Identification of Acetate-Degrading Sulfate Reducing Bacteria in Italian Rice Field Soil by rRNA based Stable Isotope Probing

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 soils, combining 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts profiling 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 labeled or non-labeled) 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 was primarily accumulated. The accumulated acetate was rapidly consumed after the depletion of propionate and butyrate. Simultaneously, Desulfovirga spp., Syntrophobacter spp., and unclassified Syntrophobacteraceae were significantly labeled with 13C, and their relative abundances were remarkably enhanced. The relatively abundance of Desulfovibrio spp. increased upon gypsum amendments. However, 13C labeling of Desulfovibrio spp. was only moderate. In addition, minor groups like Desulforhabdus spp., Desulfobacca spp., and Desulfotomaculum spp. substantially incorporated 13C into their nucleic acids. In summary, Syntrophobacteraceae affiliated species were identified as the major acetotrophic sulfate reducers (SRB) in paddy soil. They (together with Desulfobacca spp., and Desulfotomaculum spp.) coupled acetate oxidation to sulfate reduction and completely inhibited methane production 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.