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Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities
Marine infrastructure can favor the spread of non-indigenous marine biofouling species by providing a suitable habitat for them to proliferate. Cryptic organisms or those in early life stages can be difficult to distinguish by conventional morphological taxonomy. Molecular tools, such as metabarcodi...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6215007/ https://www.ncbi.nlm.nih.gov/pubmed/30389965 http://dx.doi.org/10.1038/s41598-018-34541-1 |
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author | Ammon, Ulla von Wood, Susanna A. Laroche, Olivier Zaiko, Anastasija Tait, Leigh Lavery, Shane Inglis, Graeme J. Pochon, Xavier |
author_facet | Ammon, Ulla von Wood, Susanna A. Laroche, Olivier Zaiko, Anastasija Tait, Leigh Lavery, Shane Inglis, Graeme J. Pochon, Xavier |
author_sort | Ammon, Ulla von |
collection | PubMed |
description | Marine infrastructure can favor the spread of non-indigenous marine biofouling species by providing a suitable habitat for them to proliferate. Cryptic organisms or those in early life stages can be difficult to distinguish by conventional morphological taxonomy. Molecular tools, such as metabarcoding, may improve their detection. In this study, the ability of morpho-taxonomy and metabarcoding (18S rRNA and COI) using three reference databases (PR2, BOLD and NCBI) to characterize biodiversity and detect non-indigenous species (NIS) in biofouling was compared on 60 passive samplers deployed over summer and winter in a New Zealand marina. Highest resolution of metazoan taxa was identified using 18S rRNA assigned to PR2. There were higher assignment rates to NCBI reference sequences, but poorer taxonomic identification. Using all methods, 48 potential NIS were identified. Metabarcoding detected the largest proportion of those NIS: 77% via 18S rRNA/PR2 and NCBI and 35% via COI/BOLD and NCBI. Morpho-taxonomy detected an additional 14% of all identified NIS comprising mainly of bryozoan taxa. The data highlight several on-going challenges, including: differential marker resolution, primer biases, incomplete sequence reference databases, and variations in bioinformatic pipelines. Combining morpho-taxonomy and molecular analysis methods will likely enhance the detection of NIS from complex biofouling. |
format | Online Article Text |
id | pubmed-6215007 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-62150072018-11-06 Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities Ammon, Ulla von Wood, Susanna A. Laroche, Olivier Zaiko, Anastasija Tait, Leigh Lavery, Shane Inglis, Graeme J. Pochon, Xavier Sci Rep Article Marine infrastructure can favor the spread of non-indigenous marine biofouling species by providing a suitable habitat for them to proliferate. Cryptic organisms or those in early life stages can be difficult to distinguish by conventional morphological taxonomy. Molecular tools, such as metabarcoding, may improve their detection. In this study, the ability of morpho-taxonomy and metabarcoding (18S rRNA and COI) using three reference databases (PR2, BOLD and NCBI) to characterize biodiversity and detect non-indigenous species (NIS) in biofouling was compared on 60 passive samplers deployed over summer and winter in a New Zealand marina. Highest resolution of metazoan taxa was identified using 18S rRNA assigned to PR2. There were higher assignment rates to NCBI reference sequences, but poorer taxonomic identification. Using all methods, 48 potential NIS were identified. Metabarcoding detected the largest proportion of those NIS: 77% via 18S rRNA/PR2 and NCBI and 35% via COI/BOLD and NCBI. Morpho-taxonomy detected an additional 14% of all identified NIS comprising mainly of bryozoan taxa. The data highlight several on-going challenges, including: differential marker resolution, primer biases, incomplete sequence reference databases, and variations in bioinformatic pipelines. Combining morpho-taxonomy and molecular analysis methods will likely enhance the detection of NIS from complex biofouling. Nature Publishing Group UK 2018-11-02 /pmc/articles/PMC6215007/ /pubmed/30389965 http://dx.doi.org/10.1038/s41598-018-34541-1 Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Ammon, Ulla von Wood, Susanna A. Laroche, Olivier Zaiko, Anastasija Tait, Leigh Lavery, Shane Inglis, Graeme J. Pochon, Xavier Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities |
title | Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities |
title_full | Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities |
title_fullStr | Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities |
title_full_unstemmed | Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities |
title_short | Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities |
title_sort | combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6215007/ https://www.ncbi.nlm.nih.gov/pubmed/30389965 http://dx.doi.org/10.1038/s41598-018-34541-1 |
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