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

Yi-Fan Liu; Jing Chen; Zhong-Lin Liu; Zhao-Wei Hou; Bo Liang; Li-Ying Wang; Lei Zhou; Li-Bin Shou; Dan-Dan Lin; Shi-Zhong Yang; Jin-Feng Liu; Xiao-Lin Wu; Ji-Dong Gu; Bo-Zhong Mu

Engineering (May 2023)

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

Yi-Fan Liu,
Jing Chen,
Zhong-Lin Liu,
Zhao-Wei Hou,
Bo Liang,
Li-Ying Wang,
Lei Zhou,
Li-Bin Shou,
Dan-Dan Lin,
Shi-Zhong Yang,
Jin-Feng Liu,
Xiao-Lin Wu,
Ji-Dong Gu,
Bo-Zhong Mu

Affiliations

Yi-Fan Liu: State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; Engineering Research Center of Microbial Enhanced Oil Recovery (MEOR), East China University of Science and Technology, Shanghai 200237, China
Jing Chen: State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; Engineering Research Center of Microbial Enhanced Oil Recovery (MEOR), East China University of Science and Technology, Shanghai 200237, China
Zhong-Lin Liu: State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
Zhao-Wei Hou: Exploration and Development Research Institute of Daqing Oilfield Company Limited, PetroChina, Daqing 163712, China
Bo Liang: State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; Engineering Research Center of Microbial Enhanced Oil Recovery (MEOR), East China University of Science and Technology, Shanghai 200237, China
Li-Ying Wang: State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; Engineering Research Center of Microbial Enhanced Oil Recovery (MEOR), East China University of Science and Technology, Shanghai 200237, China
Lei Zhou: State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; Engineering Research Center of Microbial Enhanced Oil Recovery (MEOR), East China University of Science and Technology, Shanghai 200237, China
Li-Bin Shou: State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; Engineering Research Center of Microbial Enhanced Oil Recovery (MEOR), East China University of Science and Technology, Shanghai 200237, China
Dan-Dan Lin: State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; Engineering Research Center of Microbial Enhanced Oil Recovery (MEOR), East China University of Science and Technology, Shanghai 200237, China
Shi-Zhong Yang: State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; Engineering Research Center of Microbial Enhanced Oil Recovery (MEOR), East China University of Science and Technology, Shanghai 200237, China
Jin-Feng Liu: State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; Engineering Research Center of Microbial Enhanced Oil Recovery (MEOR), East China University of Science and Technology, Shanghai 200237, China
Xiao-Lin Wu: Exploration and Development Research Institute of Daqing Oilfield Company Limited, PetroChina, Daqing 163712, China; Corresponding authors.
Ji-Dong Gu: Environmental Engineering and Engineering Group, Guangdong Technion Israel Institute of Technology, Shantou 515063, China
Bo-Zhong Mu: State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; Engineering Research Center of Microbial Enhanced Oil Recovery (MEOR), East China University of Science and Technology, Shanghai 200237, China; Corresponding authors.

Journal volume & issue: Vol. 24
pp. 264 – 275

Abstract

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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 H2-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.

Published in Engineering

ISSN: 2095-8099 (Print); 2096-0026 (Online)
Publisher: Elsevier
Country of publisher: China
LCC subjects: Technology: Engineering (General). Civil engineering (General)
Website: http://www.journals.elsevier.com/engineering

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