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.

Temporal Variation of Culture Independent Bacterial Diversity Based on Amplicon Sequencing of the North Sikkim Hot Spring Solfataric Soil Sediments

“…The hot spring soil ecology of the Sikkim Himalayas, had higher percentages of Gram negative bacterial phylum such as Proteobacteria and Bacteroidetes as compared to that of Gram positive bacterial phylum of Firmicutes and Actinobacteria. Interestingly, in the hot spring water samples also similar observations were reported [16,17,19]. The resident signature soil ora such as Planctomycetes and Chlorobi, which are commonly found in sulfur rich hot springs were also found here.…”

“…Those hot spring water samples, were abundant in Proteobacteria (Polok-47%; Borong-63%; Reshi-76%) and Yumthang hot spring was predominant with Actinomycetes (98%). The most abundant genera in the hot spring water of Sikkim were Acidovorax, Acinetobacter, Exiguobacterium, Flavobacterium, Ignavibacterium, Paenisporosarcina, Paracoccus, Pseudomonas, Rhodococcus, Serratia, Sulfuritalea, Thermodesulfovibrio, Thermus, and Thiobacillus [16][17][18][19].…”

Glycoside Hydrolases and Glycosyltransferases from Hyperthermophilic Archaea: Insights on Their Characteristics and Applications in Biotechnology

“…Many sequence-based analyses tried to address the biodiversity of volcanic sites and hot springs with the goal of discovering and characterizing novel hyperthermophilic CAZymes to explore their industrial and biotechnological potential [21][22][23]. GHs are abun-dant in archaeal genomes as summarized in Figure 2.…”

“…Hyperthermophilic Archaea have recently received great interest in metagenomic studies of extreme environments and constitute promising bioresource for high-temperature industrial processes. Several studies have been performed to analyze the diversity of microbial communities in hot spring systems using the metagenomic datasets that allow to study the unculturable, but significant microorganisms, to gain new insights for novel archaeal CAZymes [23,114].…”

Microbial Diversity of Terrestrial Geothermal Springs in Armenia and Nagorno-Karabakh: A Review

“…This genus appears to be present in terrestrial hot springs. Cyanobacteria have also been established as an important part of community metabolism in many continental hot springs [79][80][81][82][83][84][85]. * Phylogenetic groups representing more than 2% of the community sequences are presented.…”