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Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from...

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Autores principales: Shade, Ashley, Jones, Stuart E., Caporaso, J. Gregory, Handelsman, Jo, Knight, Rob, Fierer, Noah, Gilbert, Jack A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society of Microbiology 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4161262/
https://www.ncbi.nlm.nih.gov/pubmed/25028427
http://dx.doi.org/10.1128/mBio.01371-14
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author Shade, Ashley
Jones, Stuart E.
Caporaso, J. Gregory
Handelsman, Jo
Knight, Rob
Fierer, Noah
Gilbert, Jack A.
author_facet Shade, Ashley
Jones, Stuart E.
Caporaso, J. Gregory
Handelsman, Jo
Knight, Rob
Fierer, Noah
Gilbert, Jack A.
author_sort Shade, Ashley
collection PubMed
description Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT made up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amounts of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified “one-hit wonder” CRT that were observed at only one time point. Using a case study from a temperate lake, we gained additional insights into the ecology of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amount to microbial community dynamics than is apparent from their low proportional abundances. This observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time.
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spelling pubmed-41612622014-09-11 Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity Shade, Ashley Jones, Stuart E. Caporaso, J. Gregory Handelsman, Jo Knight, Rob Fierer, Noah Gilbert, Jack A. mBio Research Article Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT made up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amounts of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified “one-hit wonder” CRT that were observed at only one time point. Using a case study from a temperate lake, we gained additional insights into the ecology of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amount to microbial community dynamics than is apparent from their low proportional abundances. This observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time. American Society of Microbiology 2014-07-15 /pmc/articles/PMC4161262/ /pubmed/25028427 http://dx.doi.org/10.1128/mBio.01371-14 Text en Copyright © 2014 Shade et al. http://creativecommons.org/licenses/by-nc-sa/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license (http://creativecommons.org/licenses/by-nc-sa/3.0/) , which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Shade, Ashley
Jones, Stuart E.
Caporaso, J. Gregory
Handelsman, Jo
Knight, Rob
Fierer, Noah
Gilbert, Jack A.
Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity
title Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity
title_full Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity
title_fullStr Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity
title_full_unstemmed Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity
title_short Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity
title_sort conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4161262/
https://www.ncbi.nlm.nih.gov/pubmed/25028427
http://dx.doi.org/10.1128/mBio.01371-14
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