Comparative metagenomic analyses of a high-altitude Himalayan geothermal spring revealed temperature-constrained habitat-specific microbial community and metabolic dynamics

  • Nitish Kumar Mahato
  • Anukriti Sharma
  • Yogendra Singh
  • Rup LalEmail author
Original Paper


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.


Hot 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.

Supplementary material

203_2018_1616_MOESM1_ESM.docx (70 kb)
Supplementary material 1 (DOCX 69 KB)


  1. Aziz RK, Bartels D, Best AA, DeJong M, Disz T, Edwards RA et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9:75CrossRefGoogle Scholar
  2. Badhai J, Ghosh TS, Das SK (2015) Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India. Front Microbiol 6:1166CrossRefGoogle Scholar
  3. Beam JP, Jay ZJ, Kozubal MA, Inskeep WP (2014) Niche specialization of novel Thaumarchaeota to oxic and hypoxic acidic geothermal springs of Yellowstone National Park. ISME J 8:938–951CrossRefGoogle Scholar
  4. Bhatia S, Batra N, Pathak A, Green SJ, Joshi A, Chauhan A (2015) Metagenomic evaluation of bacterial and archaeal diversity in the geothermal hot springs of Manikaran, India. Genome Announc 3:e01544–e01514CrossRefGoogle Scholar
  5. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973CrossRefGoogle Scholar
  6. Chandrasekharam D, Alam MA, Minissale A (2005) Thermal discharges at Manikaran, Himachal Pradesh, India. In: Proc. World Geothermal Congress, AntalyaGoogle Scholar
  7. Cinti D, Pizzino L, Voltattorni N, Quattrocchi F, Walia V (2009) Geochemistry of thermal waters along fault segments in the Beas and Parvati valleys (north-west Himalaya, Himachal Pradesh) and in the Sohna town (Haryana), India. Geochem J 43:65–76CrossRefGoogle Scholar
  8. Clarke A, Gaston KJ (2006) Climate, energy and diversity. Proc Biol Sci 273:2257–2266CrossRefGoogle Scholar
  9. Currie DJ, Mittelbach GG, Cornell HV, Field R, Guegan JF, Hawkins BA, Kaufman DM, Kerr JT, Oberdorff T, O’Brien E, Turner JRG (2004) Predictions and tests of climate-based hypotheses of broad-scale variation in taxonomic richness. Ecol Lett 7:1121–1134CrossRefGoogle Scholar
  10. Deng Y, Cui X, Hernandez M, Dumont MG (2014) Microbial diversity in hummock and hollow soils of three wetlands on the Qinghai-Tibetan plateau revealed by 16S rRNA pyrosequencing. PLoS One 9:e103115CrossRefGoogle Scholar
  11. Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, et al (2008) Functional metagenomic profiling of nine biomes. Nature 452:629CrossRefGoogle Scholar
  12. Dwivedi V, Sangwan N, Nigam A, Garg N, Niharika N, Khurana P, Khurana JP, Lal R (2012) Draft genome sequence of Thermus sp. strain RL, isolated from a hot water spring located atop the Himalayan ranges at Manikaran, India. J Bacteriol 194:3534CrossRefGoogle Scholar
  13. Dwivedi V, Kumari K, Gupta SK, Kumari R, Tripathi C, Lata P, Niharika N, Singh AK, Kumar R, Nigam A, Garg N, Lal R (2015) Thermus parvatiensis RLT sp. nov., isolated from a Hot Water Spring, located Atop the Himalayan ranges at Manikaran, India. Indian J Microbiol 55:357–365CrossRefGoogle Scholar
  14. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797CrossRefGoogle Scholar
  15. Hanson RS, Hanson TE (1996) Methanotrophic bacteria. Microbiol Rev 60:439–471Google Scholar
  16. He Y, Xiao X, Wang F (2013) Metagenome reveals potential microbial degradation of hydrocarbon coupled with sulfate reduction in an oil-immersed chimney from Guaymas Basin. Front Microbiol 4:148CrossRefGoogle Scholar
  17. 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
  18. Huang Q, Dong CZ, Dong RM, Jiang H. Wang S, Wang G, Fang B, Ding X, Niu L, Li X, Zhang C, Dong H (2011) Archaeal and bacterial diversity in hot springs on the Tibetan plateau, China. Extremophiles 15:549–563CrossRefGoogle Scholar
  19. Jadhav A, Shanmugham B, Rajendiran A, Pan A (2014) Unraveling novel broad-spectrum antibacterial targets in food and waterborne pathogens using comparative genomics and protein interaction network analysis. Infect Genet Evol 27:300–308CrossRefGoogle Scholar
  20. Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30CrossRefGoogle Scholar
  21. Konstantinidis KT, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102:2567–2572CrossRefGoogle Scholar
  22. Kubo K, Knittel K, Amann R, Fukui M, Matsuura K (2011) Sulfur-metabolizing bacterial populations in microbial mats of the Nakabusa hot spring, Japan. Syst Appl Microbiol 34:293–302CrossRefGoogle Scholar
  23. Kumar M, Yadav AN, Tiwari R, Prasanna R, Saxena AK (2014) Deciphering the diversity of culturable thermotolerant bacteria from Manikaran hot springs. Ann Microbiol 64:741–751CrossRefGoogle Scholar
