Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
mBio. 2019 Oct 29;10(5):e02361-19. doi: 10.1128/mBio.02361-19.
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 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). 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.
对于自由生活的细菌和古菌来说，不存在与生物物种概念等效的概念，这给研究促成微生物多样化的过程带来了几个障碍。这些障碍在土壤中尤为突出，那里的高细菌多样性抑制了对密切相关基因型的研究，从而也影响了对微生物种群结构的因素的研究。在这里，我们从跨区域气候梯度的地表土壤（落叶）中分离出单一生态型内的菌株，并研究了这种基因组多样性的系统发育结构、重组和灵活的基因含量，以推断基因流动的模式。我们的结果表明，微生物种群是由基因流动不连续性划定的，不同种群在多个地点共同出现。细菌种群结构进一步由允许识别可能有助于局部适应的候选基因的基因组特征划定。这些结果表明，这种细菌的遗传结构既通过局部微环境中的生态特化（环境隔离）来维持，也通过地理位置之间的扩散限制（距离隔离）来维持。由于遗传物质的混杂交换和无性繁殖，微生物物种（以及扩展到种群）的划分仍然具有挑战性。正因为如此，绝大多数评估种群结构的微生物研究通常是在不同的选择压力下，比较来自不同环境的不同菌株。在这里，我们研究了单一细菌生态型内的种群结构，这是一个相当于真核生物物种的单位，定义为具有相同生态位的高度聚类的基因型和表型菌株。我们结合使用基因组和计算分析，评估了这种基因组多样性的系统发育结构、重组程度和灵活的基因含量，以推断基因流动的模式。据我们所知，这项研究是第一个针对一种优势土壤细菌进行的研究。我们的结果表明，类似于其他环境中的种群，土壤细菌种群是由基因流动不连续性构成的，并且表现出与距离隔离和环境隔离一致的分布模式。因此，扩散限制和局部环境都有助于解释宏观生物中观察到的密切相关土壤细菌的分化。
