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How can microbial population genomics inform community ecology?
Populations are fundamental units of ecology and evolution, but can we define them for bacteria and archaea in a biologically meaningful way? Here, we review why population structure is difficult to recognize in microbes and how recent advances in measuring contemporary gene flow allow us to identif...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Royal Society
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133533/ https://www.ncbi.nlm.nih.gov/pubmed/32200748 http://dx.doi.org/10.1098/rstb.2019.0253 |
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author | VanInsberghe, David Arevalo, Philip Chien, Diana Polz, Martin F. |
author_facet | VanInsberghe, David Arevalo, Philip Chien, Diana Polz, Martin F. |
author_sort | VanInsberghe, David |
collection | PubMed |
description | Populations are fundamental units of ecology and evolution, but can we define them for bacteria and archaea in a biologically meaningful way? Here, we review why population structure is difficult to recognize in microbes and how recent advances in measuring contemporary gene flow allow us to identify clearly delineated populations among collections of closely related genomes. Such structure can arise from preferential gene flow caused by coexistence and genetic similarity, defining populations based on biological mechanisms. We show that such gene flow units are sufficiently genetically isolated for specific adaptations to spread, making them also ecological units that are differentially adapted compared to their closest relatives. We discuss the implications of these observations for measuring bacterial and archaeal diversity in the environment. We show that operational taxonomic units defined by 16S rRNA gene sequencing have woefully poor resolution for ecologically defined populations and propose monophyletic clusters of nearly identical ribosomal protein genes as an alternative measure for population mapping in community ecological studies employing metagenomics. These population-based approaches have the potential to provide much-needed clarity in interpreting the vast microbial diversity in human and environmental microbiomes. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’. |
format | Online Article Text |
id | pubmed-7133533 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | The Royal Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-71335332020-04-07 How can microbial population genomics inform community ecology? VanInsberghe, David Arevalo, Philip Chien, Diana Polz, Martin F. Philos Trans R Soc Lond B Biol Sci Articles Populations are fundamental units of ecology and evolution, but can we define them for bacteria and archaea in a biologically meaningful way? Here, we review why population structure is difficult to recognize in microbes and how recent advances in measuring contemporary gene flow allow us to identify clearly delineated populations among collections of closely related genomes. Such structure can arise from preferential gene flow caused by coexistence and genetic similarity, defining populations based on biological mechanisms. We show that such gene flow units are sufficiently genetically isolated for specific adaptations to spread, making them also ecological units that are differentially adapted compared to their closest relatives. We discuss the implications of these observations for measuring bacterial and archaeal diversity in the environment. We show that operational taxonomic units defined by 16S rRNA gene sequencing have woefully poor resolution for ecologically defined populations and propose monophyletic clusters of nearly identical ribosomal protein genes as an alternative measure for population mapping in community ecological studies employing metagenomics. These population-based approaches have the potential to provide much-needed clarity in interpreting the vast microbial diversity in human and environmental microbiomes. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’. The Royal Society 2020-05-11 2020-03-23 /pmc/articles/PMC7133533/ /pubmed/32200748 http://dx.doi.org/10.1098/rstb.2019.0253 Text en © 2020 The Authors. http://creativecommons.org/licenses/by/4.0/ Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. |
spellingShingle | Articles VanInsberghe, David Arevalo, Philip Chien, Diana Polz, Martin F. How can microbial population genomics inform community ecology? |
title | How can microbial population genomics inform community ecology? |
title_full | How can microbial population genomics inform community ecology? |
title_fullStr | How can microbial population genomics inform community ecology? |
title_full_unstemmed | How can microbial population genomics inform community ecology? |
title_short | How can microbial population genomics inform community ecology? |
title_sort | how can microbial population genomics inform community ecology? |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133533/ https://www.ncbi.nlm.nih.gov/pubmed/32200748 http://dx.doi.org/10.1098/rstb.2019.0253 |
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