Abstract
The H2 and CO2-utilizing chemolithoautotrophic microorganisms from the deep subsurface ecosystems have gained considerable importance for their significant role in biogeochemical cycling of carbon. In this study, ten basalt and granite rocks from the deep subsurface environment of the Deccan Traps, India, have been used to enrich chemolithotrophic microorganisms. Following incubation with H2 and CO2 for 90 days at 50˚C, the enrichments showed microbial growth as evident from protein (27–157 mg/L) and carbohydrate (0.1–2.9 mg/L) contents of the enrichment cultures along with a change in pH, dissolved oxygen, and oxidation-reduction potential values. 16 S rRNA gene amplicon sequencing of the metagenomes derived from the enrichment cultures showed selective enrichment of microbial communities compared to the native rock communities. The most abundant bacterial phyla within the native rock samples were Proteobacteria, Actinobacteria, and Firmicutes, whereas the enrichment cultures showed enrichment of Proteobacteria (members of Gamma-Alpha-subdivisions), Actinobacteria, Firmicutes, and others under the chemolithoautotrophic condition. Predictive metabolic profiling using PICRUSt of enriched communities revealed the presence of genes related to H2 oxidation (hyaCD) and CO2 fixation (PGK, ccl, fhs, accABC) as well as genes for value-added product formation (ACSS, LDH, adh, acmAB, adh1, adcBDH, phaC, phbCZB, etc.). A total of 14 bacteria were isolated and identified as Mesorhizobium sp., Ralstonia spp., Massilia spp., Acidovorax spp., and Sphingobium sp. Among the bacterial isolates, Ralstonia sp., and Massilia sp. obtained from basaltic rock showed higher CO2 (up to 8 mg/L) utilization ability, and most of them can produce acetate (up to 14 mg/L). PCR analysis of the functional gene (NiFe-hyd) revealed the presence of probable H2 oxidation pathway in the isolates for their energy metabolism. The study showed the potential of H2 and CO2 utilizing deep subsurface bacterial populations in CO2 capture and value-added product formation.
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Data availability
The sequence reads of amplicon data were submitted to the short read archive (SRA) under the BioProject ID PRJNA632738. The 16 S rRNA gene sequence of the strains was submitted to NCBI GeneBank with accession numbers MT560083 to MT560091 and MT645465 to MT645469.
Abbreviations
- H2 :
-
Hydrogen
- CO2 :
-
Carbon dioxide
- SLiMEs:
-
Subsurface lithoautotrophic microbial ecosystems
- O2 :
-
Oxygen
- N2 :
-
Nitrogen
- TEA:
-
Terminal electron acceptor
- mbs:
-
Meter below surface
- MSM:
-
Minimal salt medium
- ORP:
-
Oxygen reduction potential
- DO:
-
Dissolve oxygen
- IC:
-
Ion chromatography
- CFU:
-
Colony forming unit
- BSA:
-
Bovine serum albumin
- OD:
-
Optical density
- R2A:
-
Reasoner’s 2 A
- GC:
-
Gas chromatography
- TCD:
-
Thermal conductivity detector
- P:
-
Panchgani
- PV:
-
Phansavale
- U:
-
Ukhalu
- PCR:
-
Polymerase chain reaction
- QIIME:
-
Quantitative Insights into Microbial Ecology
- OTU:
-
Operational taxonomic unit
- NSTI:
-
Nearest sequenced taxon index
- KEGG:
-
Kyoto Encyclopedia of Genes and Genomes
- NCBI:
-
National Center for Biotechnology Information
- H2CO3 :
-
Carbonic acid
- SO4 2− :
-
Sulfate
- NO3 − :
-
Nitrate
- NH4 + :
-
Ammonium
- NO2 :
-
Nitrogen dioxide
- NR:
-
Native rock
- ED:
-
Enrichment data
- PICRUSt:
-
Phylogenetic Investigation of Communities by Reconstruction of Unobserved States
- TCA:
-
Tricarboxylic acid
- CBB:
-
Calvin-Benson-Bassham
- WL:
-
Wood-Ljungdahl
- 3HP:
-
3-Hydroxypropionate
- 3HP/4HB:
-
3-Hydroxypropionate/4-hydroxybutyrate
- DC/4HB:
-
Dicarboxylate/4-hydroxybutyrate
- EPS:
-
Exopolysaccharide
- PHB:
-
Polyhydroxybutyrate
- ACSS:
-
Acyl-CoA Synthetase
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Acknowledgements
We gratefully acknowledge the Ministry of Earth Sciences (MoES), Government of India, for funding the project. We gratefully acknowledge the computational support provided by NIT Durgapur and IIT Kharagpur. Plaban Kumar Saha gratefully acknowledges the fellowship provided by NIT Durgapur. Rajendra Prasad Sahu gratefully acknowledges the fellowship provided by the Council of Scientific and Industrial Research, Government of India.
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This study was supported by the Ministry of Earth Sciences (MoES), Government of India, Project ID: MoES/P.O.(Seismo)/1(383)/2020 dated February 10, 2022.
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SKK and PS conceptualized and designed the work methodology, arranged funds and logistics, and supervised the work. PS was responsible for the sampling of the rock cores from the Koyna region, Maharashtra, India. PKS performed all experiments and data analysis. PS provided the sequencing facility. RPS and PKS performed the amplicon sequencing. PKS, SKK, and PS were responsible for manuscript preparation.
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Saha, P.K., Sahu, R.P., Sar, P. et al. Deep subsurface igneous rocks from the Deccan traps harbor H2 and CO2 utilizing chemolithoautotrophic bacteria. Biologia (2024). https://doi.org/10.1007/s11756-024-01631-7
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DOI: https://doi.org/10.1007/s11756-024-01631-7