Uncovering potential autotrophs in coal seams: characterization, enrichment, and genome-resolved metabolisms of a subsurface coal seam microbiome

Abstract

ABSTRACT Biological transformation of inorganic carbon into organic compounds is an extremely important biosynthetic process, and many organisms catalyze this reaction autotrophically, using CO2 as the sole carbon source. Natural autotrophic pathways are diverse, as are the organisms that employ them, driven in part by the varied ecological niches they inhabit. One understudied ecological niche, coal seams, contains autotrophic acetogens that catalyze an intermediate step in the conversion of coal to methane. Here, we characterize the geochemistry and microbiology of coal seam produced water (CSPW) from the Appalachian Basin and, through continued anaerobic enrichment on H2:CO2, show enhanced growth and acetate production. Specifically, the enriched CSPW microbiome was comprised of Proteiniphilum, Proteiniclasticum, Gudongella, Acetobacterium, Propionicimonas, and Mesobacillus. Genome-resolved metabolisms revealed six potential autotrophic pathways, including four natural pathways (the reductive pentose phosphate pathway, the reversed oxidative tricarboxylic acid cycle, the reductive acetyl-CoA pathway, and the reductive glycine pathway) and two proposed synthetic pathways (the serine-threonine cycle and the pyruvate formate-lyase threonine cycle), with many metagenome-assembled genomes encoding multiple pathways. Overall, these findings suggest a nuanced and adaptable carbon conversion strategy, shedding light on carbon reactions in coal seams, and the potential applications for biological production of valuable chemicals/fuels using mixed microbial communities. IMPORTANCE Coal seams harbor taxonomically diverse microorganisms, specifically acetogens and methanogens, suggesting an untapped potential for autotrophic carbon conversion. Here, we show that an enriched coal seam-produced water microbiome utilized CO2 and/or NaHCO3 for growth and produced acetate. Genome-resolved metabolisms revealed that most microorganisms encode multiple autotrophic pathways, with the reductive glycine pathway being the most prevalent. This work provides insight into potential microbial strategies for obtaining and transforming carbon in coal seams, and importantly, with proper engineering of operational parameters and reactor design, the enriched microbiome has the potential to be used as a biocatalyst for alternative carbon conversion technologies. Coal seams harbor taxonomically diverse microorganisms, specifically acetogens and methanogens, suggesting an untapped potential for autotrophic carbon conversion. Here, we show that an enriched coal seam-produced water microbiome utilized CO2 and/or NaHCO3 for growth and produced acetate. Genome-resolved metabolisms revealed that most microorganisms encode multiple autotrophic pathways, with the reductive glycine pathway being the most prevalent. This work provides insight into potential microbial strategies for obtaining and transforming carbon in coal seams, and importantly, with proper engineering of operational parameters and reactor design, the enriched microbiome has the potential to be used as a biocatalyst for alternative carbon conversion technologies.