Sympatric and allopatric differentiation delineates population structure in free-living terrestrial bacteria

Abstract

In microorganisms, specifically free-living bacteria and archaea, the equivalent of the biological species concept does not exist, creating several barriers to the study of the fine-scale genetic structure of microbial populations and thus, the processes contributing to microbial diversification. More often than not, studies attempting to delineate microbial populations overestimate traditionally-defined eukaryotic populations, or groups of individuals with the potential for contemporary interactions and exchange of genetic material. Here, we investigate the abundant leaf litter bacterium, Curtobacterium, and asked whether population structure in a free-living soil bacterium was consistent with patterns of allopatric or sympatric speciation. By investigating the fine-scale genetic structure within a single bacterial ecotype, we concluded that the distributional patterns of the populations suggest that both isolation-by-distance and isolation-by-environment contribute to Curtobacterium population structure. 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 number of clonal clusters (strains too closely-related to differentiate recombination). D = Desert, Sc = Scrubland, G/MMLR = Grassland, SS = Salton Sea, MCBA = Boston

Partners in space: Discordant population structure between legume hosts and rhizobium symbionts in their native range

“…However, metagenomic studies of microbial communities are limited in their resolution; therefore, population genomic data (Hoetzinger, Pitt, Huemer, & Hahn, 2021), coupled with spatially-structured samples of both within-and among-population variation (Whitaker & Banfield, 2006), are required for inferring population structure and gene flow, which are key to local adaptation and coevolution (Thompson 2005;Hoeksema and Forde 2008;Kraemer and Boynton 2017). Like other diverse microbial systems (Chase et al, 2019;Hoetzinger et al, 2021;Vos & Velicer, 2008), Ensifer displays both isolation by distance (chromosome) and population genetic structure (all elements); nevertheless, we found extremely closely-related strains up to 1350 km apart -indicating at least some long-distance dispersal. Large dispersal ability, together with the observation of abundant local phenotypic (Heath, 2010;Heath & Tiffin, 2009) and genomic (Bailly et al, 2011;Bailly, Olivieri, De Mita, Cleyet-Marel, & Béna, 2006) variation for symbiosis, suggests that most of the variation relevant to both bacterial adaptation and coevolution can be found at relatively small spatial scales.…”

“…The population structure and dispersal abilities of microbes remain poorly understood (Chase et al, 2019;Green, Bohannan, & Whitaker, 2008;Hanson, Fuhrman, Horner-Devine, & Martiny, 2012;Martiny et al, 2006;VanInsberghe, Arevalo, Chien, & Polz, 2020). Sequence data have revealed considerable variation in dispersal ability among microbial taxa (Locey & Lennon, 2016).…”