2009
DOI: 10.1101/gr.086645.108
|View full text |Cite
|
Sign up to set email alerts
|

On the origin of prokaryotic species

Abstract: The notion that all prokaryotes belong to genomically and phenomically cohesive clusters that we might legitimately call “species” is a contentious one. At issue are (1) whether such clusters actually exist; (2) what species definition might most reliably identify them, if they do; and (3) what species concept—by which is meant a genetic and ecological theory of speciation—might best explain species existence and rationalize a species definition, if we could agree on one. We review existing theories and some r… Show more

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
2
1
1
1

Citation Types

4
178
0
2

Year Published

2009
2009
2017
2017

Publication Types

Select...
5
4

Relationship

0
9

Authors

Journals

citations
Cited by 209 publications
(184 citation statements)
references
References 112 publications
(139 reference statements)
4
178
0
2
Order By: Relevance
“…To clarify this point, it would be necessary to study the changes within the M8/M31 genomes over time in their true ecological context, which includes not only habitat resources and physical conditions but also phages and predators as well as the substances secreted by other organisms (Cohan and Koeppel 2008). Beyond the controversy of how many microbial species exist (Pedró s-Alió, 2006), or even if they exist at all (Doolittle and Zhaxybayeva, 2009), a new 'unknown' is rising regarding the functional diversity and environmental adaptation of bacteria. This study is showing the extent of genome, phenotype and niche differentiation encoded by rather small inter-strain differences, a phenomenon that most likely is very widespread in the environment.…”
Section: Discussionmentioning
confidence: 99%
“…To clarify this point, it would be necessary to study the changes within the M8/M31 genomes over time in their true ecological context, which includes not only habitat resources and physical conditions but also phages and predators as well as the substances secreted by other organisms (Cohan and Koeppel 2008). Beyond the controversy of how many microbial species exist (Pedró s-Alió, 2006), or even if they exist at all (Doolittle and Zhaxybayeva, 2009), a new 'unknown' is rising regarding the functional diversity and environmental adaptation of bacteria. This study is showing the extent of genome, phenotype and niche differentiation encoded by rather small inter-strain differences, a phenomenon that most likely is very widespread in the environment.…”
Section: Discussionmentioning
confidence: 99%
“…Depending on the taxa examined, our data support both coupling and uncoupling between 16S phylogeny and function. This further highlights the now well-established notion that functional interpretation of 16S data should be made with great caution, as the concept that prokaryotes form ecologically distinct clusters remains controversial (Doolittle and Zhaxybayeva, 2009).…”
Section: Phylogenetic Distribution Of Biogeochemical Activitymentioning
confidence: 99%
“…During the last decade, there has been mounting evidence to suggest 16S rRNA-derived phylogeny is not a consistent proxy for functional capabilities (Doolittle and Zhaxybayeva, 2009). Chip-SIP allowed us to test this hypothesis by matching functional resource use to 16S rRNA phylogenetic relationships.…”
Section: Phylogenetic Distribution Of Biogeochemical Activitymentioning
confidence: 99%
“…Despite the long‐standing debate on whether there is a coherent species concept in the prokaryotic world (Achtman & Wagner, 2008; Doolittle & Zhaxybayeva, 2009), modern molecular technologies offer multiple operational definitions of species, as well as of subordinate levels, such as ecotypes, that are being successfully applied to aid the discovery process in microbial ecology. Some rely on genome‐wide features, such as DNA–DNA hybridization (Stackebrandt et al , 2002) or pairwise average nucleotide identity (Konstantinidis & Tiedje, 2005), while others are restricted to a specific marker gene (e.g., 16S rRNA gene, or a variable region therein) or multiple ones (Mende et al , 2013), (i.e., multilocus sequence typing).…”
Section: Introductionmentioning
confidence: 99%