Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments

Abstract

Extreme ecosystems such as hot springs are of great interest as a source of novel extremophilic species, enzymes, metabolic functions for survival and biotechnological products. India harbors hundreds of hot springs, the majority of which are not yet explored and require comprehensive studies to unravel their unknown and untapped phylogenetic and functional diversity. The aim of this study was to perform a large-scale metagenomic analysis of three major hot springs located in central India namely, Badi Anhoni, Chhoti Anhoni, and Tattapani at two geographically distinct regions (Anhoni and Tattapani), to uncover the resident microbial community and their metabolic traits. Samples were collected from seven distinct sites of the three hot spring locations with temperature ranging from 43.5 to 98°C. The 16S rRNA gene amplicon sequencing of V3 hypervariable region and shotgun metagenome sequencing uncovered a unique taxonomic and metabolic diversity of the resident thermophilic microbial community in these hot springs. Genes associated with hydrocarbon degradation pathways, such as benzoate, xylene, toluene, and benzene were observed to be abundant in the Anhoni hot springs (43.5–55°C), dominated by Pseudomonas stutzeri and Acidovorax sp., suggesting the presence of chemoorganotrophic thermophilic community with the ability to utilize complex hydrocarbons as a source of energy. A high abundance of genes belonging to methane metabolism pathway was observed at Chhoti Anhoni hot spring, where methane is reported to constitute >80% of all the emitted gases, which was marked by the high abundance of Methylococcus capsulatus. The Tattapani hot spring, with a high-temperature range (61.5–98°C), displayed a lower microbial diversity and was primarily dominated by a nitrate-reducing archaeal species Pyrobaculum aerophilum. A higher abundance of cell metabolism pathways essential for the microbial survival in extreme conditions was observed at Tattapani. Taken together, the results of this study reveal a novel consortium of microbes, genes, and pathways associated with the hot spring environment.

Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures

“…A study comparing metagenomes obtained from cold and hot deserts found thermophiles having a higher number of genes involved in metabolism and transport of carbohydrates and secondary metabolites (Le et al 2016) . Similar results were found in other studies of metagenomes from hot springs in India, where abundance of KEGG (Ogata et al 1999;Kanehisa et al 2017) pathways was investigated (Badhai, Ghosh, and Das 2015;Saxena et al 2016) .…”

“…Of the eight KEGG pathways -with significant over-representation of enzymes changing with temperature -four were previously identified as over-represented in metagenomic studies of high temperature habitats (Badhai, Ghosh, and Das 2015;Saxena et al 2016) : carbon fixation pathway in prokaryotes, pyruvate metabolism, methane metabolism and purine metabolism. The TCA cycle, another enriched KEGG pathway, is known to be extensively utilized in three thermophilic bacteria (Cordova et al 2017) .…”

Thermophilic bacterial communities inhabiting the microbial mats of “indifferent” and chalybeate (iron‐rich) thermal springs: Diversity and biotechnological analysis

“…While constituting only 21.35% and 5.9% of bacterial sequences in the CA and BV mat, respectively , Pseudomonas has also been reported in thermal springs in India where, importantly, the presence of Pseudomonas stutzeri and Acidovorax spp. was linked to the possible presence of genes associated with hydrocarbon degradation pathways in the Anhoni hot springs (43.5–55°C) (Saxena et al., ). Presumptively, this implies that thermal springs are potential reservoirs of bacterial species that can be used in the bioremediation of polluted environments.…”

Thermostable enzymes and polysaccharides produced by thermophilic bacteria isolated from Bulgarian hot springs

“…The following groups of thermophiles are commonly suggested based on their optimal growth temperature: moderate thermophiles growing between 50 and 70°C with an optimum of 55-65°C, extreme thermophiles growing optimally at temperatures between 65 and 80°C, and hyperthermophiles with Correspondence: Dr. Margarita Kambourova (margikam@ microbio.bas.bg), Institute of Microbiology, Bulgarian Academy of Sciences, Acad. Such compounds significantly contribute to biotechnological advancements in recent years [4][5][6]. 26, 1113 Sofia, Bulgaria Abbreviation: EPSs, exopolysaccharides optimum growth higher than 80°C [3].…”

“…These microorganisms have developed unique metabolic and physiological capabilities to thrive in extreme habitats and to produce particular metabolites that are rarely present in microbes of modest environments. Such compounds significantly contribute to biotechnological advancements in recent years [4][5][6]. Among compounds involved in thermophilic adaptation, enzymes and exopolysaccharides (EPSs) are of special biotechnological interest due to their unusual stability not only to high temperatures but also to detergents, organic solvents, high salt concentrations.…”