Finding the pond through the weeds: eDNA reveals underestimated diversity of pondweeds
Premise of the Study The detection of environmental DNA ( eDNA ) using high‐throughput sequencing has rapidly emerged as a method to detect organisms from environmental samples. However, eDNA studies of aquatic biomes have focused on surveillance of animal species with less emphasis on plants. Pondw...
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crwiley:10.1002/aps3.1155 2024-09-15T18:41:07+00:00 Finding the pond through the weeds: eDNA reveals underestimated diversity of pondweeds Kuzmina, Maria L. Braukmann, Thomas W. A. Zakharov, Evgeny V. Ministry of Research, Innovation and Science 2018 http://dx.doi.org/10.1002/aps3.1155 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Faps3.1155 https://onlinelibrary.wiley.com/doi/full/10.1002/aps3.1155 en eng Wiley http://creativecommons.org/licenses/by/4.0/ Applications in Plant Sciences volume 6, issue 5 ISSN 2168-0450 2168-0450 journal-article 2018 crwiley https://doi.org/10.1002/aps3.1155 2024-07-18T04:24:34Z Premise of the Study The detection of environmental DNA ( eDNA ) using high‐throughput sequencing has rapidly emerged as a method to detect organisms from environmental samples. However, eDNA studies of aquatic biomes have focused on surveillance of animal species with less emphasis on plants. Pondweeds are important bioindicators of freshwater ecosystems, although their diversity is underestimated due to difficulties in morphological identification and monitoring. Methods A protocol was developed to detect pondweeds in water samples using atpB ‐ rbcL and ITS 2 markers. The water samples were collected from the Grand River within the rare Charitable Research Reserve, Ontario ( RARE ). Short fragments were amplified using primers targeting pondweeds, sequenced on an Ion Torrent Personal Genome Machine, and assigned to the taxonomy using a local DNA reference library and GenBank. Results We detected two species earlier documented at the experimental site during ecological surveys ( Potamogeton crispus and Stuckenia pectinata ) and three species new to the RARE checklist ( P. foliosus , S. filiformis , and Zannichellia palustris ). Discussion Our targeted approach to track the species composition of pondweeds in freshwater ecosystems revealed underestimation of their diversity. This result suggests that eDNA is an effective tool for monitoring plant diversity in aquatic habitats. Article in Journal/Newspaper Zannichellia palustris Wiley Online Library Applications in Plant Sciences 6 5 |
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Wiley Online Library |
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English |
description |
Premise of the Study The detection of environmental DNA ( eDNA ) using high‐throughput sequencing has rapidly emerged as a method to detect organisms from environmental samples. However, eDNA studies of aquatic biomes have focused on surveillance of animal species with less emphasis on plants. Pondweeds are important bioindicators of freshwater ecosystems, although their diversity is underestimated due to difficulties in morphological identification and monitoring. Methods A protocol was developed to detect pondweeds in water samples using atpB ‐ rbcL and ITS 2 markers. The water samples were collected from the Grand River within the rare Charitable Research Reserve, Ontario ( RARE ). Short fragments were amplified using primers targeting pondweeds, sequenced on an Ion Torrent Personal Genome Machine, and assigned to the taxonomy using a local DNA reference library and GenBank. Results We detected two species earlier documented at the experimental site during ecological surveys ( Potamogeton crispus and Stuckenia pectinata ) and three species new to the RARE checklist ( P. foliosus , S. filiformis , and Zannichellia palustris ). Discussion Our targeted approach to track the species composition of pondweeds in freshwater ecosystems revealed underestimation of their diversity. This result suggests that eDNA is an effective tool for monitoring plant diversity in aquatic habitats. |
author2 |
Ministry of Research, Innovation and Science |
format |
Article in Journal/Newspaper |
author |
Kuzmina, Maria L. Braukmann, Thomas W. A. Zakharov, Evgeny V. |
spellingShingle |
Kuzmina, Maria L. Braukmann, Thomas W. A. Zakharov, Evgeny V. Finding the pond through the weeds: eDNA reveals underestimated diversity of pondweeds |
author_facet |
Kuzmina, Maria L. Braukmann, Thomas W. A. Zakharov, Evgeny V. |
author_sort |
Kuzmina, Maria L. |
title |
Finding the pond through the weeds: eDNA reveals underestimated diversity of pondweeds |
title_short |
Finding the pond through the weeds: eDNA reveals underestimated diversity of pondweeds |
title_full |
Finding the pond through the weeds: eDNA reveals underestimated diversity of pondweeds |
title_fullStr |
Finding the pond through the weeds: eDNA reveals underestimated diversity of pondweeds |
title_full_unstemmed |
Finding the pond through the weeds: eDNA reveals underestimated diversity of pondweeds |
title_sort |
finding the pond through the weeds: edna reveals underestimated diversity of pondweeds |
publisher |
Wiley |
publishDate |
2018 |
url |
http://dx.doi.org/10.1002/aps3.1155 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Faps3.1155 https://onlinelibrary.wiley.com/doi/full/10.1002/aps3.1155 |
genre |
Zannichellia palustris |
genre_facet |
Zannichellia palustris |
op_source |
Applications in Plant Sciences volume 6, issue 5 ISSN 2168-0450 2168-0450 |
op_rights |
http://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1002/aps3.1155 |
container_title |
Applications in Plant Sciences |
container_volume |
6 |
container_issue |
5 |
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1810485547117838336 |