Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria

Abstract

For free-living bacteria and archaea, the equivalent of the biological species concept does not exist, creating several obstacles to the study of the processes contributing to microbial diversification. These obstacles are particularly high in soil, where high bacterial diversity inhibits the study of closely related genotypes and therefore the factors structuring microbial populations. Here, we isolated strains within a single Curtobacterium ecotype from surface soil (leaf litter) across a regional climate gradient and investigated the phylogenetic structure, recombination, and flexible gene content of this genomic diversity to infer patterns of gene flow. Our results indicate that microbial populations are delineated by gene flow discontinuities, with distinct populations cooccurring at multiple sites. Bacterial population structure was further delineated by genomic features allowing for the identification of candidate genes possibly contributing to local adaptation. These results suggest that the genetic structure within this bacterium is maintained both by ecological specialization in localized microenvironments (isolation by environment) and by dispersal limitation between geographic locations (isolation by distance).IMPORTANCE Due to the promiscuous exchange of genetic material and asexual reproduction, delineating microbial species (and, by extension, populations) remains challenging. Because of this, the vast majority of microbial studies assessing population structure often compare divergent strains from disparate environments under varied selective pressures. Here, we investigated the population structure within a single bacterial ecotype, a unit equivalent to a eukaryotic species, defined as highly clustered genotypic and phenotypic strains with the same ecological niche. Using a combination of genomic and computational analyses, we assessed the phylogenetic structure, extent of recombination, and flexible gene content of this genomic diversity to infer patterns of gene flow. To our knowledge, this study is the first to do so for a dominant soil bacterium. Our results indicate that bacterial soil populations, similarly to those in other environments, are structured by gene flow discontinuities and exhibit distributional patterns consistent with both isolation by distance and isolation by environment. Thus, both dispersal limitation and local environments contribute to the divergence among closely related soil bacteria as observed in macroorganisms.

Keywords: Curtobacterium; ecotype; gene flow; microbial ecology; population structure.

FIG 1

(A) Phylogeny of the Curtobacterium ecotype, subclade IB/C, from a core genome alignment; (B) ancestral population structure estimated from admixture analysis. Bar plots reflect the proportion of an individual genome that originates from estimated ancestral gene pools (K = 4). Genome names designate the site of isolation along the climate gradient except for MCBA (Boston, MA) and MMLR (grassland isolate from 2010).

FIG 2

Recombination network across all pairwise strains. Thicker edges represent increased recombination between strains. Nodes are colored by population designation, and node size indicates the number of clonal clusters (strains too closely related to differentiate recombination). D, desert; Sc, scrubland; G/MMLR, grassland; SS, Salton Sea; MCBA, Boston, MA.

FIG 3

Flexible gene content similarity between strains. The tree is derived from a consensus neighbor-joining analysis showing only nodes with ≥750 support. Strains are colored by population assignments identified from the recombination network (Fig. 2).

FIG 4

Highly structured genomic backbones across strains. (A) Population-specific genomic backbones within all individuals in populations 1 and 3. Population-specific genes (colored in blue) are consistently flanked by highly conserved regions (in white). Putative mobile elements are also designated in boxes along the chromosome. (B) Phylogenies of a subset of conserved genes (white arrows in panel A) flanking the population-specific regions colored by the strains in each respective population.