Display options
Cite
Sahu RP, Kazy SK, Bose H, et al. Microbial diversity and function in crystalline basement beneath the Deccan Traps explored in a 3 km borehole at Koyna, western India. Environ Microbiol. 2021;doi: 10.1111/1462-2920.15867.
Sahu, R. P., Kazy, S. K., Bose, H., Mandal, S., Dutta, A., Saha, A., Roy, S., Dutta Gupta, S., Mukherjee, A., & Sar, P. (2021). Microbial diversity and function in crystalline basement beneath the Deccan Traps explored in a 3 km borehole at Koyna, western India. Environmental microbiology, . https://doi.org/10.1111/1462-2920.15867
Sahu, Rajendra Prasad, et al. "Microbial diversity and function in crystalline basement beneath the Deccan Traps explored in a 3 km borehole at Koyna, western India." Environmental microbiology vol. (2021). doi: https://doi.org/10.1111/1462-2920.15867
Sahu RP, Kazy SK, Bose H, Mandal S, Dutta A, Saha A, Roy S, Dutta Gupta S, Mukherjee A, Sar P. Microbial diversity and function in crystalline basement beneath the Deccan Traps explored in a 3 km borehole at Koyna, western India. Environ Microbiol. 2021 Dec 13; doi: 10.1111/1462-2920.15867. Epub 2021 Dec 13. PMID: 34897962.
Copy Download .nbib Format: NLM
Share it on

Environ Microbiol. 2021 Dec 13; doi: 10.1111/1462-2920.15867. Epub 2021 Dec 13.

Microbial diversity and function in crystalline basement beneath the Deccan Traps explored in a 3 km borehole at Koyna, western India.

Environmental microbiology

Rajendra Prasad Sahu, Sufia K Kazy, Himadri Bose, Sunanda Mandal, Avishek Dutta, Anumeha Saha, Sukanta Roy, Srimanti Dutta Gupta, Abhijit Mukherjee, Pinaki Sar

Affiliations

  1. Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India.
  2. Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India.
  3. Ministry of Earth Sciences, Borehole Geophysics Research Laboratory, Karad, MH, 415114, India.
  4. School of Environmental Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India.
  5. Department of Geology and Geophysics, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India.

PMID: 34897962 DOI: 10.1111/1462-2920.15867

Abstract

Deep terrestrial subsurface represents a huge repository of global prokaryotic biomass. Given its vastness and importance, microbial life within the deep subsurface continental crust remains under-represented in global studies. We characterize the microbial communities of deep, extreme and oligotrophic realm hosted by crystalline Archaean granitic rocks underneath the Deccan Traps, through sampling via 3000 m deep scientific borehole at Koyna, India through metagenomics, amplicon sequencing and cultivation-based analyses. Gene sequences 16S rRNA (7.37 × 10

© 2021 Society for Applied Microbiology and John Wiley & Sons Ltd.

