Deagle Andrea M. Polanowski Aleks Terauds Glenn J. Johnstone Jonathan S. Stark Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems
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.
format	article
author	Laurence J. Clarke Leonie Suter Bruce E. Deagle Andrea M. Polanowski Aleks Terauds Glenn J. Johnstone Jonathan S. Stark
author_facet	Laurence J. Clarke Leonie Suter Bruce E. Deagle Andrea M. Polanowski Aleks Terauds Glenn J. Johnstone Jonathan S. Stark
author_sort	Laurence J. Clarke
title	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_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_sort	environmental dna metabarcoding for monitoring metazoan biodiversity in antarctic nearshore ecosystems
publisher	PeerJ Inc.
publishDate	2021
url	https://doaj.org/article/a58b92b679b648e694f20faea5c7c248
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Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems

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