Comparative metagenomic analyses of a high-altitude Himalayan geothermal spring revealed temperature-constrained habitat-specific microbial community and metabolic dynamics
Metagenomic surveys across microbial mat (~ 55 °C) samples of high-altitude (1760 m above sea level) Himalayan geothermal springs have revealed specialized community enriched with niche-specific functions. In this study, we have performed metagenomic sequence-based analyses to get insights into taxonomic composition and functional potential of hyperthermophiles in water (~ 95 °C) and sediment samples (78–98 °C). Community analyses revealed predominance of thermophilic bacterial and archeal genera dwelling in water in contrast to microbial mats (55 °C), namely Methylophilus, Methyloversatilis, Emticicia, Caulobacter, Thermus, Enhydrobacter and Pyrobaculum. Sediment samples having surface temperature (~ 78 °C) were colonized by Pyrobaculum and Chloroflexus while genus Massilia was found to be inhabited in high-temperature sediments (~ 98 °C). Functional analyses of metagenomic sequences revealed genetic enrichment of genes such as type IV secretion system, flagellar assembly and two-component system in contrast to mats. Furthermore, inter-sample comparison of enriched microbial diversity among water, sediment and microbial mats revealed habitat-specific clustering of the samples within same environment highlighting the role of temperature dynamics in modulating community structure across different habitats in same niche. However, function-based analysis demonstrated site-specific clustering among sediment, microbial mat and water samples. Furthermore, a novel thermophilic genotype of the genus Emticicia (designated as strain MM) was reconstructed from metagenome data. This is a correlative study between three major habitats present in geothermal spring environment, i.e., water, sediment and microbial mats revealing greater phylogenetic and functional dispersion emphasizing changing habitat-specific dynamics with temperature.
KeywordsHot spring Metagenomic Thermophiles Emticicia Genome reconstruction High temperature
The authors acknowledge funds from Department of Biotechnology (DBT) (BT/PR15118/BCE/8/1141/2015) and Indian Council for Agricultural Research-National Bureau of Agriculturally Important Microorganisms (ICAR-NBAIM). NKM and AS gratefully acknowledge DBT and ICAR-NBAIM for providing research fellowships. This manuscript was revised when RL was on Executive Endeavour Fellowship at Murdoch University, Perth, Australia.
Compliance with ethical standards
Conflict of interest
The authors declare no conflict of interest.
- Chandrasekharam D, Alam MA, Minissale A (2005) Thermal discharges at Manikaran, Himachal Pradesh, India. In: Proc. World Geothermal Congress, AntalyaGoogle Scholar
- Hanson RS, Hanson TE (1996) Methanotrophic bacteria. Microbiol Rev 60:439–471Google Scholar
- Hou W, Wang S, Dong H, Jiang H, Briggs BR, Peacock JP, Huang Q, Huang L, Wu G, Zhi X, Li W, Dodsworth JA, Hedlund BP, Zhang C, Hartnett HE, Dijkstra P, Hungate BA (2013) A comprehensive census of microbial diversity in hot springs of Tengchong, Yunnan province China using 16S rRNA gene pyrosequencing. PLoS One 8:e53350CrossRefGoogle Scholar
- Mohanrao MM, Singh DP, Kanika K, Goyal E, Singh AK (2016) Deciphering the microbial diversity of Tattapani water spring using metagenomic approach. Int J Agric Sci Res 6:371–382Google Scholar
- Postma PW, Lengeler JW, Jacobson GR (1993) Phosphoenolpyruvate: carbohydrate phosphotransferase systems of bacteria. Microbiol Rev 57:543–594Google Scholar
- Ruby JG, Bellare P, Derisi JL (2013) PRICE: software for the targeted assembly of components of (meta) genomic sequence data. Genes Genom Genet 3:865–880Google Scholar
- Sharma A, Hira P, Shakarad M, Lal R (2014) Draft genome sequence of Cellulosimicrobium sp. strain MM, isolated from arsenic-rich microbial mats of a Himalayan hot spring. Genome Announc 2:e01020–e01014Google Scholar
- Tekere M, Lötter A, Olivier J, Jonker N, Venter S (2013) Metagenomic analysis of bacterial diversity of Siloam hot water spring, Limpopo, South Africa. Afr J Biotechnol 10:18005–18012Google Scholar