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Nat Microbiol. 2016 Oct 31;2:16198. doi: 10.1038/nmicrobiol.2016.198.

Genome reduction in an abundant and ubiquitous soil bacterium 'Candidatus Udaeobacter copiosus'.

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Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, USA.
Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA.
School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand.
Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637, USA.
Argonne National Laboratory, Institute for Genomic and Systems Biology, Argonne, Illinois 60439, USA.
Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA.


Although bacteria within the Verrucomicrobia phylum are pervasive in soils around the world, they are under-represented in both isolate collections and genomic databases. Here, we describe a single verrucomicrobial group within the class Spartobacteria that is not closely related to any previously described taxa. We examined more than 1,000 soils and found this spartobacterial phylotype to be ubiquitous and consistently one of the most abundant soil bacterial phylotypes, particularly in grasslands, where it was typically the most abundant. We reconstructed a nearly complete genome of this phylotype from a soil metagenome for which we propose the provisional name 'Candidatus Udaeobacter copiosus'. The Ca. U. copiosus genome is unusually small for a cosmopolitan soil bacterium, estimated by one measure to be only 2.81 Mbp, compared to the predicted effective mean genome size of 4.74 Mbp for soil bacteria. Metabolic reconstruction suggests that Ca. U. copiosus is an aerobic heterotroph with numerous putative amino acid and vitamin auxotrophies. The large population size, relatively small genome and multiple putative auxotrophies characteristic of Ca. U. copiosus suggest that it may be undergoing streamlining selection to minimize cellular architecture, a phenomenon previously thought to be restricted to aquatic bacteria. Although many soil bacteria need relatively large, complex genomes to be successful in soil, Ca. U. copiosus appears to use an alternative strategy, sacrificing metabolic versatility for efficiency to become dominant in the soil environment.

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