Metagenomics revealing molecular profiling of community structure and metabolic pathways in natural hot springs of the Sikkim Himalaya

Abstract

Background: Himalaya is an ecologically pristine environment. The geo-tectonic activities have shaped various environmental niches with diverse microbial populations throughout the Himalayan biosphere region. Albeit, limited information is available in terms of molecular insights into the microbiome, including the uncultured microbes, of the Himalayan habitat. Hence, a vast majority of genomic resources are still under-explored from this region. Metagenome analysis has simplified the extensive in-depth exploration of diverse habitats. In the present study, the culture-independent whole metagenome sequencing methodology was employed for microbial diversity exploration and identification of genes involved in various metabolic pathways in two geothermal springs located at different altitudes in the Sikkim Himalaya.

Results: The two hot springs, Polok and Reshi, have distinct abiotic conditions. The average temperature of Polok and Reshi was recorded to be 62 °C and 43 °C, respectively. Both the aquatic habitats have alkaline geochemistry with pH in the range of 7-8. Community profile analysis revealed genomic evidence of plentiful bacteria, with a minute fraction of the archaeal population in hot water reservoirs of Polok and Reshi hot spring. Mesophilic microbes belonging to Proteobacteria and Firmicutes phyla were predominant at both the sites. Polok exhibited an extravagant representation of Chloroflexi, Deinococcus-Thermus, Aquificae, and Thermotogae. Metabolic potential analysis depicted orthologous genes associated with sulfur, nitrogen, and methane metabolism, contributed by the microflora in the hydrothermal system. The genomic information of many novel carbohydrate-transforming enzymes was deciphered in the metagenomic description. Further, the genomic capacity of antimicrobial biomolecules and antibiotic resistance were discerned.

Conclusion: The study provided comprehensive molecular information about the microbial treasury as well as the metabolic features of the two geothermal sites. The thermal aquatic niches were found a potential bioresource of biocatalyst systems for biomass-processing. Overall, this study provides the whole metagenome based insights into the taxonomic and functional profiles of Polok and Reshi hot springs of the Sikkim Himalaya. The study generated a wealth of genomic data that can be explored for the discovery and characterization of novel genes encoding proteins of industrial importance.

Keywords: Antibiotic resistance; CAZymes; Functional potential; Glycosyltransferases; Hot springs; Metagenomics; Taxonomic profiling.

Fig. 1

Sampling sites and geographical positioning of Polok and Reshi hot springs. The geographical positions of the sites have been shown by using the Google Maps, 2020

Fig. 2

An overview of taxonomic profile in Polok and Reshi hot springs. a Domain level taxonomy, b phylum level taxonomy, c family level taxonomy, d genus level taxonomy

Fig. 3

Metagenomic genes mapped to methane metabolism pathway

Fig. 4

Metagenomic genes mapped to streptomycin biosynthetic pathway

Fig. 5

Network graph showing the correlation among the microbial genera and antibiotic resistance related genes. The graph represents only the positively correlated significant values (P < 0.05). Thick lines indicate relatively higher abundance

Fig. 6

Circos figure showing the relative abundance of CAZymes in Polok and Reshi metagenome with minimum 30% difference at protein level. Supportive data to the figure is given in the S17