Metatranscriptomic Evidence for Direct Interspecies Electron Transfer Between Geobacter and Methanothrix Species in Rice Paddy Sediments

The possibility that Methanothrix (formerly Methanosaeata) and Geobacter species cooperate via direct interspecies electron transfer (DIET) in terrestrial methanogenic sediments was investigated in rice paddy soils. Genes with high homology to the gene for the PilA monomer of the electrically conductive pili (e-pili) of Geobacter sulfurreducens accounted for over half of the PilA gene sequences in metagenomic libraries and 37% of the mRNA transcripts in RNAseq libraries recovered from the paddy soils.This is significant because e-pili can serve as conduits for DIET. Most of the e-pili genes and transcripts were affiliated with Geobacter species, but sequences most closely related to putative e-pili genes from such genera as Desulfobacterium, Deferribacter, Geoalkalibacter, and Desulfobacula were also detected. Analysis of metagenomic and metatranscriptomic sequences indicated ca. 20% of the bacterial community was composed of Geobacter-like species and that Geobacter was actively transcribing the gene coding for citrate synthase (gltA), indicating that Geobacter were metabolically active in the soils. Mapping the metatranscriptome to the G. sulfurreducens genome demonstrated that e-pili genes were among the most highly transcribed Geobacter genes. In addition, homologs of genes coding for the c-type cytochrome OmcS, which is associated with the e-pili of G. sulfurreducens and also required for DIET, were also highly expressed in the soils. Methanothrix species in the sediments highly expressed genes for enzymes involved in the reduction of carbon dioxide to methane. DIET is the only electron donor known to support carbon dioxide reduction in Methanothrix. Thus, these results are consistent with a model in which Geobacter species were providing electrons to Methanothrix species for methane production through an e-pili electrical connection.