Genomics, environmental genomics and the issue of microbial species

Ward, DM; Cohan, FM; Bhaya, D; Heidelberg, JF; Kühl, M; Grossman, A

Genomics, environmental genomics and the issue of microbial species

Ward, DM Cohan, FM Bhaya, D Heidelberg, JF Kühl, M

Grossman, A

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Publication Type:: Journal Article
Citation:: Heredity, 2008, 100 (2), pp. 207 - 219
Issue Date:: 2008-02-01

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Field	Value	Language
dc.contributor.author	Ward, DM	en_US
dc.contributor.author	Cohan, FM	en_US
dc.contributor.author	Bhaya, D	en_US
dc.contributor.author	Heidelberg, JF	en_US
dc.contributor.author	Kühl, M https://orcid.org/0000-0002-1792-4790	en_US
dc.contributor.author	Grossman, A	en_US
dc.date.issued	2008-02-01	en_US
dc.identifier.citation	Heredity, 2008, 100 (2), pp. 207 - 219	en_US
dc.identifier.issn	0018-067X	en_US
dc.identifier.uri	http://hdl.handle.net/10453/14963
dc.description.abstract	A microbial species concept is crucial for interpreting the variation detected by genomics and environmental genomics among cultivated microorganisms and within natural microbial populations. Comparative genomic analyses of prokaryotic species as they are presently described and named have led to the provocative idea that prokaryotes may not form species as we think about them for plants and animals. There are good reasons to doubt whether presently recognized prokaryotic species are truly species. To achieve a better understanding of microbial species, we believe it is necessary to (i) re-evaluate traditional approaches in light of evolutionary and ecological theory, (ii) consider that different microbial species may have evolved in different ways and (iii) integrate genomic, metagenomic and genome-wide expression approaches with ecological and evolutionary theory. Here, we outline how we are using genomic methods to (i) identify ecologically distinct populations (ecotypes) predicted by theory to be species-like fundamental units of microbial communities, and (ii) test their species-like character through in situ distribution and gene expression studies. By comparing metagenomic sequences obtained from well-studied hot spring cyanobacterial mats with genomic sequences of two cultivated cyanobacterial ecotypes, closely related to predominant native populations, we can conduct in situ population genetics studies that identify putative ecotypes and functional genes that determine the ecotypes' ecological distinctness. If individuals within microbial communities are found to be grouped into ecologically distinct, species-like populations, knowing about such populations should guide us to a better understanding of how genomic variation is linked to community function. © 2008 Nature Publishing Group All rights reserved.	en_US
dc.relation.ispartof	Heredity	en_US
dc.relation.isbasedon	10.1038/sj.hdy.6801011	en_US
dc.subject.classification	Evolutionary Biology	en_US
dc.subject.mesh	Cyanobacteria	en_US
dc.subject.mesh	Genetics, Population	en_US
dc.subject.mesh	Genomics	en_US
dc.subject.mesh	Environment	en_US
dc.subject.mesh	Ecosystem	en_US
dc.title	Genomics, environmental genomics and the issue of microbial species	en_US
dc.type	Journal Article
utslib.citation.volume	2	en_US
utslib.citation.volume	100	en_US
utslib.for	0604 Genetics	en_US
utslib.for	0603 Evolutionary Biology	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - C3 - Climate Change Cluster
utslib.copyright.status	closed_access
pubs.issue	2	en_US
pubs.publication-status	Published	en_US
pubs.volume	100	en_US

Abstract:

A microbial species concept is crucial for interpreting the variation detected by genomics and environmental genomics among cultivated microorganisms and within natural microbial populations. Comparative genomic analyses of prokaryotic species as they are presently described and named have led to the provocative idea that prokaryotes may not form species as we think about them for plants and animals. There are good reasons to doubt whether presently recognized prokaryotic species are truly species. To achieve a better understanding of microbial species, we believe it is necessary to (i) re-evaluate traditional approaches in light of evolutionary and ecological theory, (ii) consider that different microbial species may have evolved in different ways and (iii) integrate genomic, metagenomic and genome-wide expression approaches with ecological and evolutionary theory. Here, we outline how we are using genomic methods to (i) identify ecologically distinct populations (ecotypes) predicted by theory to be species-like fundamental units of microbial communities, and (ii) test their species-like character through in situ distribution and gene expression studies. By comparing metagenomic sequences obtained from well-studied hot spring cyanobacterial mats with genomic sequences of two cultivated cyanobacterial ecotypes, closely related to predominant native populations, we can conduct in situ population genetics studies that identify putative ecotypes and functional genes that determine the ecotypes' ecological distinctness. If individuals within microbial communities are found to be grouped into ecologically distinct, species-like populations, knowing about such populations should guide us to a better understanding of how genomic variation is linked to community function. © 2008 Nature Publishing Group All rights reserved.

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http://hdl.handle.net/10453/14963