References

  1. Banerjee, S., Schlaeppi, K., and van der Heijden, M.G.A. (2018) Keystone taxa as drivers of microbiome structure and functioning. Nat Rev Microbiol 16: 567-576. - PubMed
  2. Basen, M., and Müller, V. (2017) “Hot” acetogenesis. Extremophiles 21: 15-26. - PubMed
  3. Bates, S.T., Berg-Lyons, D., Caporaso, J.G., Walters, W.A., Knight, R., and Fierer, N. (2011) Examining the global distribution of dominant archaeal populations in soil. ISME J 5: 908-917. - PubMed
  4. Bell, E., Lamminmäki, T., Alneberg, J., Andersson, A.F., Qian, C., Xiong, W., et al. (2018) Biogeochemical cycling by a low-diversity microbial community in deep groundwater. Front Microbiol 9: 1-17. - PubMed
  5. Bell, E., Lamminmäki, T., Alneberg, J., Andersson, A.F., Qian, C., Xiong, W., et al. (2020) Active sulfur cycling in the terrestrial deep subsurface. ISME J 14: 1260-1272. - PubMed
  6. Berg, I.A. (2011) Ecological aspects of the distribution of different autotrophic CO2 fixation pathways. Appl Environ Microbiol 77: 1925-1936. - PubMed
  7. Bhaskar Rao, Y.J., Sreenivas, B., Vijaya Kumar, T., Khadke, N., Kesava Krishna, A., and Babu, E.V.S.S.K. (2017) Evidence for Neoarchean basement for the Deccan volcanic flows around Koyna-Warna region, western India: zircon U-Pb age and Hf-isotopic results. J Geol Soc India 90: 752-760. - PubMed
  8. Bull, A.T., and Goodfellow, M. (2019) Dark, rare and inspirational microbial matter in the extremobiosphere: 16000 m of bioprospecting campaigns. Microbiol (United Kingdom) 165: 1252-1264. - PubMed
  9. Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., et al. (2010) QIIME allows analysis of high-throughput community sequencing data intensity normalization improves colour calling in SOLiD sequencing. Nat Publ Gr 7: 335-336. - PubMed
  10. Cirigliano, A., Mura, F., Cecchini, A., Tomassetti, M.C., Maras, D.F., Di Paola, M., et al. (2021) Active microbial ecosystem in iron-age tombs of the Etruscan civilization. Environ Microbiol 23: 3957-3969. - PubMed
  11. Cockell, C.S., Schaefer, B., Wuchter, C., Coolen, M.J.L., Grice, K., Schnieders, L., et al. (2021) Shaping of the present-day deep biosphere at Chicxulub by the impact catastrophe that ended the cretaceous. Front Microbiol 12: 1413. - PubMed
  12. Colwell, F.S., Boyd, S., Delwiche, M.E., Reed, D.W., Phelps, T.J., and Newby, D.T. (2008) Estimates of biogenic methane production rates in deep marine sediments at hydrate ridge, Cascadia margin. Appl Environ Microbiol 74: 3444-3452. - PubMed
  13. Dutta, A., Dutta Gupta, S., Gupta, A., Sarkar, J., Roy, S., Mukherjee, A., and Sar, P. (2018) Exploration of deep terrestrial subsurface microbiome in late cretaceous Deccan traps and underlying Archean basement, India. Sci Rep 8: 1-16. - PubMed
  14. Dutta, A., Sar, P., Sarkar, J., Dutta Gupta, S., Gupta, A., Bose, H., et al. (2019) Archaeal communities in deep terrestrial subsurface underneath the Deccan traps, India. Front Microbiol 10: 1-18. - PubMed
  15. Escudero, C., Oggerin, M., and Amils, R. (2018) The deep continental subsurface: the dark biosphere. Int Microbiol 21: 3-14. - PubMed
  16. Golinska, P., Montero-Calasanz, M.d.C., Świecimska, M., Yaramis, A., Igual, J.M., Bull, A.T., and Goodfellow, M. (2020) Modestobacter excelsi sp. nov., a novel actinobacterium isolated from a high altitude Atacama Desert soil. Syst Appl Microbiol 43: 126051. - PubMed
  17. Goswami, D., Hazarika, P., and Roy, S. (2020) In situ stress orientation from 3 km borehole image logs in the Koyna Seismogenic zone, Western India: implications for transitional faulting environment. Tectonics 39: 1-17. - PubMed
  18. Goswami, D., Roy, S., and Akkiraju, V.V. (2019) Delineation of damage zones from 3 km Downhole geophysical logs in the Koyna Seismogenic zone, Western India. J Geophys Res Solid Earth 124: 6101-6120. - PubMed
  19. Gupta, H.K. (2017) Koyna, India, an ideal site for near field earthquake observations. J Geol Soc India 90: 645-652. - PubMed
  20. Gurevich, A., Saveliev, V., Vyahhi, N., and Tesler, G. (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29: 1072-1075. - PubMed
  21. Hallbeck, L., and Pedersen, K. (2008) Characterization of microbial processes in deep aquifers of the Fennoscandian shield. Appl Geochemistry 23: 1796-1819. - PubMed
