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Soil bacterial populations are shaped by recombination and gene-specific selection across a meadow

Alexander Crits-Christoph, Matthew Olm, View ORCID ProfileSpencer Diamond, Keith Bouma-Gregson, View ORCID ProfileJillian Banfield
doi: https://doi.org/10.1101/695478
Alexander Crits-Christoph
1Department of Plant and Microbial Biology, University of California, Berkeley
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Matthew Olm
1Department of Plant and Microbial Biology, University of California, Berkeley
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Spencer Diamond
1Department of Plant and Microbial Biology, University of California, Berkeley
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Keith Bouma-Gregson
1Department of Plant and Microbial Biology, University of California, Berkeley
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Jillian Banfield
2Department of Earth and Planetary Sciences, University of California, Berkeley
3Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA
4Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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  • For correspondence: jbanfield@berkeley.edu
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Abstract

Soil microbial diversity is often studied from the perspective of community composition, but less is known about genetic heterogeneity within species and how population structures are affected by dispersal, recombination, and selection. Genomic inferences about population structure can be made using the millions of sequencing reads that are assembled de novo into consensus genomes from metagenomes, as each read pair describes a short genomic sequence from a cell in the population. Here we track genome-wide population genetic variation for 19 highly abundant bacterial species sampled from across a grassland meadow. Genomic nucleotide identity of assembled genomes was significantly associated with local geography for half of the populations studied, and for a majority of populations within-sample nucleotide diversity could often be as high as meadow-wide nucleotide diversity. Genes involved in specialized metabolite biosynthesis and extracellular transport were characterized by elevated genetic diversity in multiple species. Microbial populations displayed varying degrees of homologous recombination and recombinant variants were often detected at 7-36% of loci genome-wide. Within multiple populations we identified genes with unusually high site-specific differentiation of alleles, fewer recombinant events, and lower nucleotide diversity, suggesting recent selective sweeps for gene variants. Taken together, these results indicate that recombination and gene-specific selection commonly shape local soil bacterial genetic variation.

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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-NC-ND 4.0 International license.
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Posted July 08, 2019.
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Soil bacterial populations are shaped by recombination and gene-specific selection across a meadow
Alexander Crits-Christoph, Matthew Olm, Spencer Diamond, Keith Bouma-Gregson, Jillian Banfield
bioRxiv 695478; doi: https://doi.org/10.1101/695478
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Soil bacterial populations are shaped by recombination and gene-specific selection across a meadow
Alexander Crits-Christoph, Matthew Olm, Spencer Diamond, Keith Bouma-Gregson, Jillian Banfield
bioRxiv 695478; doi: https://doi.org/10.1101/695478

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