  24. Lau MC, Aitchison JC, Pointing SB (2009) Bacterial community composition in thermophilic microbial mats from five hot springs in Central Tibet. Extremophiles 13:139–149CrossRefGoogle Scholar
  25. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760CrossRefGoogle Scholar
  26. Mackelprang R, Waldrop MP, DeAngelis KM, David MM, Chavarria KL, Blazewicz SJ, Rubin EM, Jansson JK (2011) Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480:368–373CrossRefGoogle Scholar
  27. Mahato NK, Tripathi C, Verma H, Singh N, Lal R (2014) Draft genome sequence of Deinococcus sp. strain RL isolated from sediments of a hot water spring. Genome Announc 2:e00703–e00714CrossRefGoogle Scholar
  28. 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
  29. Ondov BD, Bergman NH, Phillippy (2011) Interactive metagenomic visualization in a web browser. BMC Bioinform 12:385CrossRefGoogle Scholar
  30. Parks DH, Tyson GW, Hugenholtz P, Beiko RG (2014) STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics 30:3123–3124CrossRefGoogle Scholar
  31. Postma PW, Lengeler JW, Jacobson GR (1993) Phosphoenolpyruvate: carbohydrate phosphotransferase systems of bacteria. Microbiol Rev 57:543–594Google Scholar
  32. Raes J, Letunic I, Yamada T, Jensen LJ, Bork P (2011) Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Mol Syst Biol 7:473CrossRefGoogle Scholar
  33. Rho M, Tang H, Ye Y (2010) FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res 38:e191CrossRefGoogle Scholar
  34. 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
  35. Saha P, Chakrabarti T (2006) Emticicia oligotrophica gen. nov., sp. nov., a new member of the family ‘Flexibacteraceae’, phylum Bacteroidetes. Int J Syst Evol Microbiol 56:991–995CrossRefGoogle Scholar
  36. Sangwan N, Lambert C, Sharma A, Gupta V, Khurana P, Khurana JP, Sockett E, Gilbert JA, Lal R (2015) Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator–prey genotypes. Environ Microbiol Rep 7:812–823CrossRefGoogle Scholar
  37. 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
  38. Sharma A, Gilbert JA, Lal R (2016a) (Meta)genomic insights into the pathogenome of Cellulosimicrobium cellulans. Sci Rep 6:25527CrossRefGoogle Scholar
  39. Sharma A, Kohli P, Singh Y, Schumann P, Lal R (2016b) Fictibacillus halophilus sp. nov., from a microbial mat of a hot spring atop the Himalayan range. Int J Syst Evol Microbiol 66:2409–2416CrossRefGoogle Scholar
  40. Sharma A, Schmidt M, Kiesel B, Mahato NK, Cralle LE, Singh Y, Richnow HH, Gilbert JA, Arnold W, Lal R (2018) Bacterial and archaeal viruses of Himalayan hot springs at Manikaran modulate host genomes. Front Microbiol 9:3095CrossRefGoogle Scholar
  41. Sharp CE, Brady AL, Sharp GH, Grasby SE, Stott MB, Dunfield PF (2014) Humboldt’s spa: microbial diversity is controlled by temperature in geothermal environments. ISME J 8:1166–1174CrossRefGoogle Scholar
  42. Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690CrossRefGoogle Scholar
  43. 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
  44. Tripathi C, Mahato NK, Rani P, Singh Y, Kamra K, Lal R (2016a) Draft genome sequence of Lampropedia cohaerens strain CT6T isolated from arsenic rich microbial mats of a Himalayan hot water spring. Stand Genom Sci 11:64CrossRefGoogle Scholar
  45. Tripathi C, Mahato NK, Singh AK, Kamra K, Korpole S, Lal R (2016b) Lampropedia cohaerens sp. nov., a biofilm-forming bacterium isolated from microbial mats of a hot water spring, and emended description of the genus Lampropedia. Int J Syst Evol Microbiol 66:1156–1162CrossRefGoogle Scholar
  46. Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata N (2015) MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods 12:902–903CrossRefGoogle Scholar
  47. Wang S, Hou W, Dong H, Jiang H, Huang L, Wu G, Zhang C, Song Z, Zhang Y, Ren H, Zhang J (2013) Control of temperature on microbial community structure in hot springs of the Tibetan plateau. PLoS One 8:e62901CrossRefGoogle Scholar
  48. Warren GL, Petsko GA (1995) Composition analysis of α-helices in thermophilic organisms. Protein Eng Des Sel 8:905–913CrossRefGoogle Scholar
  49. White JR, Nagarajan N, Pop M (2009) Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5:e1000352CrossRefGoogle Scholar
  50. Ye Y, Doak TG (2009) A parsimony approach to biology pathway reconstruction/inference for genomes and metagenomes. PLoS Comput Biol 5:e1000465CrossRefGoogle Scholar
  51. Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijin graphs. Genome Res 5:821–829CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Nitish Kumar Mahato
    • 1
  • Anukriti Sharma
    • 1
  • Yogendra Singh
    • 1
  • Rup Lal
    • 1
    • 2
    Email author
  1. 1.Department of ZoologyUniversity of DelhiDelhiIndia
  2. 2.PhiXgen Pvt. LtdGurugramIndia

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