  22. Hammer, Ø., Harper, D.A., and Ryan, P.D. (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4: 9. - PubMed
  23. Hernsdorf, A.W., Amano, Y., Miyakawa, K., Ise, K., Suzuki, Y., Anantharaman, K., et al. (2017) Potential for microbial H 2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. ISME J 11: 1915-1929. - PubMed
  24. Hoehler, T.M., and Jørgensen, B.B. (2013) Microbial life under extreme energy limitation. Nat Rev Microbiol 11: 83-94. - PubMed
  25. Hubalek, V., Wu, X., Eiler, A., Buck, M., Heim, C., Dopson, M., et al. (2016) Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield. ISME J 10: 2447-2458. - PubMed
  26. Hügler, M., and Sievert, S.M. (2011) Beyond the Calvin cycle: autotrophic carbon fixation in the ocean. Ann Rev Mar Sci 3: 261-289. - PubMed
  27. Idris, H., Goodfellow, M., Sanderson, R., Asenjo, J.A., and Bull, A.T. (2017) Actinobacterial rare biospheres and dark matter revealed in habitats of the Chilean Atacama Desert. Sci Rep 7: 1-11. - PubMed
  28. Kadnikov, V.V., Mardanov, A.V., Beletsky, A.V., Banks, D., Pimenov, N.V., Frank, Y.A., et al. (2018) A metagenomic window into the 2-km-deep terrestrial subsurface aquifer revealed multiple pathways of organic matter decomposition. FEMS Microbiol Ecol 94: 1-16. - PubMed
  29. Kadnikov, V.V., Mardanov, A.V., Beletsky, A.V., Karnachuk, O.V., and Ravin, N.V. (2020) Microbial life in the deep subsurface aquifer illuminated by Metagenomics. Front Microbiol 11: 1-15. - PubMed
  30. Kanehisa, M., Sato, Y., and Morishima, K. (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and Metagenome sequences. J Mol Biol 428: 726-731. - PubMed
  31. Kazy, S.K., Sahu, R.P., Mukhopadhyay, S., Bose, H., Mandal, S., and Sar, P. (2021) Microbial life in deep terrestrial continental crust. In Extreme Environments, Pandey, A., and Sharma, A. (eds). Boca Raton: CRC Press, pp. 263-291. - PubMed
  32. Kieft, T.L. (2016) Microbiology of the deep continental biosphere. In Their World: A Diversity of Microbial Environments. Advances in Environmental Microbiology, Vol. 1, Hurst, C. (ed). Cham: Springer, pp. 225-249. - PubMed
  33. Kietäväinen, R., and Purkamo, L. (2015) The origin, source, and cycling of methane in deep crystalline rock biosphere. Front Microbiol 6: 725. - PubMed
  34. Lau, M.C.Y., Cameron, C., Magnabosco, C., Brown, C.T., Schilkey, F., Grim, S., et al. (2014) Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships. Front Microbiol 5: 1-17. - PubMed
  35. Lau, M.C.Y., Kieft, T.L., Kuloyo, O., Linage-Alvarez, B., Van Heerden, E., Lindsay, M.R., et al. (2016) An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers. Proc Natl Acad Sci U S A 113: E7927-E7936. - PubMed
  36. Lever, M.A., Rouxel, O., Alt, J.C., Shimizu, N., Ono, S., Coggon, R.M., et al. (2013) Evidence for microbial carbon and sulfur cycling in deeply buried ridge flank basalt. Science 339: 1305-1309. - PubMed
  37. Lloyd, K.G., Sheik, C.S., García-Moreno, B., and Royer, C.A. (2019) The genetics, biochemistry, and biophysics of carbon cycling by deep life. Deep Carbon: 556-584. - PubMed
  38. López-García, P., and Moreira, D. (2020) The Syntrophy hypothesis for the origin of eukaryotes revisited. Nat Microbiol 5: 655-667. - PubMed
  39. Magnabosco, C., Lin, L.H., Dong, H., Bomberg, M., Ghiorse, W., Stan-Lotter, H., et al. (2018) The biomass and biodiversity of the continental subsurface. Nat Geosci 11: 707-717. - PubMed
  40. Magnabosco, C., Ryan, K., Lau, M.C.Y., Kuloyo, O., Sherwood Lollar, B., Kieft, T.L., et al. (2016) A metagenomic window into carbon metabolism at 3 km depth in precambrian continental crust. ISME J 10: 730-741. - PubMed
  41. McMahon, S., and Parnell, J. (2014) Weighing the deep continental biosphere. FEMS Microbiol Ecol 87: 113-120. - PubMed
  42. Moffett, J.R., Puthillathu, N., Vengilote, R., Jaworski, D.M., and Namboodiri, A.M. (2020) Acetate revisited: a key biomolecule at the nexus of metabolism, epigenetics and oncogenesis part 1: acetyl-CoA, acetogenesis and acyl-CoA short-chain Synthetases. Front Physiol 11: 1-24. - PubMed
  43. Mohan, S.V., Raghavulu, S.V., Goud, R.K., Srikanth, S., Babu, V.L., and Sarma, P.N. (2010) Microbial diversity analysis of long term operated biofilm configured anaerobic reactor producing biohydrogen from wastewater under diverse conditions. Int J Hydrogen Energy 35: 12208-12215. - PubMed
