Metatranscriptomic Evidence for Direct Interspecies Electron Transfer between Geobacter and Methanothrix Species in Methanogenic Rice Paddy Soils

Abstract

The possibility that (formerly) and species 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) of accounted 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 with species, but sequences most closely related to putative e-pilin genes from genera such as, ,, and , were also detected. Approximately 17% of all metagenomic and metatranscriptomic bacterial sequences clustered with species, and the finding that spp. 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 transcribed genes. In addition, homologs of genes encoding OmcS, a -type cytochrome associated with the e-pili of and required for DIET, were also highly expressed in the soils. species 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 CO reduction in Thus, these results are consistent with a model in which species were providing electrons to species for methane production through electrical connections of e-pili. species 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 for in methanogenic rice paddy soils is important because it demonstrates that the contribution that makes to methane production in terrestrial environments may extend beyond the conversion of acetate to methane. Furthermore, defined coculture studies have suggested that when species receive some of their energy from DIET, they grow faster than when acetate is their sole energy source. Thus, growth and metabolism in methanogenic soils may be faster and more robust than generally considered. The results also suggest that the reason that species are repeatedly found to be among the most metabolically active microorganisms in methanogenic soils is that they grow syntrophically in cooperation with spp., and possibly other methanogens, via DIET.

A Membrane-Bound Cytochrome EnablesMethanosarcina acetivoransto Conserve Energy to Support Growth from Extracellular Electron Transfer

“…Diversion of electron flux from methane production to extracellular electron transfer may influence the extent of methane production and metal geochemistry in anaerobic soils and sediments. Methanogens such as Methanothrix (formerly Methanosaeta ) and Methanosarcina species can accept electrons via direct interspecies electron transfer from electron-donating partners, such as Geobacter species in important methanogenic environments such as anaerobic digesters and rice paddy soils (10–12). Anaerobic methane oxidation also plays an important role in the global carbon cycle and diverse anaerobic methane-oxidizing archaea (ANME) transfer electrons derived from methane oxidation to extracellular electron acceptors, such as other microbial species, Fe(III), or extracellular quinones (13–19).…”

Elucidating syntrophic butyrate-degrading populations in anaerobic digesters using stable isotope-informed genome-resolved metagenomics

“…The only gene lacking in the CO 2 -reducing pathway was a F 420 -dependent N 5 N 10 -methylene-tetrahydromethanopterin dehydrogenase (Mtd). While Methanothrix are thought to be obligate aceticlastic methanogens (53, 54), the presence and expression of the CO 2 -reducing pathway in Methanothrix was previously reported (60–62) and was hypothesized to be involved in methane formation via DIET. However, the mechanism through which Methanothrix would directly accept electrons from its syntrophic partner has not been identified (60, 61).…”

Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes

“…While the aromatically dense pilins in this study met the bioinformatic thresholds for e-pili, it is possible that they are used for another function, such as DIET (Holmes et al, 2017; Walker et al, 2019a) or cellular detection of solid surfaces via electrical communication (Lovley, 2017). Evaluation of the conductivity of the putative e-pilins awaits testing by genetic complementation of Δ pilA in G. sulfurreducens , as in Walker et al (2018).…”