Genomic analysis of the mesophilic Thermotogae genus Mesotoga reveals phylogeographic structure and genomic determinants of its distinct metabolism

Summary The genus Mesotoga, the only described mesophilic Thermotogae lineage, is common in mesothermic anaerobic hydrocarbon-rich environments. Besides mesophily, Mesotoga displays lineage-specific phenotypes, such as no or little H2 production and dependence on sulfur-compound reduction, which may influence its ecological role. We used comparative genomics of 18 Mesotoga strains (pairwise 16S rRNA identity > 99%) and a transcriptome of M. prima to investigate how life at moderate temperatures affects phylogeography and to interrogate the genomic features of its lineage-specific metabolism. We propose that Mesotoga accomplish H2 oxidation and thiosulfate reduction using a sulfide dehydrogenase and a hydrogenase-complex and that a pyruvate:ferredoxin oxidoreductase acquired from Clostridia is responsible for oxidizing acetate. Phylogenetic analysis revealed three distinct Mesotoga lineages (89.6-99.9% average nucleotide identity [ANI] within lineages, 79.3-87.6% ANI between lineages) having different geographic distribution patterns and high levels of intra-lineage recombination but little geneflow between lineages. Including data from metagenomes, phylogeographic patterns suggest that geographical separation historically has been more important for Mesotoga than hyperthermophilic Thermotoga and we hypothesize that distribution of Mesotoga is constrained by their anaerobic lifestyle. Our data also suggest that recent anthropogenic activities and environments (e.g., wastewater treatment, oil exploration) have expanded Mesotoga habitats and dispersal capabilities. Originality-Significance Statement This study comprises one of the first whole-genome-based phylogeographic analyses of anaerobic mesophiles, and our data suggest that such microbes are more restricted by geography than are thermophiles (and mesophilic aerobes). This is likely to be a general trait for similar anaerobic organisms – and therefore broadly relevant to and testable in other environments. Moreover, Mesotoga bacteria are part of the largely understudied subsurface ecosystem that has relatively recently been recognized as a new and important biosphere. Understanding the forces responsible for the distribution of organisms in the subsurface, as well as the identification of genes responsible for Mesotoga’s distinct metabolism, will contribute to the understanding of these communities.