Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA.
ISME J. 2022 Apr;16(4):915-926. doi: 10.1038/s41396-021-01139-x. Epub 2021 Oct 23.
Microbial metabolisms and interactions that facilitate subsurface conversions of recalcitrant carbon to methane are poorly understood. We deployed an in situ enrichment device in a subsurface coal seam in the Powder River Basin (PRB), USA, and used BONCAT-FACS-Metagenomics to identify translationally active populations involved in methane generation from a variety of coal-derived aromatic hydrocarbons. From the active fraction, high-quality metagenome-assembled genomes (MAGs) were recovered for the acetoclastic methanogen, Methanothrix paradoxum, and a novel member of the Chlorobi with the potential to generate acetate via the Pta-Ack pathway. Members of the Bacteroides and Geobacter also encoded Pta-Ack and together, all four populations had the putative ability to degrade ethylbenzene, phenylphosphate, phenylethanol, toluene, xylene, and phenol. Metabolic reconstructions, gene analyses, and environmental parameters also indicated that redox fluctuations likely promote facultative energy metabolisms in the coal seam. The active "Chlorobi PRB" MAG encoded enzymes for fermentation, nitrate reduction, and multiple oxygenases with varying binding affinities for oxygen. "M. paradoxum PRB" encoded an extradiol dioxygenase for aerobic phenylacetate degradation, which was also present in previously published Methanothrix genomes. These observations outline underlying processes for bio-methane from subbituminous coal by translationally active populations and demonstrate activity-based metagenomics as a powerful strategy in next generation physiology to understand ecologically relevant microbial populations.
微生物代谢和相互作用促进了难降解碳向甲烷的地下转化，但这一过程仍知之甚少。我们在美国粉河盆地（PRB）的地下煤层中部署了一个原位富集装置，并使用 BONCAT-FACS-Metagenomics 来鉴定参与各种煤衍生芳烃生成甲烷的翻译活性种群。从活性部分中，我们回收了高质量的宏基因组组装基因组（MAG），用于产乙酸甲烷菌 Methanothrix paradoxum 和具有通过 Pta-Ack 途径生成乙酸盐潜力的 Chlorobi 的新成员。拟杆菌和 Geobacter 的成员也编码了 Pta-Ack，这四个种群都有可能降解乙苯、苯膦酸、苯乙醇、甲苯、二甲苯和苯酚。代谢重建、基因分析和环境参数也表明，氧化还原波动可能促进了煤层中兼性能量代谢。活跃的“PRB Chlorobi”MAG 编码了发酵、硝酸盐还原和多种具有不同氧结合亲和力的加氧酶的酶。“PRB Methanothrix paradoxum”编码了用于有氧苯乙酸降解的外二醇加氧酶，该酶也存在于之前发表的 Methanothrix 基因组中。这些观察结果概述了通过翻译活性种群从亚烟煤中生物甲烷的潜在过程，并展示了基于活性的宏基因组学作为下一代生理学中理解生态相关微生物种群的强大策略。
