Limnohabitans populations in Lake Michigan

Most freshwater bacterial communities are characterized by a few dominant taxa, which are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic basis underlying this pattern is limited to a subset of taxa. Here, we investigated the genomic basis 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 metagenome assembled genomes (MAGs) from this genus 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 two of the primary drivers of 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 cultured Limnohabitans strains. 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.