Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India.
Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India.
Environ Microbiol. 2022 Jun;24(6):2837-2853. doi: 10.1111/1462-2920.15867. Epub 2021 Dec 20.
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 × 10 ) 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.
深层陆地地下代表了全球原核生物生物量的巨大储存库。考虑到其巨大的规模和重要性，深部大陆地壳中的微生物生命在全球研究中仍然代表性不足。我们通过在印度科伊纳的 3000 米深的科学钻孔中进行采样，通过宏基因组学、扩增子测序和基于培养的分析，对德干高原下太古花岗质岩石中深层、极端和贫营养领域的微生物群落进行了表征。16S rRNA 基因序列（7.37×10）显示出相当大的细菌多样性和核心微生物组（在总共 118064 个 OTU 中有 5724 个保守的操作分类单位）的存在，这些 OTU 跨越了不同的深度。核心微生物组中不同分类群的相对丰度随深度而变化，以响应流行的岩性和地球化学。共生网络分析和培养尝试阐明自养和异养细菌之间的密切相互作用。鸟枪法宏基因组学揭示了通过 Wood-Ljungdahl 途径进行自养碳固定和负责能量和碳代谢的基因的主要作用。更深入的分析表明存在“乙酸开关”，协调生物合成和细胞内稳态。我们得出结论，在营养和能量有限的深部花岗质地壳中的微生物生命受到深度的限制，并通过自养和异养之间的密切相互作用由少数核心成员来管理。
