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Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments

Author

Listed:
  • Xiyang Dong

    (University of Calgary)

  • Chris Greening

    (Monash University)

  • Jayne E. Rattray

    (University of Calgary)

  • Anirban Chakraborty

    (University of Calgary)

  • Maria Chuvochina

    (Monash University)

  • Daisuke Mayumi

    (University of Calgary
    National Institute of Advanced Industrial Science and Technology (AIST))

  • Jan Dolfing

    (Newcastle University)

  • Carmen Li

    (University of Calgary)

  • James M. Brooks

    (TDI Brooks International)

  • Bernie B. Bernard

    (TDI Brooks International)

  • Ryan A. Groves

    (University of Calgary)

  • Ian A. Lewis

    (University of Calgary)

  • Casey R. J. Hubert

    (University of Calgary)

Abstract

The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.

Suggested Citation

  • Xiyang Dong & Chris Greening & Jayne E. Rattray & Anirban Chakraborty & Maria Chuvochina & Daisuke Mayumi & Jan Dolfing & Carmen Li & James M. Brooks & Bernie B. Bernard & Ryan A. Groves & Ian A. Lewi, 2019. "Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-09747-0
    DOI: 10.1038/s41467-019-09747-0
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    Cited by:

    1. Xiyang Dong & Yongyi Peng & Muhua Wang & Laura Woods & Wenxue Wu & Yong Wang & Xi Xiao & Jiwei Li & Kuntong Jia & Chris Greening & Zongze Shao & Casey R. J. Hubert, 2023. "Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Ying-Li Zhou & Paraskevi Mara & Guo-Jie Cui & Virginia P. Edgcomb & Yong Wang, 2022. "Microbiomes in the Challenger Deep slope and bottom-axis sediments," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    3. Xiyang Dong & Chuwen Zhang & Yongyi Peng & Hong-Xi Zhang & Ling-Dong Shi & Guangshan Wei & Casey R. J. Hubert & Yong Wang & Chris Greening, 2022. "Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

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