Long-Term Cultivation and Meta-Omics Reveal Methylotrophic Methanogenesis in Hydrocarbon-Impacted Habitats

Yi-Fan Liu^a,d,e, Jing Chen^a,e, Zhong-Lin Liu^a, Zhao-Wei Hou^b, Bo Liang^a,e

State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China.

The microbial conversion of alkanes to methane in hydrocarbon-contaminated environments is an intrinsic bioremediation strategy under anoxic conditions. However, the mechanism of microbial methanogenic alkane degradation is currently unclear. Under ten-years of continuous efforts, we obtained a methanogenic n-alkane-degrading (C₁₅–C₂₀) enrichment culture that exhibited sustained improvements in the kinetic properties of methane production. The integrated metagenomic and metatranscriptomic analyses revealed that n-alkanes were mainly attacked by members of Desulfosarcinaceae, Firmicutes, and Synergistetes using the fumarate addition strategy, and were then further degraded in a common effort by Tepidiphilus members. Meanwhile, the abundant members of Anaerolineaceae were mainly responsible for cell debris recycling. However, according to the metatranscriptomic analyses, methane was predicted to be produced mainly via H₂₅-dependent methylotrophic methanogenesis, primarily from necromass-derived trimethylamine mediated by Methanomethyliaceae within the candidate phylum Verstraetearchaeota. These findings reveal that H₂-dependent methylotrophic methanogens, as well as methylotrophic methanogens, may play important ecological roles in the carbon cycle of hydrocarbon enriched subsurface ecosystems.

Keywords: Methanogenic hydrocarbon degradation, Oily sludge, Bioremediation, Alkanes.