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Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water

Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water
Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water
Environmental DnA (eDnA) surveys are increasingly being used for biodiversity monitoring, principally because they are sensitive and can provide high resolution community composition data. Despite considerable progress in recent years, eDNA studies examining how different environmental sample types can affect species detectability remain rare. Comparisons of environmental samples are especially important for providing best practice guidance on early detection and subsequent mitigation of non-indigenous species. Here we used eDnA metabarcoding of coi (cytochrome c oxidase subunit i) and 18S (nuclear small subunit ribosomal DNA) genes to compare community composition between sediment and water samples in artificial coastal sites across the United Kingdom. We first detected markedly different communities and a consistently greater number of distinct operational taxonomic units in sediment compared to water. We then compared our eDNA datasets with previously published rapid assessment biodiversity surveys and found excellent concordance among the different survey techniques. finally, our eDnA surveys detected many non-indigenous species, including several newly introduced species, highlighting the utility of eDnA metabarcoding for both early detection and temporal / spatial monitoring of non-indigenous species. We conclude that careful consideration on environmental sample type is needed when conducting eDnA surveys, especially for studies assessing community change
2045-2322
1-10
Holman, Luke E.
3d57aba8-c261-413b-a053-e7bed35adba0
de Bruyn, Mark
bda81f81-e206-4d64-8a93-541e253d0497
Creer, Simon
d032cd75-9ed6-4bb8-b55b-926afb575321
Carvalho, Gary R.
fe03b393-a1af-4639-8a93-684e58d3434a
Robidart, Julie
a9b8d49c-c1e3-4a3b-a53c-685a0f2c7f93
Rius, Marc
c4e88345-4b4e-4428-b4b2-37229155f68d
Holman, Luke E.
3d57aba8-c261-413b-a053-e7bed35adba0
de Bruyn, Mark
bda81f81-e206-4d64-8a93-541e253d0497
Creer, Simon
d032cd75-9ed6-4bb8-b55b-926afb575321
Carvalho, Gary R.
fe03b393-a1af-4639-8a93-684e58d3434a
Robidart, Julie
a9b8d49c-c1e3-4a3b-a53c-685a0f2c7f93
Rius, Marc
c4e88345-4b4e-4428-b4b2-37229155f68d

Holman, Luke E., de Bruyn, Mark, Creer, Simon, Carvalho, Gary R., Robidart, Julie and Rius, Marc (2019) Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water. Scientific Reports, 9, 1-10. (doi:10.1038/s41598-019-47899-7).

Record type: Article

Abstract

Environmental DnA (eDnA) surveys are increasingly being used for biodiversity monitoring, principally because they are sensitive and can provide high resolution community composition data. Despite considerable progress in recent years, eDNA studies examining how different environmental sample types can affect species detectability remain rare. Comparisons of environmental samples are especially important for providing best practice guidance on early detection and subsequent mitigation of non-indigenous species. Here we used eDnA metabarcoding of coi (cytochrome c oxidase subunit i) and 18S (nuclear small subunit ribosomal DNA) genes to compare community composition between sediment and water samples in artificial coastal sites across the United Kingdom. We first detected markedly different communities and a consistently greater number of distinct operational taxonomic units in sediment compared to water. We then compared our eDNA datasets with previously published rapid assessment biodiversity surveys and found excellent concordance among the different survey techniques. finally, our eDnA surveys detected many non-indigenous species, including several newly introduced species, highlighting the utility of eDnA metabarcoding for both early detection and temporal / spatial monitoring of non-indigenous species. We conclude that careful consideration on environmental sample type is needed when conducting eDnA surveys, especially for studies assessing community change

Text
Holman et al 2019 Sci Rep - Version of Record
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Accepted/In Press date: 25 July 2019
Published date: 9 August 2019

Identifiers

Local EPrints ID: 433322
URI: https://eprints.soton.ac.uk/id/eprint/433322
ISSN: 2045-2322
PURE UUID: 9814d9fd-124f-4d85-a752-b3f7a11cabdd
ORCID for Luke E. Holman: ORCID iD orcid.org/0000-0002-8139-3760

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Date deposited: 14 Aug 2019 16:30
Last modified: 10 Dec 2019 02:00

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Contributors

Author: Luke E. Holman ORCID iD
Author: Mark de Bruyn
Author: Simon Creer
Author: Gary R. Carvalho
Author: Julie Robidart
Author: Marc Rius

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