Bacterial diversity and functional metagenomics expounding the diversity of xenobiotics, stress, defense and CRISPR gene ontology providing eco-efficiency to Himalayan Hot Springs

• Published in: Functional & integrative genomics Vol. 20; no. 4; pp. 479 - 496
• Main Authors: Najar, Ishfaq Nabi, Sherpa, Mingma Thundu, Das, Sayak, Thakur, Nagendra
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.07.2020; Springer Nature B.V
• Subjects: Animal Genetics and Genomics; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; beta-Lactamases - genetics; beta-Lactamases - metabolism; Biochemistry; Biodegradation; Bioinformatics; Biomedical and Life Sciences; Cell Biology; Chlorobenzene; CRISPR; Endodeoxyribonucleases - genetics; Endodeoxyribonucleases - metabolism; Firmicutes; Gene families; Genes; Gram-positive bacteria; Heat shock; Hot springs; Hot Springs - microbiology; Life Sciences; Membrane Transport Proteins - genetics; Membrane Transport Proteins - metabolism; Metagenome; Metagenomics; Microbial Genetics and Genomics; Microbiota; Multidrug resistance; Original Article; Plant Genetics and Genomics; Stress, Physiological; Sulfur; Xenobiotics; Xenobiotics - metabolism; Xylene; NGS (next-generation sequencing); Functional metagenomics; CRISPR (clustered regularly interspaced short palindromic repeats); Phospholipid fatty acid analysis (PLFA); Hot springs; Thermophiles
• ISSN: 1438-793X; 1438-7948
• DOI: 10.1007/s10142-019-00723-x

Sikkim is one of the bio-diverse states of India, which harbors diverse alkaline and sulfur rich hot springs in its vicinity. However, there is a dearth of data present in terms of microbial and its functional diversity as only a few hot springs have been studied in this area. Thus, in this regard, microbial and functional diversity of two hot springs by NGS, PLFA, and culture-independent approaches were carried out. PLFA and culture-dependent analysis was complementary as the Gram-positive bacteria were abundant in both the hot springs with the dominance of phylum Firmicutes with Geobacillus . Metagenomic analysis revealed the abundance of Proteobacteria, Actinobacteria, and Firmicutes in both hot springs. Functional metagenomics suggested that both Yumthang and Reshi hot spring possess a diverse set of genes analogous to stress such as genes allied to osmotic, heat shock, and acid stresses; defense analogies such as multidrug resistance efflux pump, multidrug transport system, and β-lactamase; and CRISPR analogues such as related to Cas1, Cas2, Cas3, cmr1-5 proteins, CT1972, and CT1133 gene families. The xenobiotic analogues were found against benzoate, nitrotolune, xylene, DDT, and chlorocyclohexane/chlorobenzene degradation. Thus, these defensive mechanisms against environmental and anthropogenic hiccups and hindrances provide the eco-efficiency to such thermal habitats. The higher enzymatic, degradation, defense, stress potential and the lower percentage identity (< 95%) of isolates encourage the further exploration and exploitation of these habitats for industrial and biotechnological purposes.