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 meter deep scientific borehole at Koyna, India through metagenomics, amplicon sequencing, and cultivation-based analyses. 16S rRNA gene sequences (7.37 × 106 ) show considerable bacterial diversity and existence of a core microbiome (5724 operational taxonomic units conserved out of a total 118064 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 elucidate close interactions among autotrophic and organotrophic bacteria. Shotgun metagenomics reveals 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. This article is protected by copyright. All rights reserved.