Anaerobic Degradation of Paraffins by Thermophilic Actinobacteria under Methanogenic Conditions

Abstract

Microbial anaerobic alkane degradation is a key process in subsurface oil reservoirs and anoxic environments contaminated with petroleum, with a major impact on global carbon cycling. However, the thermophiles capable of water-insoluble paraffins (>C 17 ) degradation under methanogenic conditions has remained understudied. Here, we established thermophilic (55 °C) n-paraffins-degrading (C 21 −C 30 ) cultures from an oil reservoir. After over 900 days of incubation, the even-numbered n-paraffins were biodegraded to methane. The bacterial communities are dominated by a novel class-level lineage of actinobacteria, 'Candidatus Syntraliphaticia'. These 'Ca. Syntraliphaticia'-like metagenome-assembled genomes (MAGs) encode a complete alkylsuccinate synthases (ASS) gene operon, as well as hydrogenases and formate dehydrogenase, and several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. Metatranscriptomic analysis suggests that n-paraffins are activated via fumarate addition reaction, and oxidized into carbon dioxide, hydrogen/formate and acetate by 'Ca. Syntraliphaticia', that could be further converted to methane by the abundant hydrogenotrophic and acetoclastic methanogens. We also found a divergent methyl-CoM reductase-like complex (MCR) and a canonical MCR in two MAGs representing 'Ca. Methanosuratus' (within candidate phylum Verstraetearchaeota), indicating the capability of methane and short-chain alkane metabolism in the oil reservoir. Ultimately, this result offers new insights into the degradability and the mechanisms of n-paraffins under methanogenic conditions at high temperatures.

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

“…Members of Actinobacteria were identified in various methanogenic crude oil-degrading consortia [14,23]. In the syntrophic thermophilic methanogenic community growing on crude oil, actinobacteria 'Candidatus Syntraliphaticia' were found, probably belonging to a new class of the phylum Actinobacteria [23].…”

“…Members of Actinobacteria were identified in various methanogenic crude oil-degrading consortia [14,23]. In the syntrophic thermophilic methanogenic community growing on crude oil, actinobacteria 'Candidatus Syntraliphaticia' were found, probably belonging to a new class of the phylum Actinobacteria [23]. Metatranscriptomic analysis indicated their ability to carry out anaerobic alkane degradation by activation with fumarate and subsequent oxidation to CO2, H2/formate, and acetate, which were then utilized by methanogens.…”

Petroleum NAPL Depletion Estimates and Selection of Marker Constituents from Compositional Analysis

“…Biodegradation of n-paraffins (>C10 up to C50) by mixed microbial cultures in methanogenic conditions has been observed for oil-impacted sediments and oil reservoir fluids in microcosm studies (Zengler et al 1999;Anderson and Lovley 2000;Jones et al 2008;Siddique et al 2011;Wawrik et al 2016;Liu et al 2020) with measured production of methane in the range of 75% to 94% of that predicted by Equation 19. In the example cases and in similar NAPL releases, we may also expect production of methane, with oxidation of some produced methane to carbon dioxide in aerobic soil zones surrounding the NAPL.…”

Genomic remnants of ancestral hydrogen and methane metabolism in Archaea drive anaerobic carbon cycling

“…The JdFR metagenomes also contain JdFR-11, one of the Bathyarchaeota with canonical Mtr. We found two additional NRA7 MAGs (Archaeoglobi MAG-15, Archaeoglobi MAG-16) from the Shengli oil field metagenomes 32 that were submitted to NCBI after we created our local genomic databases, and were thus not included in other phylogenomic analyses. We downloaded the JdFR and Shengli metagenomic reads from SRA, reassembled, rebinned them, and manually curated the genomes, improving upon their NCBI counterparts.…”

“…We assembled the reads using metaSPADES v3.14.1 64 . The JdFR metagenomes were assembled individually, while the Shengli metagenomes were co-assembled, as in the original publication 32 . Both JdFR and Shengli metagenomes were then processed identically using the uBin helper scripts 65 .…”