Quantification of Desulfovibrio vulgaris Dissimilatory Sulfite Reductase Gene Expression during Electron Donor- and Electron Acceptor-Limited Growth

Harvard FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
Applied and Environmental Microbiology (Impact Factor: 3.67). 09/2008; 74(18):5850-3. DOI: 10.1128/AEM.00399-08
Source: PubMed


Previous studies have suggested that levels of transcripts for dsrA, a gene encoding a subunit of the dissimilatory sulfite reductase, are not directly related to the rates of sulfate reduction
in sediments under all conditions. This phenomenon was further investigated with chemostat-grown Desulfovibrio vulgaris. Under sulfate-limiting conditions, dsrA transcript levels increased as the bulk rates of sulfate reduction in the chemostat increased, but transcript levels were
similar at all sulfate reduction rates under electron donor-limiting conditions. When both electron donor- and electron acceptor-limiting
conditions were considered, there was a direct correspondence between dsrA transcript levels and the rates of sulfate reduction per cell. These results suggest that dsrA transcript levels may provide important information on the metabolic state of sulfate reducers.

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Available from: Laura Villanueva, Mar 10, 2014
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    • "The dissimilatory (bi)sulfite reductase (dsrAB) gene is highly conserved among sulfate-reducing prokaryotes (Bacteria and Archaea) and codes for the dissimilatory (bi)sulfite reductase, which is responsible for the rate-limiting step of sulfate reduction (Wagner et al., 1998). Levels of mRNA for dsrAB genes were shown to increase in pure culture studies of dissimilatory SRB as rates of sulfate reduction increased (Neretin et al., 2003; Villanueva et al., 2008) and correlated with the activity of SRB in petroleum-contaminated marine harbor sediments (Chin et al., 2008). In the case of Fe(III) reduction, no single respiration pathway has been identified as FeRB can reduce insoluble Fe(III) oxides via direct enzymatic reduction, electron shuttling pathways, or by solubilizing metals with organic ligands (DiChristina, 2005a). "
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    ABSTRACT: Though iron- and sulfate-reducing bacteria are well known for mediating uranium(VI) reduction in contaminated subsurface environments, quantifying the in situ activity of the microbial groups responsible remains a challenge. The objective of this study was to demonstrate the use of quantitative molecular tools that target mRNA transcripts of key genes related to Fe(III) and sulfate reduction pathways in order to monitor these processes during in situ U(VI) remediation in the subsurface. Expression of the Geobacteraceae-specific citrate synthase gene (gltA) and the dissimilatory (bi)sulfite reductase gene (dsrA), were correlated with the activity of iron- or sulfate-reducing microorganisms, respectively, under stimulated bioremediation conditions in microcosms of sediments sampled from the U.S. Department of Energy's Oak Ridge Integrated Field Research Challenge (OR-IFRC) site at Oak Ridge, TN, USA. In addition, Geobacteraceae-specific gltA and dsrA transcript levels were determined in parallel with the predominant electron acceptors present in moderately and highly contaminated subsurface sediments from the OR-IFRC. Phylogenetic analysis of the cDNA generated from dsrA mRNA, sulfate-reducing bacteria-specific 16S rRNA, and gltA mRNA identified activity of specific microbial groups. Active sulfate reducers were members of the Desulfovibrio, Desulfobacterium, and Desulfotomaculum genera. Members of the subsurface Geobacter clade, closely related to uranium-reducing Geobacter uraniireducens and Geobacter daltonii, were the metabolically active iron-reducers in biostimulated microcosms and in situ core samples. Direct correlation of transcripts and process rates demonstrated evidence of competition between the functional guilds in subsurface sediments. We further showed that active populations of Fe(III)-reducing bacteria and sulfate-reducing bacteria are present in OR-IFRC sediments and are good potential targets for in situ bioremediation.
    Full-text · Article · Aug 2012 · Frontiers in Microbiology
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    • "Perhaps the greatest unknown in applying functional gene expression to estimating rates of microbial metabolism is the diversity of sulfate reducers in natural environments. To date dsr expression has been tested in only two pure sulfate reducing strains, D. vulgaris (Strattan, 2010; Villanueva et al., 2008) and Desulfobacterium autotrophicum (Neretin et al., 2003), and no attempt yet has been made to determine whether a given csSRR is reflected by the same level of dsr expression in each. Such a comparison would not immediately confirm the widespread applicability of this approach, but could be useful to determine its feasibility. "

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    ABSTRACT: In the human gastrointestinal system, dietary components, including fiber, that reach the colon are fermented principally to short-chain fatty acids, hydrogen and carbon dioxide. Microbial disposal of the hydrogen generated during anaerobic fermentation in the human colon is critical to the functioning of this ecosystem. Methanogenesis by methanogenic Archaea and sulfate reduction by sulfate reducing bacteria (SRB) are the major hydrogenotrophic pathways in the human colon. Hydrogen metabolism by these microbes has an important impact on the colonic health. Methanogenic status of mammals is suggested to be under evolutionary rather than dietary control. However, information is lacking regarding the dynamics of hydrogenotrophic microbial communities among different primate species. Here I analyzed the composition of methanogens and SRB in various species of primates using PCR-DGGE fingerprinting targeting Archaea and Desulfovibrionales 16S rDNA, clone library construction of Archaea 16S rDNA and mcrA gene, and quantitative real-time PCR targeting mcrA and dsrA genes. Functionality of methanogens was determined by detection of methane from in vitro incubation of fresh feces. The results showed that the host species-specific hydrogenotrophic microbiota can be observed in some, but not all, of the captive primate species. A human colonic methanogen, Methanobrevibacter smithii, was detected in all captive hominoid species, indicating high similarity of methanogenic microbiota among these primates and humans. Comparison of wild and captive primates indicated that captive condition can be a major determinant of hydrogenotrophic microbial composition that overrides the genetic or early environmental effects, indicating the importance of proper captive management on the maintenance of colonic health.
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