Most freshwater bacterial communities are characterized by a few dominant taxa that are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic diversity within these taxonomic groups is limited to a subset of taxa. Here, we investigated the genomic diversity that enables Limnohabitans, a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight putative Limnohabitans metagenome assembled genomes (MAGs) from stations located along broad environmental gradients existing in Lake Michigan, part of Earth's largest surface freshwater system. De novo strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with co-occurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust in situ strain-delineation had not previously been achieved. Our data show that temperature and nutrient levels may be important environmental parameters associated with microdiversification within the Limnohabitans genus. Additionally, strains predominant in low and high phosphorus conditions had larger genomic divergence than strains abundant under different temperatures. Comparative genomics and gene expression analysis yielded evidence for the ability of LimB populations to exhibit cellular motility and chemotaxis, a phenotype not yet associated with available Limnohabitans isolates. Our findings broaden historical marker gene-based surveys of Limnohabitans microdiversification, and provide in situ evidence of genome diversity and its functional implications across freshwater gradients.

Importance Limnohabitans is an important bacterial taxonomic group for cycling carbon in freshwater ecosystems worldwide. Here we examined the genomic diversity of different Limnohabitans lineages. We focused on the LimB lineage of this genus, which is globally distributed and often abundant, and its abundance has shown to be largely invariant to environmental change. Our data show that the LimB lineage is actually comprised of multiple co-occurring populations of which the composition and genomic characteristics are associated with variations in temperature and nutrient levels. The gene expression profiles of this lineage suggest the importance of chemotaxis and motility, traits that had not yet been associated with the Limnohabitans genus, in adapting to environmental conditions.

大多数淡水细菌群落的特征是在世界各地的淡水生物群落中普遍存在的少数优势类群。我们对这些分类组中的基因组多样性的了解仅限于一个分类单元。在这里，我们研究了基因组多样性，该多样性使Limnohabitans（一种使初级生产者的碳汇入较高营养水平的淡水属钥匙）能够实现丰度和普遍性。我们从位于地球上最大的地面淡水系统一部分的密歇根湖中存在的广泛环境梯度中的站中重建了八个推定的Limnohabitans metagenome组装基因组（MAGs）。从头开始菌株推论分析从这些MAG中共解析了23个菌株，这些菌株被强烈分为两个特定于生境的簇，并且来自不同谱系的共生菌株。数量最多的菌株属于丰富的LimB谱系，对此以前尚未实现可靠的原位菌株鉴定。我们的数据表明温度和营养水平可能是与Limnohabitans内的微生物多样性相关的重要环境参数属。另外，在低磷和高磷条件下占优势的菌株比在不同温度下富集的菌株具有更大的基因组差异。比较基因组学和基因表达分析产生了LimB群体表现出细胞运动性和趋化性的能力的证据，该表型尚未与可用的Limnohabitans分离株相关。我们的发现扩大了基于历史标记基因的Limnohabitans微生物多样性的调查范围，并提供了基因组多样性及其在整个淡水梯度中的功能含义的现场证据。

重要性 Limnohabitans是在全球淡水生态系统中循环碳循环的重要细菌分类学类别。在这里，我们检查了不同Limnohabitans谱系的基因组多样性。我们关注了该属的LimB谱系，该谱系在全球范围内分布且通常很丰富，并且其丰富程度已显示出对环境变化的大部分不变性。我们的数据表明，LimB谱系实际上由多个同时出现的种群组成，这些种群的组成和基因组特征与温度和营养水平的变化相关。该谱系的基因表达谱表明趋化性和运动性的重要性，尚未与Limnohabitans相关的特征 属，适应环境条件。