Summary 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 × 106) show considerable bacterial diversity and the existence of a core microbiome (5724 operational taxonomic units conserved out of a total 118,064 OTUs) across the depths. Relative abundance of different taxa of core microbiome varies with depth in response to prevailing lithology and geochemistry. Co‐occurrence network analysis and cultivation attempt to elucidate close interactions among autotrophic and organotrophic bacteria. Shotgun metagenomics reveals a major role of autotrophic carbon fixation via the Wood–Ljungdahl pathway and genes responsible for energy and carbon metabolism. Deeper analysis suggests the existence of an ‘acetate switch’, coordinating biosynthesis and cellular homeostasis. We conclude that the microbial life in the nutrient‐ and energy‐limited deep granitic crust is constrained by the depth and managed by a few core members via a close interplay between autotrophy and organotrophy.

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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.

In the last few decades, the demand for introducing biological resources into the multifaceted industry of medicine, food, cosmetics, textiles among others for manufacturing useful products has received immense consideration. Incidentally, fungal mycelium-based resources can act as an important instrument for the same. For example, cultivation of Ganoderma lucidum (Curtis)P. Karst. on a mixture which includes wheat straws and polypropylene embedded with spores from Bacillus amyloliquefaciens subsp. amyloliquefaciens resulted in a very unique biomaterial. This biomaterial is safe, inert, renewable, natural, biodegradable and could be molded in a desired shape. Also, they have high potential as thermal insulation material for applications in building sectors. Another example is of the billion-dollar cosmetic industry which seems to be in awe with byproducts of the fungal organisms for the development of antiaging products. A plus point with these fungal based products is that they are eco-friendly and are cost effective. These fungal organisms are extremely helpful in degrading the wastes produced by humans thus helping in curbing environmental contamination and also performing natural green auditing. This review is an attempt to emphasize the importance of mycelium-based bio-products in cosmetic, medicinal, packaging, enzyme, prebiotic, alkaloid, steroid, pigment, biopolymer, antibiotic, construction, vitamin based and organic acid industries.

<p>Scientific drilling within the deep continental crust provides the unique opportunity for characterizing subsurface microorganisms from deep crystalline rocks and is of major scientific interest owing to the crucial role of these microorganism in global carbon cycles. Scientific drilling in Koyna seismogenic zone enables characaterization of deep Earth crust microbiome and provides a new insight into their biogeochemical role. In this study, we investigated the microbial populations reactivated (enriched) from the deep [1679 - 2908 meters below surface (mbs)] granitic rocks underneath the Deccan Traps with inorganic [CO<sub>2 </sub>(+H<sub>2</sub>)/ HCO<sub>3</sub><sup>- </sup>] and organic carbon (CH<sub>4</sub> / Organic carbon mix/ Polymeric carbon mix) sources under hot (50°C), anaerobic conditions (180 days). Estimation of total protein, ATP and 16S rRNA gene qPCR suggested considerable microbial growth in all the enrichment setups. 16S rRNA gene amplicon sequencing showed a depth-wide distribution of diverse chemolithotrophic (and a few fermentative) organisms in the inorganic enrichments, whereas a substrate specific response was observed under the heterotrophic conditions with organic carbon sources. <em>Comamonas, Burkholderia-Caballeronia-Paraburkholderia,</em> <em>Ralstonia</em>, <em>Klebsiella</em>, unclassified Burkholderiaceae and Enterobacteriaceae were reactivated as dominant organisms from the enrichments of the deeper rocks (2335 - 2908 mbs) with both CO<sub>2</sub> and HCO<sub>3</sub><sup>-</sup>. From shallower depths, organisms of varied taxa were enriched. <em>Pseudomonas, Rhodanobacter,</em> <em>Methyloversatilis, </em>and Thaumarchaeota were major CO<sub>2 </sub>(+H<sub>2</sub>) utilizers, while <em>Nocardioides, Sphingomonas, Aeromonas</em> responded towards HCO<sub>3</sub><sup>-</sup>. Enrichments with CH<sub>4</sub> reactivated <em>Actinophytocola, Pseudomonas, Methylobacterium, Nocardiodes </em>members, while with the organic carbons, <em>Bacillus</em> and <em>Thermoactinomyces</em> were the most abundant taxa. <em>Gemella</em>, <em>Pseudomonas</em> and <em>Nocardiodes </em>got enriched with the polymeric carbon mix. Interestingly, enrichment of Cyanobacteria were observed mostly with CO<sub>2</sub> (+H<sub>2</sub>), CH<sub>4  </sub>and polymeric carbon mix, which could be attributed to their ecological versatility, potential for H<sub>2</sub>-based lithoautotrophic metabolism and their ability to switch to fermentative lifestyle. Statistical analyses depicted depth-wise and substrate-wise distinct cladding of chemolithotrophic and chemoorganotrophic microbial communities, respectively. Phylogenetic analyses of the operational taxonomic units, showed similarities with sequences retrieved from other extreme deep subsurface environments. Co-occurrence networks suggested close interaction between chemolithototrophic and chemoorganotrophic/fermentative organisms. Predictive metabolic profiling revealed the presence of various genes for carbon and energy metabolisms as well as for valuable chemicals. The subsurface microorganisms showed the potential for answering the fundamental questions of deep life and for their exploitation as resources of valuable chemicals.</p>

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