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

Shun’ichi Ishii (), Shino Suzuki, Trina M. Norden-Krichmar, Aaron Tenney, Patrick S. G. Chain, Matthew B. Scholz, Kenneth H. Nealson and Orianna Bretschger
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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
Aaron Tenney: Microbial and Environmental Genomics, J. Craig Venter Institute
Patrick S. G. Chain: Genome Sciences, Los Alamos National Laboratory
Matthew B. Scholz: Genome Sciences, Los Alamos National Laboratory
Kenneth H. Nealson: Microbial and Environmental Genomics, J. Craig Venter Institute
Orianna Bretschger: Microbial and Environmental Genomics, J. Craig Venter Institute

Nature Communications, 2013, vol. 4, issue 1, 1-10

Abstract: 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.

Date: 2013
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DOI: 10.1038/ncomms2615

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