Abstract
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.
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Data availability
Genomic sequence data associated with Total-sorted and BONCAT-sorted cells are available on the Integrated Microbial Genomes & Microbiomes (IMG) site under GOLD Study ID Gs014100. High quality MAGs for Methanothrix paradoxum PRB and Chlorobi PRB were submitted to JGI under GOLD Analysis IDs Ga0496496 and Ga0496497, respectively. Environmental metagenomes for FG11 and FGP wells are available on IMG under GOLD Project IDs Gp0406117 and Gp0406116, respectively.
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Acknowledgements
BONCAT-FACS and metagenomic sequencing were conducted under CSP503725 by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, which is supported under Contract No. DE-AC02-05CH11231. The authors (LJM, HJS, MWF) appreciate support from ENIGMA- Ecosystems and Networks Integrated with Genes and Molecular Assemblies (http://enigma.lbl.gov), a Science Focus Area Program at Lawrence Berkeley National Laboratory. We would like to thank Dr. Steven Singer at Lawrence Berkeley National Laboratory for sharing information regarding the Chlorobi NICIL-2 genome for comparison with Chlorobi PRB. We appreciate assistance in field work from Dr. Katie Davis and George Platt, and we are grateful to Dr. Jennifer MacIntosh and Dr. Daniel Ritter for geochemical analyses and discussion. We also acknowledge the USGS Energy Resources Program (Alicia Lindauer, Program Coordinator), the USGS National Innovation Center (Jonathan Stock, Director) and Montana Emergent Technologies for assistance in the field and SES development. Disclaimer: Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
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HJS, HDS, EPB, LJM, and MWF designed the study. EPB, HJS, and HDS performed field sampling. HJS and HDS conducted laboratory experiments. RRM and DG performed cell sorting and sequencing. LJM, HDS, EPB, HJS, and MWF analyzed and interpreted the data. LJM, HJS, and EPB wrote the paper. All authors reviewed and edited the paper.
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McKay, L.J., Smith, H.J., Barnhart, E.P. et al. Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane. ISME J 16, 915–926 (2022). https://doi.org/10.1038/s41396-021-01139-x
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DOI: https://doi.org/10.1038/s41396-021-01139-x
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