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Extracellular DNA as a genetic recorder of microbial diversity in benthic deep-sea ecosystems

Extracellular DNA in deep-sea sediments represents a major repository of genes, which previously belonged to living organisms. However, the extent to which these extracellular genes influence current estimates of prokaryotic biodiversity is unknown. We investigated the abundance and diversity of 16S...

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Autores principales: Corinaldesi, C., Tangherlini, M., Manea, E., Dell’Anno, A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5789842/
https://www.ncbi.nlm.nih.gov/pubmed/29382896
http://dx.doi.org/10.1038/s41598-018-20302-7
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author Corinaldesi, C.
Tangherlini, M.
Manea, E.
Dell’Anno, A.
author_facet Corinaldesi, C.
Tangherlini, M.
Manea, E.
Dell’Anno, A.
author_sort Corinaldesi, C.
collection PubMed
description Extracellular DNA in deep-sea sediments represents a major repository of genes, which previously belonged to living organisms. However, the extent to which these extracellular genes influence current estimates of prokaryotic biodiversity is unknown. We investigated the abundance and diversity of 16S rDNA sequences contained within extracellular DNA from continental margins of different biogeographic regions. We also compared the taxonomic composition of microbial assemblages through the analysis of extracellular DNA and DNA associated with living cells. 16S rDNA contained in the extracellular DNA pool contributed up to 50% of the total 16S rDNA copy number determined in the sediments. Ca. 4% of extracellular Operational Taxonomic Units (OTUs) were shared among the different biogeographic regions revealing the presence of a core of preserved OTUs. A higher fraction of OTUs was exclusive of each region potentially due to its geographic and thermohaline characteristics. Ca. one third of the OTUs identified in the extracellular DNA were absent from living prokaryotic assemblages, possibly representing the signatures of past assemblages. Our findings expand the knowledge of the contribution of extracellular microbial sequences to current estimates of prokaryotic diversity obtained through the analyses of “environmental DNA”, and open new perspectives for understanding microbial successions in benthic ecosystems.
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spelling pubmed-57898422018-02-15 Extracellular DNA as a genetic recorder of microbial diversity in benthic deep-sea ecosystems Corinaldesi, C. Tangherlini, M. Manea, E. Dell’Anno, A. Sci Rep Article Extracellular DNA in deep-sea sediments represents a major repository of genes, which previously belonged to living organisms. However, the extent to which these extracellular genes influence current estimates of prokaryotic biodiversity is unknown. We investigated the abundance and diversity of 16S rDNA sequences contained within extracellular DNA from continental margins of different biogeographic regions. We also compared the taxonomic composition of microbial assemblages through the analysis of extracellular DNA and DNA associated with living cells. 16S rDNA contained in the extracellular DNA pool contributed up to 50% of the total 16S rDNA copy number determined in the sediments. Ca. 4% of extracellular Operational Taxonomic Units (OTUs) were shared among the different biogeographic regions revealing the presence of a core of preserved OTUs. A higher fraction of OTUs was exclusive of each region potentially due to its geographic and thermohaline characteristics. Ca. one third of the OTUs identified in the extracellular DNA were absent from living prokaryotic assemblages, possibly representing the signatures of past assemblages. Our findings expand the knowledge of the contribution of extracellular microbial sequences to current estimates of prokaryotic diversity obtained through the analyses of “environmental DNA”, and open new perspectives for understanding microbial successions in benthic ecosystems. Nature Publishing Group UK 2018-01-30 /pmc/articles/PMC5789842/ /pubmed/29382896 http://dx.doi.org/10.1038/s41598-018-20302-7 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
Corinaldesi, C.
Tangherlini, M.
Manea, E.
Dell’Anno, A.
Extracellular DNA as a genetic recorder of microbial diversity in benthic deep-sea ecosystems
title Extracellular DNA as a genetic recorder of microbial diversity in benthic deep-sea ecosystems
title_full Extracellular DNA as a genetic recorder of microbial diversity in benthic deep-sea ecosystems
title_fullStr Extracellular DNA as a genetic recorder of microbial diversity in benthic deep-sea ecosystems
title_full_unstemmed Extracellular DNA as a genetic recorder of microbial diversity in benthic deep-sea ecosystems
title_short Extracellular DNA as a genetic recorder of microbial diversity in benthic deep-sea ecosystems
title_sort extracellular dna as a genetic recorder of microbial diversity in benthic deep-sea ecosystems
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5789842/
https://www.ncbi.nlm.nih.gov/pubmed/29382896
http://dx.doi.org/10.1038/s41598-018-20302-7
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