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DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers

Biodiversity assessment of marine hard-bottom communities is hindered by the high diversity and size-ranges of the organisms present. We developed a DNA metabarcoding protocol for biodiversity characterization of structurally complex natural marine hard-bottom communities. We used two molecular mark...

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Autores principales: Wangensteen, Owen S., Palacín, Creu, Guardiola, Magdalena, Turon, Xavier
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5937484/
https://www.ncbi.nlm.nih.gov/pubmed/29740514
http://dx.doi.org/10.7717/peerj.4705
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author Wangensteen, Owen S.
Palacín, Creu
Guardiola, Magdalena
Turon, Xavier
author_facet Wangensteen, Owen S.
Palacín, Creu
Guardiola, Magdalena
Turon, Xavier
author_sort Wangensteen, Owen S.
collection PubMed
description Biodiversity assessment of marine hard-bottom communities is hindered by the high diversity and size-ranges of the organisms present. We developed a DNA metabarcoding protocol for biodiversity characterization of structurally complex natural marine hard-bottom communities. We used two molecular markers: the “Leray fragment” of mitochondrial cytochrome c oxidase (COI), for which a novel primer set was developed, and the V7 region of the nuclear small subunit ribosomal RNA (18S). Eight different shallow marine littoral communities from two National Parks in Spain (one in the Atlantic Ocean and another in the Mediterranean Sea) were studied. Samples were sieved into three size fractions from where DNA was extracted separately. Bayesian clustering was used for delimiting molecular operational taxonomic units (MOTUs) and custom reference databases were constructed for taxonomic assignment. Despite applying stringent filters, we found high values for MOTU richness (2,510 and 9,679 MOTUs with 18S and COI, respectively), suggesting that these communities host a large amount of yet undescribed eukaryotic biodiversity. Significant gaps are still found in sequence reference databases, which currently prevent the complete taxonomic assignment of the detected sequences. In our dataset, 85% of 18S MOTUs and 64% of COI MOTUs could be identified to phylum or lower taxonomic level. Nevertheless, those unassigned were mostly rare MOTUs with low numbers of reads, and assigned MOTUs comprised over 90% of the total sequence reads. The identification rate might be significantly improved in the future, as reference databases are further completed. Our results show that marine metabarcoding, currently applied mostly to plankton or sediments, can be adapted to structurally complex hard bottom samples. Thus, eukaryotic metabarcoding emerges as a robust, fast, objective and affordable method to comprehensively characterize the diversity of marine benthic communities dominated by macroscopic seaweeds and colonial or modular sessile metazoans. The 18S marker lacks species-level resolution and thus cannot be recommended to assess the detailed taxonomic composition of these communities. Our new universal primers for COI can potentially be used for biodiversity assessment with high taxonomic resolution in a wide array of marine, terrestrial or freshwater eukaryotic communities.
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spelling pubmed-59374842018-05-08 DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers Wangensteen, Owen S. Palacín, Creu Guardiola, Magdalena Turon, Xavier PeerJ Biodiversity Biodiversity assessment of marine hard-bottom communities is hindered by the high diversity and size-ranges of the organisms present. We developed a DNA metabarcoding protocol for biodiversity characterization of structurally complex natural marine hard-bottom communities. We used two molecular markers: the “Leray fragment” of mitochondrial cytochrome c oxidase (COI), for which a novel primer set was developed, and the V7 region of the nuclear small subunit ribosomal RNA (18S). Eight different shallow marine littoral communities from two National Parks in Spain (one in the Atlantic Ocean and another in the Mediterranean Sea) were studied. Samples were sieved into three size fractions from where DNA was extracted separately. Bayesian clustering was used for delimiting molecular operational taxonomic units (MOTUs) and custom reference databases were constructed for taxonomic assignment. Despite applying stringent filters, we found high values for MOTU richness (2,510 and 9,679 MOTUs with 18S and COI, respectively), suggesting that these communities host a large amount of yet undescribed eukaryotic biodiversity. Significant gaps are still found in sequence reference databases, which currently prevent the complete taxonomic assignment of the detected sequences. In our dataset, 85% of 18S MOTUs and 64% of COI MOTUs could be identified to phylum or lower taxonomic level. Nevertheless, those unassigned were mostly rare MOTUs with low numbers of reads, and assigned MOTUs comprised over 90% of the total sequence reads. The identification rate might be significantly improved in the future, as reference databases are further completed. Our results show that marine metabarcoding, currently applied mostly to plankton or sediments, can be adapted to structurally complex hard bottom samples. Thus, eukaryotic metabarcoding emerges as a robust, fast, objective and affordable method to comprehensively characterize the diversity of marine benthic communities dominated by macroscopic seaweeds and colonial or modular sessile metazoans. The 18S marker lacks species-level resolution and thus cannot be recommended to assess the detailed taxonomic composition of these communities. Our new universal primers for COI can potentially be used for biodiversity assessment with high taxonomic resolution in a wide array of marine, terrestrial or freshwater eukaryotic communities. PeerJ Inc. 2018-05-04 /pmc/articles/PMC5937484/ /pubmed/29740514 http://dx.doi.org/10.7717/peerj.4705 Text en ©2018 Wangensteen et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Biodiversity
Wangensteen, Owen S.
Palacín, Creu
Guardiola, Magdalena
Turon, Xavier
DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers
title DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers
title_full DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers
title_fullStr DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers
title_full_unstemmed DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers
title_short DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers
title_sort dna metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers
topic Biodiversity
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5937484/
https://www.ncbi.nlm.nih.gov/pubmed/29740514
http://dx.doi.org/10.7717/peerj.4705
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