title: Microbial metabolic networks in a complex electrogenic biofilm recovered from a stimulus-induced metatranscriptomics approach.
abstract: Microorganisms almost always exist as mixed communities in nature. While the significance of microbial community activities is well appreciated, a thorough understanding about how microbial communities respond to environmental perturbations has not yet been achieved. Here we have used a combination of metagenomic, genome binning, and stimulus-induced metatranscriptomic approaches to estimate the metabolic network and stimuli-induced metabolic switches existing in a complex microbial biofilm that was producing electrical current via extracellular electron transfer (EET) to a solid electrode surface. Two stimuli were employed: to increase EET and to stop EET. An analysis of cell activity marker genes after stimuli exposure revealed that only two strains within eleven binned genomes had strong transcriptional responses to increased EET rates, with one responding positively and the other responding negatively. Potential metabolic switches between eleven dominant members were mainly observed for acetate, hydrogen, and ethanol metabolisms. These results have enabled the estimation of a multi-species metabolic network and the associated short-term responses to EET stimuli that induce changes to metabolic flow and cooperative or competitive microbial interactions. This systematic meta-omics approach represents a next step towards understanding complex microbial roles within a community and how community members respond to specific environmental stimuli.
authors.affiliation: Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA.|R&D Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502.
authors.forename: Shun'ichi
authors.initials: S
authors.lastname: Ishii
authors.affiliation: Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA.|Kochi Institute for Core Sample Research, JAMSTEC, Nankoku, Kochi 783-8502.|Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Nankoku, Kochi 783-8502.|Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Shino
authors.initials: S
authors.lastname: Suzuki
authors.affiliation: Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: Aaron
authors.initials: A
authors.lastname: Tenney
authors.affiliation: Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: Trina M
authors.initials: TM
authors.lastname: Norden-Krichmar
authors.affiliation: Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Nealson
authors.affiliation: Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: Orianna
authors.initials: O
authors.lastname: Bretschger
mesh_terms: D018441:Biofilms; D004579:Electron Transport; D004583:Electrons; D020869:Gene Expression Profiling; D005798:Genes, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D053858:Metabolic Networks and Pathways; D056186:Metagenomics; D056265:Microbial Interactions; D059467:Transcriptome