Exploring the one-carbon metabolism of a novel, dichloromethane-fermenting bacterium, 'Candidatus Formamonas warabiya'

Abstract

Anaerobic microbial metabolism of dichloromethane (DCM; CH2Cl2), quaternary amines, and methanol has important implications for carbon and nitrogen cycling in oligotrophic environments and the atmospheric flux of climate-active trace gasses. A novel, strictly anaerobic member of the Peptococcaceae family, strain DCMF, is the dominant organism in a DCM-fermenting enrichment culture (DFE) and one of very few known bacteria capable of fermenting DCM to the innocuous end product acetate. Long read, whole genome sequencing provided a single, circularised 6.44 Mb chromosome for strain DCMF, which contains 5,772 predicted protein-coding genes including an abundance of MttB superfamily methyltransferases. Genomic comparison of anaerobic, DCM-degrading bacteria provided a relatively small core genome, including the Wood-Ljungdahl pathway. Strain DCMF is the first non-obligate anaerobic DCM-degrading bacterium. Genomic, physiological and proteomic experiments confirmed that it is an anaerobic methylotroph, able to metabolise DCM, methanol, and methyl groups from quaternary amines via the Wood-Ljungdahl pathway. The quaternary amine choline was converted to glycine betaine, which was demethylated to sarcosine with a glycine betaine methyltransferase, then reductively cleaved to methylamine and acetate. Methanol (via a methanol methyltransferase) and DCM were fermented to acetate. Comparative proteomics revealed a methyltransferase system that was significantly more abundant in cells grown with DCM than glycine betaine. The novel, putative DCM methyltransferase genes are highly conserved between anaerobic DCM-degrading bacteria. Genomic and physiological evidence support placement of strain DCMF in a novel genus, for which we propose the name ‘Candidatus Formamonas warabiya’. Cohabiting bacteria in the DFE community have persisted despite repeated attempts to isolate strain DCMF, yet strain DCMF-free enrichments demonstrated that most are unable to utilise DCM, quaternary amines, or methanol. Five MAGs were generated from the long-read sequencing data and a metaproteogenomic approach suggested that the cohabiting organisms persist in the culture via necromass fermentation, i.e. oxidation of carbohydrates, proteins, and sugars released from expired strain DCMF cells. The DFE culture is a long-term stable-state community that highlights interactions between foundation species and supporting bacteria, as well as important pathways of carbon and nitrogen cycling.