A census-based estimate of Earth's bacterial and archaeal diversity.

The global diversity of Bacteria and Archaea, the most ancient and most widespread forms of life on Earth, is a subject of intense controversy. This controversy stems largely from the fact that existing estimates are entirely based on theoretical models or extrapolations from small and biased data s...

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Autores principales:	Stilianos Louca, Florent Mazel, Michael Doebeli, Laura Wegener Parfrey
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2019
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/1fcfd451b50646a6abc8363648f4a383
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spelling	oai:doaj.org-article:1fcfd451b50646a6abc8363648f4a3832021-12-02T19:54:19ZA census-based estimate of Earth's bacterial and archaeal diversity.1544-91731545-788510.1371/journal.pbio.3000106https://doaj.org/article/1fcfd451b50646a6abc8363648f4a3832019-02-01T00:00:00Zhttps://doi.org/10.1371/journal.pbio.3000106https://doaj.org/toc/1544-9173https://doaj.org/toc/1545-7885The global diversity of Bacteria and Archaea, the most ancient and most widespread forms of life on Earth, is a subject of intense controversy. This controversy stems largely from the fact that existing estimates are entirely based on theoretical models or extrapolations from small and biased data sets. Here, in an attempt to census the bulk of Earth's bacterial and archaeal ("prokaryotic") clades and to estimate their overall global richness, we analyzed over 1.7 billion 16S ribosomal RNA amplicon sequences in the V4 hypervariable region obtained from 492 studies worldwide, covering a multitude of environments and using multiple alternative primers. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs, 16S-V4 gene clusters at 97% similarity), a commonly used measure of microbial richness. Using several statistical approaches, we estimate that there exist globally about 0.8-1.6 million prokaryotic OTUs, of which we recovered somewhere between 47%-96%, representing >99.98% of prokaryotic cells. Consistent with this conclusion, our data set independently "recaptured" 91%-93% of 16S sequences from multiple previous global surveys, including PCR-independent metagenomic surveys. The distribution of relative OTU abundances is consistent with a log-normal model commonly observed in larger organisms; the total number of OTUs predicted by this model is also consistent with our global richness estimates. By combining our estimates with the ratio of full-length versus partial-length (V4) sequence diversity in the SILVA sequence database, we further estimate that there exist about 2.2-4.3 million full-length OTUs worldwide. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar richness estimates as for the global data set, suggesting that most OTUs are globally distributed. Qualitatively similar results are also obtained for other 16S similarity thresholds (90%, 95%, and 99%). Our estimates constrain the extent of a poorly quantified rare microbial biosphere and refute recent predictions that there exist trillions of prokaryotic OTUs.Stilianos LoucaFlorent MazelMichael DoebeliLaura Wegener ParfreyPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Biology, Vol 17, Iss 2, p e3000106 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Stilianos Louca Florent Mazel Michael Doebeli Laura Wegener Parfrey A census-based estimate of Earth's bacterial and archaeal diversity.
description	The global diversity of Bacteria and Archaea, the most ancient and most widespread forms of life on Earth, is a subject of intense controversy. This controversy stems largely from the fact that existing estimates are entirely based on theoretical models or extrapolations from small and biased data sets. Here, in an attempt to census the bulk of Earth's bacterial and archaeal ("prokaryotic") clades and to estimate their overall global richness, we analyzed over 1.7 billion 16S ribosomal RNA amplicon sequences in the V4 hypervariable region obtained from 492 studies worldwide, covering a multitude of environments and using multiple alternative primers. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs, 16S-V4 gene clusters at 97% similarity), a commonly used measure of microbial richness. Using several statistical approaches, we estimate that there exist globally about 0.8-1.6 million prokaryotic OTUs, of which we recovered somewhere between 47%-96%, representing >99.98% of prokaryotic cells. Consistent with this conclusion, our data set independently "recaptured" 91%-93% of 16S sequences from multiple previous global surveys, including PCR-independent metagenomic surveys. The distribution of relative OTU abundances is consistent with a log-normal model commonly observed in larger organisms; the total number of OTUs predicted by this model is also consistent with our global richness estimates. By combining our estimates with the ratio of full-length versus partial-length (V4) sequence diversity in the SILVA sequence database, we further estimate that there exist about 2.2-4.3 million full-length OTUs worldwide. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar richness estimates as for the global data set, suggesting that most OTUs are globally distributed. Qualitatively similar results are also obtained for other 16S similarity thresholds (90%, 95%, and 99%). Our estimates constrain the extent of a poorly quantified rare microbial biosphere and refute recent predictions that there exist trillions of prokaryotic OTUs.
format	article
author	Stilianos Louca Florent Mazel Michael Doebeli Laura Wegener Parfrey
author_facet	Stilianos Louca Florent Mazel Michael Doebeli Laura Wegener Parfrey
author_sort	Stilianos Louca
title	A census-based estimate of Earth's bacterial and archaeal diversity.
title_short	A census-based estimate of Earth's bacterial and archaeal diversity.
title_full	A census-based estimate of Earth's bacterial and archaeal diversity.
title_fullStr	A census-based estimate of Earth's bacterial and archaeal diversity.
title_full_unstemmed	A census-based estimate of Earth's bacterial and archaeal diversity.
title_sort	census-based estimate of earth's bacterial and archaeal diversity.
publisher	Public Library of Science (PLoS)
publishDate	2019
url	https://doaj.org/article/1fcfd451b50646a6abc8363648f4a383
work_keys_str_mv	AT stilianoslouca acensusbasedestimateofearthsbacterialandarchaealdiversity AT florentmazel acensusbasedestimateofearthsbacterialandarchaealdiversity AT michaeldoebeli acensusbasedestimateofearthsbacterialandarchaealdiversity AT laurawegenerparfrey acensusbasedestimateofearthsbacterialandarchaealdiversity AT stilianoslouca censusbasedestimateofearthsbacterialandarchaealdiversity AT florentmazel censusbasedestimateofearthsbacterialandarchaealdiversity AT michaeldoebeli censusbasedestimateofearthsbacterialandarchaealdiversity AT laurawegenerparfrey censusbasedestimateofearthsbacterialandarchaealdiversity
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A census-based estimate of Earth's bacterial and archaeal diversity.

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