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

Abstract

AbstractTrans-Himalayan hot spring waters rich in sulfur, boron, sodium and chlorine (but poor in calcium and silicon) are known based on PCR-amplified 16S rRNA gene sequence data to harbor high diversities of infiltrating bacterial mesophiles. Yet, little is known about the population dynamics, primary productivity, mutual interactions, and thermal adaptations of the microorganisms present in the steaming waters discharged by these geochemically peculiar spring systems. We revealed these aspects of a bacteria-dominated microbiome thriving in the boiling (85°C) fluid vented by a sulfur-borax spring called Lotus Pond, situated at 4436 m above the mean sea-level, in the Puga valley of eastern Ladakh, on the Changthang plateau. Assembly, annotation, and population-binning of >15-GB metagenomic sequence illuminated the numeral predominance of Aquificae (particularly, the generaHydrogenobacterandSulfurihydrogenibium), even as Proteobacteria, and Firmicutes, Cyanobacteria, Chloroflexi and Bacteroidetes, contributed most of the genetic diversity of the microbiome; prevalence and diversity of Deinococcus-Thermus, Thermotogae, Thermodesulfobacteria, Crenarchaeota and Euryarchaeota were far less. Perpetual presence of bacterial mesophiles in Lotus Pond’s vent-water was evident from the detection of 51 such genera that had been discovered in previous 16S-amplicon-based investigations of the habitat, but have no member with laboratory growth at >45°C. The metagenome was replete with genes crucial for hydrothermal, and other stress, adaptations, and a majority of them were attributed to phylogenetic relatives of mesophilic bacteria; examples included genes encoding heat shock proteins, molecular chaperones, and chaperonin complexes; proteins controlling/modulating/inhibiting DNA gyrase; universal stress proteins; methionine sulfoxide reductases; fatty acid desaturases; different toxin–antitoxin systems; enzymes protecting against oxidative damage; proteins conferring flagellar structure/function, chemotaxis, cell adhesion/aggregation, biofilm formation, and quorum sensing. The Lotus Pond Aquificae not only dominated the microbiome numerically but also acted potentially as the main primary producers of the ecosystem, with chemolithotrophic sulfur oxidation (Sox) being the fundamental bioenergetic mechanism, and reductive tricarboxylic acid (rTCA) cycle the predominant carbon fixation pathway. Furthermore, the Aquificae members presentin situcontained copious genes for virulence functions, and biosynthesis of the antibiotics monobactams, streptomycin, prodigiosin, acarbose and validamycin, novobiocin, carbapenems, and vancomycin (a few genes were there for phenazine, and neomycin/kanamycin/gentamicin as well). The Lotus Pond Aquificae also contained copious genes for resistance against beta-lactam antibiotics (penicillins, cephalosporins, monobactams, and carbapenems) cationic antimicrobial peptides, vancomycin, aminoglycosides (streptomycin and neomycin/kanamycin/gentamicin), and fluoroquinolones; they also had several genes for multidrug resistance efflux pumps. Among the other thermophiles present, only Thermodesulfobacteria and Deinococcus-Thermus had genes for all these functions, albeit at much lesser frequencies; the Archaea and Thermotogae were either devoid of, or had very few genes for, the aforesaid functions. The Lotus Pond mesophiles, led by Alphaproteobacteria and Gammaproteobacteria, possessed a slightly wider variety, and higher abundance, of antibiotic synthesis/resistance genes, compared with the Aquificae, besides having a more uniform gene count across the antibiotics synthesized/resisted. We hypothesize that antibiosis helped Aquificae avoid niche overlap with other thermophiles/hyperthermophiles, especially the Archaea, besides exacerbating the bioenergetic costs of thermal endurance for the mesophiles infiltrating the system, thereby keeping the potential proliferation of these intruders at bay.