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A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer

Author

Listed:
  • Shun’ichi Ishii

    (Microbial and Environmental Genomics, J. Craig Venter Institute)

  • Shino Suzuki

    (Microbial and Environmental Genomics, J. Craig Venter Institute)

  • Trina M. Norden-Krichmar

    (Microbial and Environmental Genomics, J. Craig Venter Institute
    Present address: Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA)

  • Aaron Tenney

    (Microbial and Environmental Genomics, J. Craig Venter Institute)

  • Patrick S. G. Chain

    (Genome Sciences, Los Alamos National Laboratory
    Joint Genome Institute)

  • Matthew B. Scholz

    (Genome Sciences, Los Alamos National Laboratory
    Joint Genome Institute)

  • Kenneth H. Nealson

    (Microbial and Environmental Genomics, J. Craig Venter Institute
    University Southern California)

  • Orianna Bretschger

    (Microbial and Environmental Genomics, J. Craig Venter Institute)

Abstract

Microbial respiration via extracellular electron transfer (EET) is a ubiquitous reaction that occurs throughout anoxic environments and is a driving force behind global biogeochemical cycling of metals. Here we identify specific EET-active microbes and genes in a diverse biofilm using an innovative approach to analyse the dynamic community-wide response to changing EET rates. We find that the most significant gene expression responses to applied EET stimuli occur in only two microbial groups, Desulfobulbaceae and Desulfuromonadales. Metagenomic analyses reveal high coverage draft genomes of these abundant and active microbes. Our metatranscriptomic results show known and unknown genes that are highly responsive to EET stimuli and associated with our identified draft genomes. This new approach yields a comprehensive image of functional microbes and genes related to EET activity in a diverse community, representing the next step towards unravelling complex microbial roles within a community and how microbes adapt to specific environmental stimuli.

Suggested Citation

  • Shun’ichi Ishii & Shino Suzuki & Trina M. Norden-Krichmar & Aaron Tenney & Patrick S. G. Chain & Matthew B. Scholz & Kenneth H. Nealson & Orianna Bretschger, 2013. "A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer," Nature Communications, Nature, vol. 4(1), pages 1-10, June.
    • Handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms2615
    DOI: 10.1038/ncomms2615
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    Cited by:

    1. Taku Omura & Noriyuki Isobe & Takamasa Miura & Shun’ichi Ishii & Mihoko Mori & Yoshiyuki Ishitani & Satoshi Kimura & Kohei Hidaka & Katsuya Komiyama & Miwa Suzuki & Ken-ichi Kasuya & Hidetaka Nomaki &, 2024. "Microbial decomposition of biodegradable plastics on the deep-sea floor," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Jafar Ali & Aaqib Sohail & Lei Wang & Muhammad Rizwan Haider & Shahi Mulk & Gang Pan, 2018. "Electro-Microbiology as a Promising Approach Towards Renewable Energy and Environmental Sustainability," Energies, MDPI, vol. 11(7), pages 1-30, July.

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