title: Metatranscriptomic Evidence for Direct Interspecies Electron Transfer between Geobacter and Methanothrix Species in Methanogenic Rice Paddy Soils.
abstract: The possibility thatMethanothrix(formerlyMethanosaeta) andGeobacterspecies cooperate via direct interspecies electron transfer (DIET) in terrestrial methanogenic environments was investigated in rice paddy soils. Genes with high sequence similarity to the gene for the PilA pilin monomer of the electrically conductive pili (e-pili) ofGeobacter sulfurreducensaccounted for over half of the PilA gene sequences in metagenomic libraries and 42% of the mRNA transcripts in RNA sequencing (RNA-seq) libraries. This abundance of e-pilin genes and transcripts is significant because e-pili can serve as conduits for DIET. Most of the e-pilin genes and transcripts were affiliated withGeobacterspecies, but sequences most closely related to putative e-pilin genes from genera such asDesulfobacterium,Deferribacter,Geoalkalibacter, andDesulfobacula, were also detected. Approximately 17% of all metagenomic and metatranscriptomic bacterial sequences clustered withGeobacterspecies, and the finding thatGeobacterspp. were actively transcribing growth-related genes indicated that they were metabolically active in the soils. Genes coding for e-pilin were among the most highly transcribedGeobactergenes. In addition, homologs of genes encoding OmcS, ac-type cytochrome associated with the e-pili ofG. sulfurreducensand required for DIET, were also highly expressed in the soils.Methanothrixspecies in the soils highly expressed genes for enzymes involved in the reduction of carbon dioxide to methane. DIET is the only electron donor known to support CO2reduction inMethanothrixThus, these results are consistent with a model in whichGeobacterspecies were providing electrons toMethanothrixspecies for methane production through electrical connections of e-pili.IMPORTANCEMethanothrixspecies are some of the most important microbial contributors to global methane production, but surprisingly little is known about their physiology and ecology. The possibility that DIET is a source of electrons forMethanothrixin methanogenic rice paddy soils is important because it demonstrates that the contribution thatMethanothrixmakes to methane production in terrestrial environments may extend beyond the conversion of acetate to methane. Furthermore, defined coculture studies have suggested that whenMethanothrixspecies receive some of their energy from DIET, they grow faster than when acetate is their sole energy source. Thus,Methanothrixgrowth and metabolism in methanogenic soils may be faster and more robust than generally considered. The results also suggest that the reason thatGeobacterspecies are repeatedly found to be among the most metabolically active microorganisms in methanogenic soils is that they grow syntrophically in cooperation withMethanothrixspp., and possibly other methanogens, via DIET.
authors.affiliation: Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA dholmes@wne.edu.|Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts, USA.
authors.forename: Dawn E
authors.initials: DE
authors.lastname: Holmes
authors.affiliation: Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA.|Energy Biosciences Institute, University of California Berkeley, Berkeley, California, USA.
authors.forename: Pravin M
authors.initials: PM
authors.lastname: Shrestha
authors.affiliation: Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA.
authors.forename: David J F
authors.initials: DJF
authors.lastname: Walker
authors.affiliation: Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA.
authors.forename: Yan
authors.identifier: http://orcid.org/0000-0002-0126-7503
authors.initials: Y
authors.lastname: Dang
authors.affiliation: Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA.
authors.forename: Kelly P
authors.initials: KP
authors.lastname: Nevin
authors.affiliation: Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA.
authors.forename: Trevor L
authors.initials: TL
authors.lastname: Woodard
authors.affiliation: Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA.
authors.forename: Derek R
authors.identifier: http://orcid.org/0000-0001-7158-3555
authors.initials: DR
authors.lastname: Lovley
mesh_terms: D002245:Carbon Dioxide / Q000378:metabolism; D004579:Electron Transport; D036781:Fimbriae Proteins / Q000032:analysis / Q000235:genetics; D020869:Gene Expression Profiling; D045302:Geobacter / Q000254:growth & development / Q000378:metabolism*; D054892:Metagenome; D008697:Methane / Q000378:metabolism; D017019:Methanosarcinaceae / Q000254:growth & development / Q000378:metabolism*; D012275:Oryza / Q000254:growth & development; D012988:Soil Microbiology
chemical_list: D002245:Carbon Dioxide; D036781:Fimbriae Proteins; D008697:Methane
keywords: DIET; Geobacter; Methanothrix (Methanosaeta); direct interspecies electron transfer; metatranscriptomics; methane; methanogenesis