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eDNA as a tool for non-invasive monitoring of the fauna of a turbid, well-mixed system, the Elbe estuary in Germany

The Elbe is one of the longest European rivers and features a large, turbid and well-mixed estuary, which runs through the inner city of Hamburg. The Elbe has been closely monitored using classical catch techniques in the past. Here we tested a COI-based eDNA approach for assessing the biodiversity...

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Autores principales: Schwentner, Martin, Zahiri, Reza, Yamamoto, Satoshi, Husemann, Martin, Kullmann, Björn, Thiel, Ralf
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8051793/
https://www.ncbi.nlm.nih.gov/pubmed/33861810
http://dx.doi.org/10.1371/journal.pone.0250452
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author Schwentner, Martin
Zahiri, Reza
Yamamoto, Satoshi
Husemann, Martin
Kullmann, Björn
Thiel, Ralf
author_facet Schwentner, Martin
Zahiri, Reza
Yamamoto, Satoshi
Husemann, Martin
Kullmann, Björn
Thiel, Ralf
author_sort Schwentner, Martin
collection PubMed
description The Elbe is one of the longest European rivers and features a large, turbid and well-mixed estuary, which runs through the inner city of Hamburg. The Elbe has been closely monitored using classical catch techniques in the past. Here we tested a COI-based eDNA approach for assessing the biodiversity within the Elbe. We sampled three stations in the Elbe, included low and high tide events, as well as two adjoining lakes to compare the recovered faunas. To analyze the data, we employed two different pipelines: the automated mBRAVE pipeline utilizing the BOLD database and one including NCBI BLAST. The number of OTUs with species or higher-level identifications were similar between both approaches with 352 OTUs and 355 OTUs for BLAST and mBRAVE, respectively, however, BLAST searches recovered another 942 unidentified metazoan OTUs. Many taxa were well represented; however, fish species were poorly represented, especially in the Elbe estuary samples. This could be a result of the universal COI primers, which also yielded high read numbers for non-metazoan OTUs, and small-bodies taxa like Rotifera, which might have been sampled together with the eDNA. Our results show a strong tidal influence on the recovered taxa. During low tide, downstream stations resembled sites further upstream, but the former showed a very different OTU composition during high tide and early tide. Such differences might be due to varying impacts of upstream-originating eDNA during tide cycles. Such factors need to be considered when routinely employing eDNA for monitoring programs.
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spelling pubmed-80517932021-04-28 eDNA as a tool for non-invasive monitoring of the fauna of a turbid, well-mixed system, the Elbe estuary in Germany Schwentner, Martin Zahiri, Reza Yamamoto, Satoshi Husemann, Martin Kullmann, Björn Thiel, Ralf PLoS One Research Article The Elbe is one of the longest European rivers and features a large, turbid and well-mixed estuary, which runs through the inner city of Hamburg. The Elbe has been closely monitored using classical catch techniques in the past. Here we tested a COI-based eDNA approach for assessing the biodiversity within the Elbe. We sampled three stations in the Elbe, included low and high tide events, as well as two adjoining lakes to compare the recovered faunas. To analyze the data, we employed two different pipelines: the automated mBRAVE pipeline utilizing the BOLD database and one including NCBI BLAST. The number of OTUs with species or higher-level identifications were similar between both approaches with 352 OTUs and 355 OTUs for BLAST and mBRAVE, respectively, however, BLAST searches recovered another 942 unidentified metazoan OTUs. Many taxa were well represented; however, fish species were poorly represented, especially in the Elbe estuary samples. This could be a result of the universal COI primers, which also yielded high read numbers for non-metazoan OTUs, and small-bodies taxa like Rotifera, which might have been sampled together with the eDNA. Our results show a strong tidal influence on the recovered taxa. During low tide, downstream stations resembled sites further upstream, but the former showed a very different OTU composition during high tide and early tide. Such differences might be due to varying impacts of upstream-originating eDNA during tide cycles. Such factors need to be considered when routinely employing eDNA for monitoring programs. Public Library of Science 2021-04-16 /pmc/articles/PMC8051793/ /pubmed/33861810 http://dx.doi.org/10.1371/journal.pone.0250452 Text en © 2021 Schwentner 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, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Schwentner, Martin
Zahiri, Reza
Yamamoto, Satoshi
Husemann, Martin
Kullmann, Björn
Thiel, Ralf
eDNA as a tool for non-invasive monitoring of the fauna of a turbid, well-mixed system, the Elbe estuary in Germany
title eDNA as a tool for non-invasive monitoring of the fauna of a turbid, well-mixed system, the Elbe estuary in Germany
title_full eDNA as a tool for non-invasive monitoring of the fauna of a turbid, well-mixed system, the Elbe estuary in Germany
title_fullStr eDNA as a tool for non-invasive monitoring of the fauna of a turbid, well-mixed system, the Elbe estuary in Germany
title_full_unstemmed eDNA as a tool for non-invasive monitoring of the fauna of a turbid, well-mixed system, the Elbe estuary in Germany
title_short eDNA as a tool for non-invasive monitoring of the fauna of a turbid, well-mixed system, the Elbe estuary in Germany
title_sort edna as a tool for non-invasive monitoring of the fauna of a turbid, well-mixed system, the elbe estuary in germany
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8051793/
https://www.ncbi.nlm.nih.gov/pubmed/33861810
http://dx.doi.org/10.1371/journal.pone.0250452
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