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Identification of Syntrophobacteraceae as major acetate‐degrading sulfate reducing bacteria in Italian paddy soil

Liu, Pengfei, Pommerenke, Bianca, Conrad, Ralf
Environmental microbiology 2018 v.20 no.1 pp. 337-354
Desulfobacca, Desulforhabdus, Desulfotomaculum, Desulfovibrio, Desulfovirga, Syntrophobacter, acetates, butyrates, carbon, fluorides, genes, greenhouse gas emissions, greenhouse gases, gypsum, isotope labeling, methane, methane production, methanogens, microbial communities, paddies, paddy soils, propionic acid, ribosomal RNA, stable isotopes, sulfate-reducing bacteria, sulfates, sulfites
Methane is an important greenhouse gas and acetate is the most important intermediate (average 70%) of the carbon flow to CH₄ in paddy fields. Sulfate (e.g., gypsum) application can reduce CH₄ emissions up to 70%. However, the effect of gypsum application on acetate degradation and the microbial communities involved are unclear. Therefore, we studied acetate‐dependent sulfate reduction in anoxic microcosms of Italian rice paddy soil, combining profiling of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts and rRNA based stable isotope probing (SIP) analysis. Methane production was completely inhibited by gypsum in the absence of exogenous acetate. Amended acetate (either ¹³C labelled or non‐labelled) was stoichiometrically coupled to sulfate reduction or CH₄ production. With methyl fluoride in the presence of sulfate, added propionate and butyrate were incompletely oxidized to acetate, which transiently accumulated. After the depletion of propionate and butyrate the accumulated acetate was rapidly consumed. The relative abundance of dsrB and 16S rRNA genes and transcripts from Syntrophobacteraceae (Desulfovirga spp., Syntrophobacter spp. and unclassified Syntrophobacteraceae) increased upon addition of gypsum and acetate. Simultaneously, Syntrophobacteraceae affiliated species were significantly labelled with ¹³C. In addition, minor groups like Desulforhabdus spp., Desulfobacca spp. and Desulfotomaculum spp. substantially incorporated ¹³C into their nucleic acids. The relative abundance of Desulfovibrio spp. slightly increased upon gypsum amendments. However, ¹³C labelling of Desulfovibrio spp. was only moderate. In summary, Syntrophobacteraceae affiliated species were identified as the major acetotrophic sulfate reducers (SRB) in Italian paddy soil. The identification of these SRB as dominant acetate degraders well explained the scenarios of competition between SRB and acetoclastic methanogens as observed in rice paddy soil.