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Genome reduction in an abundant and ubiquitous soil bacterial lineage

Tess E Brewer, Kim M Handley, Paul Carini, Jack A Gibert, Noah Fierer
doi: https://doi.org/10.1101/053942
Tess E Brewer
1Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309;
2Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309;
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Kim M Handley
3School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand;
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Paul Carini
1Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309;
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Jack A Gibert
4Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637;
5Argonne National Laboratory, Institute for Genomic and Systems Biology, Argonne, IL 60439;
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Noah Fierer
1Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309;
6Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309
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  • For correspondence: noah.fierer@colorado.edu
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Abstract

Although bacteria within the Verrucomicrobia phylum are pervasive in soils around the world, they are underrepresented in both isolate collections and genomic databases. Here we describe a single verrucomicrobial phylotype within the class Spartobacteria that is not closely related to any previously described taxa. We examined >1000 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 phylotype. 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 soil bacteria, estimated 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 chemoorganoheterotroph with numerous amino acid and vitamin auxotrophies. The large population size, relatively small genome and multiple putative auxotrophies characteristic of Ca. U. copiosus suggests 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 have identified an alternate strategy, sacrificing metabolic versatility for efficiency to become dominant in the soil environment.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted May 18, 2016.
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Genome reduction in an abundant and ubiquitous soil bacterial lineage
Tess E Brewer, Kim M Handley, Paul Carini, Jack A Gibert, Noah Fierer
bioRxiv 053942; doi: https://doi.org/10.1101/053942
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Genome reduction in an abundant and ubiquitous soil bacterial lineage
Tess E Brewer, Kim M Handley, Paul Carini, Jack A Gibert, Noah Fierer
bioRxiv 053942; doi: https://doi.org/10.1101/053942

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