Aquificae overcomes competition by archaeal thermophiles, and crowding by bacterial mesophiles, to dominate the boiling vent-water of a Trans-Himalayan sulfur-borax spring

Abstract

Little is known about the relative abundance and metabolisms of microorganisms present in the vent-waters of Trans-Himalayan hot springs. This study revealed a Bacteria-dominated microbiome in the ~84°C vent-water (microbial cell density ~8.5 * 104mL-1; live:dead cell ratio 17:10) of a sulfur-borax spring called Lotus Pond, situated at 4436 m, in Puga Valley. Aquificae accounted for 80% of all 16S rRNA-encoding reads within the metagenomic dataset, while only 14% of such reads were attributed to Proteobacteria. Post assembly, only 25% of all protein-coding genes identified were attributable to Aquificae, and ~41% to Proteobacteria. Annotation of raw metagenomic reads encoding 16S rRNAs, and/or PCR-amplified 16S rRNA genes, identified 163 bacterial genera, out of which 66 had been detected in past investigations of Lotus Pond′s vent-water via 16S amplicon sequencing. Among these 66,Fervidobacterium,Halomonas,Hydrogenobacter,Paracoccus,Sulfurihydrogenibium,Tepidimonas,ThermusandThiofaba(or their close phylogenomic relatives) were presently detected as metagenome-assembled genomes (MAGs). Remarkably, the MAG related to Hydrogenobacter alone accounted for ~56% of the entire metagenome, even as literature survey showed that only 15 out of the 66 genera consistently present in Lotus Pond have strains growing in the laboratory at >45°C, reflecting the continued existence of diverse mesophiles in the habitat. Most genes annotated within the MAGs/assembled-metagenome rendered bioenergetic functions (especially oxidative phosphorylation and rTCA/TCA cycles), while many (especially from Aquificae) conferred virulence functions and antibiotics synthesis/resistance. These could help the Aquificae outcompete other native thermophiles, and contain the proliferation of the bacterial mesophiles that infiltrate the ecosystem.