Non-Sulfate-Reducing, Syntrophic Bacteria Affiliated with Desulfotomaculum Cluster I Are Widely Distributed in Methanogenic Environments

Abstract

The classical perception of members of the gram-positive Desulfotomaculum cluster I as sulfate-reducing bacteria was recently challenged by the isolation of new representatives lacking the ability for anaerobic sulfate respiration. For example, the two described syntrophic propionate-oxidizing species of the genus Pelotomaculum form the novel Desulfotomaculum subcluster Ih. In the present study, we applied a polyphasic approach by using cultivation-independent and culturing techniques in order to further characterize the occurrence, abundance, and physiological properties of subcluster Ih bacteria in low-sulfate, methanogenic environments. 16S rRNA (gene)-based cloning, quantitative fluorescence in situ hybridization, and real-time PCR analyses showed that the subcluster Ih population composed a considerable part of the Desulfotomaculum cluster I community in almost all samples examined. Additionally, five propionate-degrading syntrophic enrichments of subcluster Ih bacteria were successfully established, from one of which the new strain MGP was isolated in coculture with a hydrogenotrophic methanogen. None of the cultures analyzed, including previously described Pelotomaculum species and strain MGP, consumed sulfite, sulfate, or organosulfonates. In accordance with these phenotypic observations, a PCR-based screening for dsrAB (key genes of the sulfate respiration pathway encoding the alpha and beta subunits of the dissimilatory sulfite reductase) of all enrichments/(co)cultures was negative with one exception. Surprisingly, strain MGP contained dsrAB, which were transcribed in the presence and absence of sulfate. Based on these and previous findings, we hypothesize that members of Desulfotomaculum subcluster Ih have recently adopted a syntrophic lifestyle to thrive in low-sulfate, methanogenic environments and thus have lost their ancestral ability for dissimilatory sulfate/sulfite reduction.Members of Desulfotomaculum cluster I have been generally known as gram-positive, spore-forming, sulfate-reducing bacteria (50, 56) and have frequently been found in various anoxic environments, such as sediments, rice paddy soil, human feces, and anaerobic sludges (for examples, see references 21, 42, 56, 57). The genus Desulfotomaculum includes over 20 validly described mesophilic and thermophilic species, all of which share the ability to oxidize various organic substances, like shortchain fatty acids, alcohols, and aromatic compounds with sulfate as a terminal electron acceptor (56). Due to these physiological traits, members of Desulfotomaculum cluster I have been considered important in sulfidogenic, anoxic environments, where they play crucial roles in the degradation of organic compounds, as well as in the biogeochemical cycling of sulfur (56).On the basis of comparative 16S rRNA gene sequence analysis, Desulfotomaculum cluster I was considered to be comprised of seven well-separated subclusters, Ia to Ig (27,50,52,57). Although it has been argued that each subcluster could be treated taxonomically as an individual...

Phylogeny of the alpha and beta subunits of the dissimilatory adenosine-5′-phosphosulfate (APS) reductase from sulfate-reducing prokaryotes – origin and evolution of the dissimilatory sulfate-reduction pathway

“…However, in the DsrAB-based tree, the deltaproteobacterial SRB group was monophyletic and the Desulfobacterium anilini-related SRB group was suggested to be the donor lineage for the xenologous dsrAB genes of the Desulfotomaculum subclusters Ib, Ic, Id and Ie, as well as Moorella thermoacetica (member of the Thermoanaerobacteriales). Desulfosporosinus and the Desulfotomaculum subclusters Ia, If and Ih have been postulated to represent the DsrAB-'authentic' Gram-positive SRB clades that were not affected by LGT (Imachi et al, 2006;Klein et al, 2001;Zverlov et al, 2005). The xenologous gene displacements of the orthologous dsrAB genes in subclusters Ib-Ie are supported by the AprB/A phylogeny of this study, because Desulfotomaculum subclusters Ia/If and Desulfosporosinus consistently branch close to the root of the DsrAB-and AprB/A-based trees.…”

Microbial methane production in deep aquifer associated with the accretionary prism in Southwest Japan

“…It is known that these sulfate reducers are able to grow by fermentation in low-sulfate environments (Henry et al, 1994;Nazina et al, 2005). In addition, a few members of the genus Desulfotomaculum degrade organic matter to H 2 and CO 2 through fermentation process and grow in syntrophic association with hydrogenotrophic methanogens in the absence of sulfate (Imachi et al, 2006). The dominant species related to sulfate-reducing bacteria in the clone library (SMD-B01 and SMD-B02) may grow by fermentation and degrade organic matter to H 2 and CO 2 in the deep aquifer, because the groundwater has low concentrations of sulfate and sulfide (Supplementary Table S2).…”

Agricultural biogas production in Germany - from practice to microbiology basics

“…However, some SRB appear to have adopted a facultative syntrophic lifestyle in the absence of sulfate [33], degrading e.g. propionic acid with methanogenic Archaea, whereas some erstwhile SRB appear to have lost the ability to reduce sulfate [36]. This indicates that adaptation upon selection pressure and niche occupation is an ongoing mechanism also in biogas microbiology and may be exploited in respective biotechnological developments.…”