Exploring the piezotolerant/piezophilic microbial community and genomic basis of piezotolerance within the deep subsurface Deccan traps

Abstract

The deep biosphere is often characterized by multiple extreme physical–chemical conditions, of which pressure is an important parameter that influences life but remains less studied. This geomicrobiology study was designed to understand the response of a subterranean microbial community of the Deccan traps to high-pressure conditions and to elucidate their genomic properties. Groundwater from a deep basaltic aquifer of the Deccan traps was used to ascertain the community response to 25 MPa and 50 MPa pressure following enrichment in high-salt and low-salt organic media. Quantitative PCR data indicated a decrease in bacterial and archaeal cell numbers with increasing pressure. 16S rRNA gene sequencing displayed substantial changes in the microbial community in which Acidovorax appeared to be the most dominant genus in the low-salt medium and Microbacteriaceae emerged as the major family in the high-salt medium under both pressure conditions. Genes present in metagenome-associated genomes which have previously been associated with piezotolerance include those related to nutrient uptake and extracytoplasmic stress (omp, rseC), protein folding and unfolding (dnaK, groEL and others), and DNA repair mechanisms (mutT, uvr and others). We hypothesize that these genes facilitate tolerance to high pressure by certain groups of microbes residing in subsurface Deccan traps.

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Acknowledgements

This work was supported by the Ministry of Earth Sciences, India (Project ID: MoES/P.O.(Seismo)/1(181)/2013). We thank the Director and all the investigators and participants from CSIR-National Geophysical Research Institute, Hyderabad, engaged in the exploratory scientific drilling operations at the Koyna–Warna region of Deccan traps. We are grateful to Harsh Gupta (NGRI), Shailesh Nayak (MoES), B.K. Bansal (MoES) and Sukanta Roy (NGRI) for their unstinted support. Next generation sequencing facility created at PS’s laboratory was funded by the Indian Institute of Technology Kharagpur Challenge Grant (IIT/SRIC/BT/ODM/2015-16/141). The authors thankfully acknowledge the support received from Deep Carbon Observatory (DCO) for AD’s visit to Scripps Institution of Oceanography, UC San Diego and performing experiments related to high-pressure microbiology there. The authors acknowledge Prof Abhijit Mukherjee and Srimanti Dutta Gupta of School of Environmental Studies, IIT Kharagpur, for their help in geochemical analysis of the groundwater sample. AD gratefully acknowledges IIT Kharagpur for providing fellowship (IIT/ACAD (PGS&R)/F.II/2/14/BS/91R01). AG thanks the Department of Biotechnology, Government of India for providing fellowship under DBT-JRF category (DBT/2014/IITKH/113).

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Dutta, A., Peoples, L.M., Gupta, A. et al. Exploring the piezotolerant/piezophilic microbial community and genomic basis of piezotolerance within the deep subsurface Deccan traps. Extremophiles 23, 421–433 (2019). https://doi.org/10.1007/s00792-019-01094-8

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Keywords

  • Piezotolerant/piezophilic microbes
  • Terrestrial deep biosphere
  • Pressure adaptation
  • Deccan traps