Abstract
Dichloromethane (DCM; CH2Cl2) is a toxic groundwater pollutant that also has a detrimental effect on atmospheric ozone levels. As a dense non-aqueous phase liquid, DCM migrates vertically through groundwater to low redox zones, yet information on anaerobic microbial DCM transformation remains scarce due to a lack of cultured organisms. We report here the characterisation of DCMF, the dominant organism in an anaerobic enrichment culture (DFE) capable of fermenting DCM to the environmentally benign product acetate. Stable carbon isotope experiments demonstrated that the organism assimilated carbon from DCM and bicarbonate via the Wood–Ljungdahl pathway. DCMF is the first anaerobic DCM-degrading population also shown to metabolise non-chlorinated substrates. It appears to be a methylotroph utilising the Wood–Ljungdahl pathway for metabolism of methyl groups from methanol, choline, and glycine betaine. The flux of these substrates from subsurface environments may either directly (DCM, methanol) or indirectly (choline, glycine betaine) affect the climate. Community profiling and cultivation of cohabiting taxa in culture DFE without DCMF suggest that DCMF is the sole organism in this culture responsible for substrate metabolism, while the cohabitants persist via necromass recycling. Genomic and physiological evidence support placement of DCMF in a novel genus within the Peptococcaceae family, ‘Candidatus Formimonas warabiya’.
Highlights
Dichloromethane (DCM, CH2Cl2) is one of the most commonly encountered subsurface pollutants in industrial areas [1]
Following quantitative real-time PCR (qPCR) confirmation that the DCMF 16S rRNA gene was below the limit of detection in the lowest active dilution culture, these cultures were subject to Illumina 16 rRNA gene amplicon sequencing and used to inoculate triplicate microcosms amended with one of: 1 mM DCM, 5 mM choline chloride, or 5 mM glycine betaine (Fig. S1), which were monitored for 8 weeks
DCMF is a novel candidate species present in enrichment culture DFE, which has been maintained with DCM as sole external energy source for 5 years and at least 20 consecutive transfers [24]
Summary
Dichloromethane (DCM, CH2Cl2) is one of the most commonly encountered subsurface pollutants in industrial areas [1]. Elyunquensis’ strain RM has been characterised [19, 20] Both D. formicoaceticum and ‘Ca. Dichloromethanomonas elyunquensis’ are obligate anaerobic DCM-degrading bacteria and have genome sequences available [15, 19, 21, 22]. A combination of genomic, physiological, and proteomic work has demonstrated the central role of the Wood–Ljungdahl pathway (WLP) in DCM metabolism in both organisms, variations on the pathway result in different end products [15, 20, 23]. We report that DCMF is the first non-obligate anaerobic DCM-degrading bacterium and characterise its metabolism of DCM, quaternary amines, and methanol, whilst considering the role of the cohabiting bacteria in culture DFE. Using contemporary molecular and traditional cultivation techniques, this study represents a thorough and robust characterisation of a novel bacterium despite its presence in a multi-lineage enrichment culture
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