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Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane
The ISME Journal ( IF 11.0 ) Pub Date : 2021-10-23 , DOI: 10.1038/s41396-021-01139-x
Luke J McKay 1, 2, 3 , Heidi J Smith 1, 4 , Elliott P Barnhart 5 , Hannah D Schweitzer 1, 4, 6 , Rex R Malmstrom 7 , Danielle Goudeau 7 , Matthew W Fields 1, 4
Affiliation  

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.



中文翻译:

基于活动的、基因组解析的宏基因组学揭示了煤炭地下转化为甲烷所涉及的关键种群和途径

人们对促进顽固碳在地下转化为甲烷的微生物代谢和相互作用知之甚少。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-宏基因组学来识别参与从各种煤衍生芳烃中产生甲烷的转化活性种群。从活性部分,回收了高质量的宏基因组组装基因组 (MAGs),用于产甲烷菌Methanothrix paradoxumChlorobi的一个新成员,该成员有可能通过 Pta-Ack 途径产生乙酸盐。拟杆菌属地杆菌属的成员还编码 Pta-Ack,所有四个种群都具有降解乙苯、磷酸苯酯、苯乙醇、甲苯、二甲苯和苯酚的推定能力。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煤层中的兼性能量代谢。活性“ Chlorobi PRB”MAG 编码用于发酵、硝酸盐还原的酶,以及具有不同氧结合亲和力的多种加氧酶。“ M. paradoxum PRB”编码了一种用于有氧苯乙酸降解的二醇双加氧酶,该酶也存在于之前发表的甲烷丝菌中基因组。这些观察概述了转化活性种群从次烟煤中提取生物甲烷的潜在过程,并证明了基于活性的宏基因组学是下一代生理学中了解生态相关微生物种群的强大策略。

更新日期:2021-10-24
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