Genomic Variations in Hydrogenophilus thermoluteolus Genomes Across a Small-Scale Hot Spring Soil Gradient and Global Geothermal Environments

The facultative, chemolithotrophic bacteria Hydrogenophilus thermoluteolus is an understudied thermophilic, hydrogen- and thiosulfate- oxidizing microorganism that has been found globally in hot spring environments. It was identified in a series of four soil samples collected around the Polloquere hot spring of Lauca National Park, Chile, in 10m intervals from the hot spring water line. Metagenome-assembled genomes (MAGs) of H. thermoluteolus were reconstructed from each sample, exhibiting high completion and a 98% average nucleotide identity with the reference genome of the cultured H. thermoluteolus isolate. In this study, we collected and analyzed publicly available genomes of H. thermoluteolus and other members of the Hydrogenophilceae family derived from cultures and metagenomes from a diverse set of geothermal environments for pangenomic comparison with the Polloquere MAGs. The Polloquere soils are characterized by distinct changes to the environmental chemistry and biology across the 30m distance from the hot spring. In particular, increased aridity and pH, as well as lower temperatures and biomass, coincided with a shift from a characteristic geothermal microbial population, to that of an arid desert community. Notably, however, the presence and relative abundance of H. thermoluteolus remained stable over the same distance (~0.1% of the total community). Using pangenomics, we were able to deduce several genomic differences between soil samples closest (0m) and furthest (30m) from the hot spring, as well as between the Polloquere MAGs and the cultured reference. Functionally, the 30m MAG lacked carbon fixation capabilities, while all of the soil MAGs showed added genomic capacity for denitrification not present in the reference genome. These results contribute significantly to the pool of genomic data for H. thermoluteolus, adding to our understanding of the organism's high metabolic flexibility. The Polloquere MAGs also represent a rare example of this organism appearing in a dry, colder, soil environment, presumably transported from the local hot spring. This study investigates how the genomes and metabolisms of H. thermoluteolus vary between environments from a biogeographical perspective, both globally and across a small spatial distance defined by a steep environmental gradient.