Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species

Abstract

The methanogenic degradation of oil hydrocarbons can proceed through syntrophic partnerships of hydrocarbon-degrading bacteria and methanogenic archaea [1][2][3] . However, recent culture-independent studies have suggested that the archaeon 'Candidatus Methanoliparum' alone can combine the degradation of long-chain alkanes with methanogenesis 4,5 . Here we cultured Ca. Methanoliparum from a subsurface oil reservoir. Molecular analyses revealed that Ca. Methanoliparum contains and overexpresses genes encoding alkyl-coenzyme M reductases and methyl-coenzyme M reductases, the marker genes for archaeal multicarbon alkane and methane metabolism. Incubation experiments with different substrates and mass spectrometric detection of coenzyme-M-bound intermediates confirm that Ca. Methanoliparum thrives not only on a variety of long-chain alkanes, but also on n-alkylcyclohexanes and n-alkylbenzenes with long n-alkyl (C ≥13 ) moieties. By contrast, short-chain alkanes (such as ethane to octane) or aromatics with short alkyl chains (C ≤12 ) were not consumed. The wide distribution of Ca. Methanoliparum 4-6 in oil-rich environments indicates that this alkylotrophic methanogen may have a crucial role in the transformation of hydrocarbons into methane.In subsurface oil reservoirs and marine oil seep sediments, microorganisms use hydrocarbons as a source of energy and carbon 7,8 . The microorganisms preferentially consume alkanes, cyclic and aromatic compounds, leaving an unresolved complex mixture as residue and thereby altering the quality of the oil 7,8 . In the absence of sulfate, microorganisms couple anaerobic hydrocarbon degradation to methane formation 1,9,10 . This reaction was originally demonstrated by Zengler et al 2 as methanogenic 'microbial alkane cracking', and a large number of studies have shown that it can be performed in syntrophic interactions of bacteria and archaea 11 . In this syntrophy, the bacteria ferment the oil to acetate, carbon dioxide and hydrogen, while hydrogenotrophic and/or acetotrophic methanogenic archaea use the products for methanogenesis 1,2,11 .Diverse anaerobic hydrocarbon activation mechanisms exist, including the well-studied fumarate addition pathway catalysed by glycyl radical enzymes 12 . This mechanism is widespread among bacteria that thrive on alkanes of various chain lengths and other hydrocarbons 12,13 . By contrast, several archaeal lineages activate gaseous alkanes with the help of a specific type of methyl-coenzyme M reductase (MCR), an enzyme that was originally described to catalyse the reduction of methyl-coenzyme M (methyl-CoM) to methane in methanogens 14 . Anaerobic methanotrophic archaea use canonical MCRs to activate methane into methyl-CoM, which is then oxidized to CO 2 . Short-chain alkane-oxidizing archaea contain divergent variants of this enzyme, which are known as alkyl-CoM reductases (ACRs). Analogous to the methane-activating MCR, ACRs activate multicarbon alkanes to form CoM-bound alkyl units [15][16][17] . The cultured alkane-oxidizing archaea oxidize sho...

Physiological and Genomic Characterization of Actinotalea subterranea sp. nov. from Oil-Degrading Methanogenic Enrichment and Reclassification of the Family Actinotaleaceae

“…Bacteria of the genera Smithella and Syntrophus degrade alkanes in consortia with methanogens [11]. Recently the archaeon 'Candidatus Methanoliparum' was shown to be able to combine the degradation of long-chain alkanes with methanogenesis [22].…”

“…Using metagenomic analysis in syntrophic oil-degrading communities, in addition to the known species, new uncultured bacteria such as 'Atribacteria' or archaea 'Candidatus Methanoliparia', 'Candidatus Argoarchaeum', and 'Candidatus Syntrophoarchaeum' were revealed [19][20][21]. Moreover, recently non-syntrophic hydrocarbon degradation by the methanogenic archaeon 'Candidatus Methanoliparum' was shown, which essentially changes our view on anaerobic oil transformation in petroleum reservoirs [22].…”

Overview of Diverse Methyl/Alkyl-Coenzyme M Reductases and Considerations for Their Potential Heterologous Expression

“…Metagenomic and transcriptomic data indicated the presence of several different species, which contain and expresses genes encoding putative ACRs as well as MCRs. Additionally, the presence of hexadecyl-S-CoM and other long-chain alkane R-S-CoM derivatives were confirmed by mass spectrometry, thus indicating the involvement of an ACR in alkane activation ( Zhou et al, 2022 ).…”

“…In addition to the involvement of ACRs in short-chain alkane oxidation, recently published work suggests the use of ACRs to activate long-chain alkanes in oil reservoirs ( Zhou et al, 2022 ). Ca.…”

“…This reaction is proposed to occur in reverse in ANME that anaerobically oxidize methane to CO 2 via reverse methanogenesis ( Hallam et al, 2004 ; Shima and Thauer, 2005 ; Scheller et al, 2010 ; Timmers et al, 2017 ). In addition to methane formation and oxidation, variants of MCR are also involved in the anaerobic oxidation of short- and long-chain alkanes ( Borrel et al, 2019 ; Wang et al, 2021 ; Zhou et al, 2022 ).…”