Implications of geographic separation and temporal dynamics on the evolution of free-living bacterial species are widely unclear. However, the vast amount of metagenome sequencing data generated during the last decades from various habitats around the world provides an unprecedented opportunity for such investigations. Here we exploited publicly available and new freshwater metagenomes in combination with genomes of abundant freshwater bacteria to reveal geographic and temporal population structure. We focused on species that were detected across broad geographic ranges at high enough sequence coverage for meaningful population genomic analyses, associated to the predominant freshwater taxa acI, LD12, Polynucleobacter and Ca. Methylopumilus. Despite the broad geographic ranges, each species appeared as sequence-discrete cluster, in contrast to abundant marine taxa, for which continuous diversity structures were reported on global scale. Population differentiation increased significantly with spatial distance in all species, but notable dispersal barriers (e.g. oceanic) were not apparent. Yet, the different species showed contrasting rates of geographic divergence and strikingly different intra-population dynamics in time series within individual habitats. Change of an LD12 population over seven years was minor (FST = 0.04) compared to differentiation between lakes, whereas a Polynucleobacter population displayed strong changes within merely two months (FST up to 0.54), similar in scale to differentiation between populations separated by thousands of kilometers. The slowly and steadily evolving LD12 population showed high strain diversity, whereas the dynamic Polynucleobacter population exhibited alternating clonal expansions of mostly two strains only. Based on the contrasting population structures we propose distinct models of speciation.

中文翻译：

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全球丰富的淡水细菌的地理种群结构和独特的种群内动态


地理分离和时间动态对自由生活细菌物种进化的影响尚不清楚。然而，过去几十年从世界各地不同栖息地产生的大量宏基因组测序数据为此类研究提供了前所未有的机会。在这里，我们利用公开的和新的淡水宏基因组与丰富的淡水细菌的基因组相结合来揭示地理和时间的种群结构。我们重点关注在广泛的地理范围内以足够高的序列覆盖率检测到的物种，以进行有意义的群体基因组分析，这些物种与主要的淡水类群 acI、LD12、多核杆菌和 Ca 相关。甲基小叶属。尽管地理范围广泛，但每个物种都表现为序列离散的簇，这与丰富的海洋类群形成鲜明对比，在全球范围内报告了连续的多样性结构。所有物种的种群分化随着空间距离的增加而显着增加，但显着的扩散障碍（例如海洋）并不明显。然而，不同物种在各个栖息地的时间序列中表现出截然不同的地理差异率和显着不同的种群内动态。与湖泊之间的分化相比，LD12 种群在七年内的变化很小（FST = 0.04），而多核杆菌种群在短短两个月内就表现出强烈的变化（FST 高达 0.54），其规模与相隔数千个种群之间的分化相似。公里。缓慢而稳定进化的 LD12 群体表现出高度的菌株多样性，而动态多核杆菌群体则表现出大多数仅两种菌株的交替克隆扩增。 基于对比的种群结构，我们提出了不同的物种形成模型。