  44. Momper, L., Jungbluth, S.P., Lee, M.D., and Amend, J.P. (2017) Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community. ISME J 11: 2319-2333. - PubMed
  45. Nixon, S.L., Daly, R.A., Borton, M.A., Solden, L.M., Welch, S.A., Cole, D.R., et al. (2019) Genome-resolved Metagenomics extends the environmental distribution of the Verrucomicrobia phylum to the deep terrestrial subsurface. mSphere 4: e00613-e00619. - PubMed
  46. Nurk, S., Meleshko, D., Korobeynikov, A., and Pevzner, P.A. (2017) MetaSPAdes: a new versatile metagenomic assembler. Genome Res 27: 824-834. - PubMed
  47. Nyyssönen, M., Hultman, J., Ahonen, L., Kukkonen, I., Paulin, L., Laine, P., et al. (2014) Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the fennoscandian shield. ISME J 8: 126-138. - PubMed
  48. Parnell, J., and McMahon, S. (2016) Physical and chemical controls on habitats for life in the deep subsurface beneath continents and ice. Philos Trans R Soc A Math Phys Eng Sci 374: 20140293. - PubMed
  49. Podugu, N., Mishra, S., Wiersberg, T., and Roy, S. (2019) Chemical and noble gas isotope compositions of formation gases from a 3 km deep scientific borehole in the Koyna Seismogenic zone, Western India. Geofluids 2019: 1-16. - PubMed
  50. Puente-Sánchez, F., Arce-Rodríguez, A., Oggerin, M., García-Villadangos, M., Moreno-Paz, M., Blanco, Y., et al. (2018) Viable cyanobacteria in the deep continental subsurface. Proc Natl Acad Sci U S A 115: 10702-10707. - PubMed
  51. Purkamo, L., Bomberg, M., Nyyssönen, M., Kukkonen, I., Ahonen, L., and Itävaara, M. (2015) Heterotrophic communities supplied by ancient organic carbon predominate in deep Fennoscandian bedrock fluids. Microb Ecol 69: 319-332. - PubMed
  52. Purkamo, L., Kietäväinen, R., Nuppunen-Puputti, M., Bomberg, M., and Cousins, C. (2020) Ultradeep microbial communities at 4.4 km within crystalline bedrock: implications for habitability in a planetary context. Life (Basel) 10: 2. - PubMed
  53. R Development Core Team. (2017) R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. - PubMed
  54. Roy, S. (2017) Scientific drilling in Koyna region, Maharashtra. Curr Sci 112: 2181-2181. - PubMed
  55. Sanz, J.L., Rodriguez, N., Escudero, C., Carrizo, D., and Amils, R. (2021) Biological production of H2, CH4 and CO2 in the deep subsurface of the Iberian Pyrite Belt. Environ Microbiol 23: 3913-3922. - PubMed
  56. Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541. - PubMed
  57. Schoene, B., Samperton, K.M., Eddy, M.P., Keller, G., Adatte, T., Bowring, S.A., et al. (2015) U-Pb geochronology of the Deccan traps and relation to the end-cretaceous mass extinction. Science 347: 182-184. - PubMed
  58. Schuchmann, K., and Müller, V. (2014) Autotrophy at the thermodynamic limit of life: a model for energy conservation in acetogenic bacteria. Nat Rev Microbiol 12: 809-821. - PubMed
  59. Shade, A., and Handelsman, J. (2012) Beyond the Venn diagram: the hunt for a core microbiome. Environ Microbiol 14: 4-12. - PubMed
  60. Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504. - PubMed
  61. Sheik, C.S., Reese, B.K., Twing, K.I., Sylvan, J.B., Grim, S.L., Schrenk, M.O., et al. (2018) Identification and removal of contaminant sequences from ribosomal gene databases: lessons from the census of deep life. Front Microbiol 9: 1-14. - PubMed
  62. Stevens, T.O., and McKinley, J.P. (1995) Lithoautotrophic microbial ecosystems in deep basalt aquifers. Science 270: 450-455. - PubMed
  63. Westphal, L., Wiechmann, A., Baker, J., Minton, N.P., and Müller, V. (2018) The Rnf complex is an energy-coupled transhydrogenase essential to reversibly link cellular NADH and ferredoxin pools in the acetogen Acetobacterium woodii. J Bacteriol 200: e00357-e00318. - PubMed
  64. Wolfe, A.J. (2005) The acetate switch. Microbiol Mol Biol Rev 69: 12-50. - PubMed
  65. Wu, X., Holmfeldt, K., Hubalek, V., Lundin, D., Åström, M., Bertilsson, S., and Dopson, M. (2016) Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations. ISME J 10: 1192-1203. - PubMed
  66. Yan, L., Herrmann, M., Kampe, B., Lehmann, R., Totsche, K.U., and Küsel, K. (2020) Environmental selection shapes the formation of near-surface groundwater microbiomes. Water Res 170: 115341. - PubMed

Publication Types

Grant support