Depth wide distribution and metabolic potential of chemolithoautotrophic microorganisms reactivated from deep continental granitic crust underneath the Deccan Traps at Koyna, India

Abstract

Characterization of inorganic carbon (C) utilizing microorganisms from deep crystalline rocks is of major scientific interest owing to their crucial role in global carbon and other elemental cycles. In this study we investigate the microbial populations from the deep [up to 2,908 meters below surface (mbs)] granitic rocks within the Koyna seismogenic zone, reactivated (enriched) under anaerobic, high temperature (50°C), chemolithoautotrophic conditions. Subsurface rock samples from six different depths (1,679–2,908 mbs) are incubated (180 days) with CO2 (+H2) or HCO3− as the sole C source. Estimation of total protein, ATP, utilization of NO3- and SO42− and 16S rRNA gene qPCR suggests considerable microbial growth within the chemolithotrophic conditions. We note a better response of rock hosted community towards CO2 (+H2) over HCO3−. 16S rRNA gene amplicon sequencing shows a depth-wide distribution of diverse chemolithotrophic (and a few fermentative) Bacteria and Archaea. Comamonas, Burkholderia-Caballeronia-Paraburkholderia, Ralstonia, Klebsiella, unclassified Burkholderiaceae and Enterobacteriaceae are reactivated as dominant organisms from the enrichments of the deeper rocks (2335–2,908 mbs) with both CO2 and HCO3−. For the rock samples from shallower depths, organisms of varied taxa are enriched under CO2 (+H2) and HCO3−. Pseudomonas, Rhodanobacter, Methyloversatilis, and Thaumarchaeota are major CO2 (+H2) utilizers, while Nocardioides, Sphingomonas, Aeromonas, respond towards HCO3−. H2 oxidizing Cupriavidus, Hydrogenophilus, Hydrogenophaga, CO2 fixing Cyanobacteria Rhodobacter, Clostridium, Desulfovibrio and methanogenic archaea are also enriched. Enriched chemolithoautotrophic members show good correlation with CO2, CH4 and H2 concentrations of the native rock environments, while the organisms from upper horizons correlate more to NO3−, SO42−, Fe and TIC levels of the rocks. Co-occurrence networks suggest close interaction between chemolithoautotrophic and chemoorganotrophic/fermentative organisms. Carbon fixing 3-HP and DC/HB cycles, hydrogen, sulfur oxidation, CH4 and acetate metabolisms are predicted in the enriched communities. Our study elucidates the presence of live, C and H2 utilizing Bacteria and Archaea in deep subsurface granitic rocks, which are enriched successfully. Significant impact of depth and geochemical controls on relative distribution of various chemolithotrophic species enriched and their C and H2 metabolism are highlighted. These endolithic microorganisms show great potential for answering the fundamental questions of deep life and their exploitation in CO2 capture and conversion to useful products.

Deep subsurface microbial life in impact‐altered Late Paleozoic granitoid rocks from the Chicxulub impact crater

“…Hydrothermally altered shocked granites, nutritionally rich non-granite rocks (e.g., intercalated intervals of pre-impact subvolcanic, suevite, and impact melt rocks), and cross-cut mineral veins of anhydrite and silica were analyzed from this core section. All three sample categories were dominated by Proteobacteria (notably Gammaproteobacteria), followed by Bacteroidota, Firmicutes, and Actinobacteriota, which is consistent with the predominant microbial communities previously recorded from the main lithologies of the Chicxulub Impact crater (Cockell et al, 2021) and those associated with deep subsurface igneous rocks such as basalt, granite, and inactive hydrothermal vents (e.g., Dutta et al, 2018;Hou et al, 2020;Jørgensen & Zhao, 2016;Mandal et al, 2022;Zhang et al, 2016).…”

“…The presence of Enterobacteriaceae in environmental 16S rRNA sequence data is usually considered contamination of the sampling location with sewage material. However, slow‐growing thermophilic chemolithoautotrophic Enterobacteriaceae were recently cultivated from deep continental granitic crust underneath the Deccan Traps (Koyna, India) using H 2 as electron donor and nitrate, Mn(IV), Fe(III), or sulfate as suitable electron acceptors (Mandal et al., 2022). The Enterobacteriaceae in our core could not be classified beyond the family level but showed 98.4% sequence similarity with the chemolithoautotrophic isolates from the deep Deccan trap granites (Table S6).…”