Sulfur and methane oxidation by a single microorganism

Abstract

Natural and anthropogenic wetlands are major sources of the atmospheric greenhouse gas methane. Methane emissions from wetlands are mitigated by methanotrophic bacteria at the oxic–anoxic interface, a zone of intense redox cycling of carbon, sulfur, and nitrogen compounds. Here, we report on the isolation of an aerobic methanotrophic bacterium, ‘ Methylovirgula thiovorans ' strain HY1, which possesses metabolic capabilities never before found in any methanotroph. Most notably, strain HY1 is the first bacterium shown to aerobically oxidize both methane and reduced sulfur compounds for growth. Genomic and proteomic analyses showed that soluble methane monooxygenase and XoxF-type alcohol dehydrogenases are responsible for methane and methanol oxidation, respectively. Various pathways for respiratory sulfur oxidation were present, including the Sox–rDsr pathway and the S 4 I system. Strain HY1 employed the Calvin–Benson–Bassham cycle for CO 2 fixation during chemolithoautotrophic growth on reduced sulfur compounds. Proteomic and microrespirometry analyses showed that the metabolic pathways for methane and thiosulfate oxidation were induced in the presence of the respective substrates. Methane and thiosulfate could therefore be independently or simultaneously oxidized. The discovery of this versatile bacterium demonstrates that methanotrophy and thiotrophy are compatible in a single microorganism and underpins the intimate interactions of methane and sulfur cycles in oxic–anoxic interface environments.

Methanotrophs are vigorous H2S oxidizers using a sulfide:quinone oxidoreductase and a ba3-type terminal oxidase

“…Different types of putative SQRs were detected in a large variety of proteobacterial genera in which a pMMO and/or sMMO was present, such as Methylobacter , Methylocaldum , Methylocapsa , Methylococcus , Methylocystis , Methylomagnum , Methylomarinum , Methylomicrobium , Methylomonas , Methyloprofundus , Methylosinus , Methylospira , Methyloterricola , Methylotetracoccus , Methylotuvimicrobium and Methylovulum . In addition, the recently isolated alphaproteobacterium ‘ Methylovirgula thiovorans ’ strain HY1 encodes a type I SQR (Gwak et al, 2022). In contrast, verrucomicrobial methanotrophs possess genes encoding a type III SQR, comprising bacterial and archaeal SQRs of which the least is known (Marcia et al, 2010).…”

“…SAD2, isolated from a sulfide-rich anaerobic digester, was slightly inhibited (44-60% decrease in methanol production) in the presence of 0.1% H 2 S, but the mechanism was not explored (Zhang et al, 2016; Wei et al, 2017). ‘ Methylovirgula thiovorans ’ strain HY1A was recently shown to be able to consume various reduced sulfur compounds together with CH 4 , but a simultaneous oxidation of CH 4 and H 2 S could not be observed (Gwak et al, 2022). The H 2 S concentration was below the detection limit in the peatland where strain HY1A was isolated from, suggesting that a vigorous H 2 S detoxification might not be necessary.…”

“…H 2 S is known to bind to metals such as copper and iron, which could lead to inhibition of the CH 4 oxidation capacity of the copper-dependent pMMO and terminal oxidases involved in the reduction of O 2 (Bagarinao, 1992; Pietri et al, 2011; Barton et al, 2014; Landry et al, 2021). Interestingly, ‘ Methylovirgula thiovorans ’ strain HY1A only encodes an iron-dependent sMMO (Gwak et al, 2022), whereas M. fumariolicum SolV encodes multiple copper-dependent pMMOs (Schmitz et al, 2021). The former strain does not simultaneously oxidize H 2 S and CH 4 , while the latter has a rapid H 2 S detoxification system to alleviate inhibition of methanotrophy.…”

“…The observation that M. fumariolicum SolV reduced elemental sulfur to H 2 S in the presence of H 2 or methanol is intriguing. ‘ Methylovirgula thiovorans ’ strain HY1A grown on thiosulfate increasingly produced an enzyme that resembles a protein known to possess sulfhydrogenase activity (Gwak et al, 2022). Interestingly, this enzyme clusters with the group 3b [NiFe] hydrogenase of M. fumariolicum SolV, thought to be involved in the production of NAD(P)H for CO 2 fixation (Carere et al, 2017).…”

“…Recently, it was demonstrated that pure cultures of the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV can consume methanethiol (CH3SH), with concomitant substoichiometric formation of H 2 S, which indicated that strain SolV partly metabolized this toxic intermediate (Schmitz et al, 2022). Subsequently, the elegant study of Gwak et al (2022) demonstrated that also proteobacterial methanotrophs can oxidize H 2 S. They isolated the versatile alphaproteobacterium ‘ Methylovirgula thiovorans ’ strain HY1 from a peatland in South Korea that could grow on thiosulfate (S 2 O 3 2− ), tetrathionate (S 4 O 6 2− ), elemental sulfur (S 0 ), and a range of carbon compounds. However, growth on H 2 S was not studied.…”