Department of Biological Sciences, University of Calgary, Calgary, Canada.
Faculty of Science and Technology, Athabasca University, Athabasca, Canada.
mSystems. 2023 Apr 27;8(2):e0088422. doi: 10.1128/msystems.00884-22. Epub 2023 Feb 14.
Petroleum reservoirs within the deep biosphere are extreme environments inhabited by diverse microbial communities and represent biogeochemical hot spots in the subsurface. Despite the ecological and industrial importance of oil reservoir microbiomes, systematic study of core microbial taxa and their associated genomic attributes spanning different environmental conditions is limited. Here, we compile and compare 343 16S rRNA gene amplicon libraries and 25 shotgun metagenomic libraries from oil reservoirs in different parts of the world to test for the presence of core taxa and functions. These oil reservoir libraries do not share any core taxa at the species, genus, family, or order levels, and was the only taxonomic class detected in all samples. Instead, taxonomic composition varies among reservoirs with different physicochemical characteristics and with geographic distance highlighting environmental selection and biogeography in these deep biosphere habitats. Gene-centric metagenomic analysis reveals a functional core of metabolic pathways including carbon acquisition and energy-yielding strategies consistent with biogeochemical cycling in other subsurface environments. Genes for anaerobic hydrocarbon degradation are observed in a subset of the samples and are therefore not considered to represent core functions in oil reservoirs despite hydrocarbons representing an abundant source of carbon in these deep biosphere settings. Overall, this work reveals common and divergent features of oil reservoir microbiomes that are shaped by and responsive to environmental factors, highlighting controls on subsurface microbial community assembly. This comprehensive analysis showcases how environmental selection and geographic distance influence the microbiome of subsurface petroleum reservoirs. We reveal substantial differences in the taxonomy of the inhabiting microbes but shared metabolic function between reservoirs with different temperatures and between reservoirs separated by large distances. The study helps understand and advance the field of deep biosphere science by providing an ecological framework and footing for geologists, chemists, and microbiologists studying these habitats to elucidate major controls on deep biosphere microbial ecology.
油藏深部生物圈是由多种微生物群落栖息的极端环境，是地下的生物地球化学热点。尽管油藏微生物组具有生态和工业重要性，但对跨越不同环境条件的核心微生物类群及其相关基因组属性的系统研究是有限的。在这里，我们编译并比较了来自世界不同地区的 343 个 16S rRNA 基因扩增子文库和 25 个 shotgun 宏基因组文库，以检验核心分类群和功能的存在。这些油藏文库在物种、属、科和目水平上没有共享任何核心分类群，而是在所有样本中都检测到了 是唯一的分类类群。相反，具有不同理化特性的油藏和地理距离的分类组成差异突出了这些深部生物圈生境中的环境选择和生物地理学。基于基因的宏基因组分析揭示了代谢途径的功能核心，包括碳获取和能量产生策略，与其他地下环境的生物地球化学循环一致。在一部分样品中观察到了厌氧烃降解基因，因此尽管烃类在这些深部生物圈环境中是丰富的碳源，但它们不被认为代表油藏中的核心功能。总的来说，这项工作揭示了油藏微生物组的共同和不同特征，这些特征是由环境因素塑造和响应的，突出了对地下微生物群落组装的控制。这项综合分析展示了环境选择和地理距离如何影响地下石油储层的微生物组。我们揭示了栖息微生物的分类学上的巨大差异，但在不同温度的储层之间以及相距较远的储层之间存在共享的代谢功能。该研究通过为研究这些栖息地的地质学家、化学家和微生物学家提供生态框架和基础，有助于理解和推进深部生物圈科学领域，阐明深部生物圈微生物生态学的主要控制因素。
