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The ecological coherence of high bacterial taxonomic ranks

Abstract

The species is a fundamental unit of biological organization, but its relevance for Bacteria and Archaea is still hotly debated. Even more controversial is whether the deeper branches of the ribosomal RNA-derived phylogenetic tree, such as the phyla, have ecological importance. Here, we discuss the ecological coherence of high bacterial taxa in the light of genome analyses and present examples of niche differentiation between deeply diverging groups in terrestrial and aquatic systems. The ecological relevance of high bacterial taxa has implications for bacterial taxonomy, evolution and ecology.

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Figure 1: Habitat–phylotype associations for the Alphaproteobacteria.
Figure 2: Niche differentiation at the phylum and class levels.
Figure 3: Microbial succession at the order level in the human small-bowel lumen.
Figure 4: Habitat–phylotype associations.

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Acknowledgements

L.P. gratefully acknowledges the Environment and Agronomy research division and the International Relations Department of the Institut National de la Recherche Agronomique, France, and the Department of Microbiology of the Swedish University of Agricultural Sciences in Uppsala for supporting and hosting his sabbatical in Sweden. T.J.B. was supported by the Lake Ecosystems Response to Environmental Change (LEREC) programme (which is funded by the Swedish Research Council Formas) while at the University of Uppsala. S.H. is supported by the Swedish Research Council and the Swedish Research Council Formas, which finance the Uppsala Monitoring Centre, and S.G.E.A. is supported by the Swedish Research Council, the Göran Gustafsson Foundation, the Swedish Foundation for Strategic Research and the Knut and Alice Wallenberg Foundation. J.P. acknowledges support from the Royal Society of Edinburgh, and W.B.W. from the US Department of Agriculture and the US National Science Foundation.

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Correspondence to Laurent Philippot.

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DATABASES

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Escherichia coli

Ralstonia solanacearum

Takifugu rubripes

FURTHER INFORMATION

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Glossary

Biogeography

The distribution of organisms over space and time, including where they live, at what abundance, and why; these data offer insights into the mechanisms that generate and maintain diversity.

Clade

A phylogenetically coherent bacterial group.

Deep sequencing

High-throughput sequencing designed to maximize the amount of sequence information that can be gained from an environmental sample, the ultimate aim being exhaustive sequencing.

High taxonomic level

A taxonomic level from genus to phylum.

Horizontal gene transfer

The acquisition of a new DNA fragment from another organism.

Ileostomy

A surgical opening between the abdominal wall and the ileum (small intestine).

Lineage

A group of taxa that are related by descent from a common ancestor.

Niche

The particular set of resources and environmental conditions that an individual species exploits.

Phylogeny

The inferred evolutionary relationships among a group of organisms (most often inferred on the basis of molecular data).

Phylotype

A taxon-neutral term referring to an organism with a unique genetic make-up according to its evolutionary relationship to other organisms.

Species

A generally accepted species definition has yet to be established for microorganisms. For the purposes of taxonomy, an ad hoc definition on the basis of DNA hybridization is widely used. This definition is based on degrees of relatedness, without an underlying biological principle.

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Philippot, L., Andersson, S., Battin, T. et al. The ecological coherence of high bacterial taxonomic ranks. Nat Rev Microbiol 8, 523–529 (2010). https://doi.org/10.1038/nrmicro2367

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