Effects of sulfate reducing bacteria and sulfate concentrations on mercury methylation in freshwater sediments

Methylmercury (MeHg) is the most poisonous form of mercury (Hg) and it enters the human body primarily through consumption of Hg contaminated fish. Sulfate reducing bacteria (SRB) are major producers of MeHg in anoxic sediments. The dsrAB gene was isolated from freshwater fish pond sediments. Sequence analyses showed that the SRB in sediments was mainly composed of Desulfobulbus propionicus and Desulfovibrio vulgaris. The two species of SRB were cultured from freshwater sediments. The addition of inorganic Hg to these freshwater sediments caused an increase in MeHg concentrations at 30 days incubation. MeHg levels were sensitive to sulfate concentrations; a medium sulfate level (0.11 mg/g) produced higher levels than treatments lacking sulfate addition or when amended with 0.55 mg/g. Assessment of bacterial levels by PCR measurements of microbial DNA indicated that the MeHg levels were correlated with cell growth.

Reclassification of the sulfate- and nitrate-reducing bacterium Desulfovibrio vulgaris subsp. oxamicus as Desulfovibrio oxamicus sp. nov., comb. nov

Desulfovibrio vulgaris subsp. oxamicus (type strain, DSM 1925(T)) was found to use nitrate as a terminal electron acceptor, the latter being reduced to ammonium. Phylogenetic studies indicated that strain DSM 1925(T) was distantly related to the type strain of Desulfovibrio vulgaris (95.4 % similarity of the small-subunit rRNA gene) and had as its closest phylogenetic relatives two other nitrate- and sulfate-reducing bacteria, namely Desulfovibrio termitidis (99.4 % similarity) and Desulfovibrio longreachensis (98.4 % similarity). Additional experiments were conducted to characterize better strain DSM 1925(T). This strain incompletely oxidized lactate and ethanol to acetate. It also oxidized butanol, pyruvate and citrate, but not glucose, fructose, acetate, propionate, butyrate, methanol, glycerol or peptone. The optimum temperature for growth was 37 degrees C (range 16-50 degrees C) and the optimum NaCl concentration for growth was 0.1 % (range 0-5 %). Because of significant genotypic and phenotypic differences from Desulfovibrio termitidis and Desulfovibrio longreachensis, reclassification of Desulfovibrio vulgaris subsp. oxamicus as Desulfovibrio oxamicus sp. nov., comb. nov., is proposed. The type strain is strain Monticello 2(T) (=DSM 1925(T)=NCIMB 9442(T)=ATCC 33405(T)).

Spectroelectrochemical Characterization of the [NiFe] Hydrogenase of Desulfovibrio vulgaris Miyazaki F

The active site in the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F has been investigated by Fourier transform infrared (FTIR) spectroscopy. Analysis of the spectra allowed the three diatomic inorganic ligands to Fe in this enzyme to be identified as one CO molecule and two CN(-) molecules. Furthermore, pH-dependent redox titrations were performed to determine the midpoint potentials as well as the pK value of the respective reactions and revealed that each single-electron redox transition is accompanied by a single-proton transfer step. The comparison of these spectra with those published for other [NiFe] hydrogenases shows that the electronic structure of the active sites of these enzymes and their redox processes are essentially the same. Nevertheless, differences with respect to the frequency of the CO band and the pH dependence of the Ni-R states have been observed. Finally, the frequency shifts of the bands in the IR spectra were interpreted with respect to the electronic configuration of the redox intermediates in the catalytic cycle.

Redox-coupled conformational alternations in cytochrome c(3) from D. vulgaris Miyazaki F on the basis of its reduced solution structure

Heteronuclear NMR spectroscopy was performed to determine the solution structure of (15)N-labeled ferrocytochrome c(3) from Desulfovibrio vulgaris Miyazaki F (DvMF). Although the folding of the reduced cytochrome c(3) in solution was similar to that of the oxidized one in the crystal structure, the region involving hemes 1 and 2 was different. The redox-coupled conformational change is consistent with the reported solution structure of D. vulgaris Hildenborough ferrocytochrome c(3), but is different from those of other cytochromes c(3). The former is homologous with DvMF cytochrome c(3) in amino acid sequence. Small displacements of hemes 1 and 2 relative to hemes 3 and 4 were observed. This observation is consistent with the unusual behavior of the 2(1)CH(3) signal of heme 3 reported previously. As shown by the (15)N relaxation parameters of the backbone, a region between hemes 1 and 2 has more flexibility than the other regions. The results of this work strongly suggest that the cooperative reduction of hemes 1 and 2 is based on the conformational changes of the C-13 propionate of heme 1 and the aromatic ring of Tyr43, and the interaction between His34 and His 35 through covalent and coordination bonds.

Modeling reduction of uranium U(VI) under variable sulfate concentrations by sulfate-reducing bacteria

The kinetics for the reduction of sulfate alone and for concurrent uranium [U(VI)] and sulfate reduction, by mixed and pure cultures of sulfate-reducing bacteria (SRB) at 21 +/- 3 degrees C were studied. The mixed culture contained the SRB Desulfovibrio vulgaris along with a Clostridium sp. determined via 16S ribosomal DNA analysis. The pure culture was Desulfovibrio desulfuricans (ATCC 7757). A zero-order model best fit the data for the reduction of sulfate from 0.1 to 10 mM. A lag time occurred below cell concentrations of 0.1 mg (dry weight) of cells/ml. For the mixed culture, average values for the maximum specific reaction rate, V(max), ranged from 2.4 +/- 0.2 micromol of sulfate/mg (dry weight) of SRB. h(-1)) at 0.25 mM sulfate to 5.0 +/- 1.1 micromol of sulfate/mg (dry weight) of SRB. h(-1) at 10 mM sulfate (average cell concentration, 0.52 mg [dry weight]/ml). For the pure culture, V(max) was 1.6 +/- 0.2 micromol of sulfate/mg (dry weight) of SRB. h(-1) at 1 mM sulfate (0.29 mg [dry weight] of cells/ml). When both electron acceptors were present, sulfate reduction remained zero order for both cultures, while uranium reduction was first order, with rate constants of 0.071 +/- 0.003 mg (dry weight) of cells/ml. min(-1) for the mixed culture and 0.137 +/- 0.016 mg (dry weight) of cells/ml. min(-1) (U(0) = 1 mM) for the D. desulfuricans culture. Both cultures exhibited a faster rate of uranium reduction in the presence of sulfate and no lag time until the onset of U reduction in contrast to U alone. This kinetics information can be used to design an SRB-dominated biotreatment scheme for the removal of U(VI) from an aqueous source.

Rapid comparison of the cytochrome c3 gene from nine strains of Desulfovibrio vulgaris using polymerase chain reaction amplification

Polymerase chain reaction amplification was used to compare different regions of the cytochrome c3 gene from nine strains of Desulfovibrio vulgaris, to examine homology within the species. Six 30-base polymerase chain reaction primers and three probes were synthesized on the basis of the published nucleic acid sequence of the cytochrome c3 gene from D. vulgaris, NCIMB 8303. Amplifications were performed on genomic DNA isolated from NCIMB 8303 as well as eight other strains. Six strains, NCIMB 8302, 8305, 8306, 8311, 11779, and DSM 2119, showed amplification products of equal size and quantity to those of strain 8303. Two other strains, NCIMB 8456 and DSM 1744, either showed reduced levels or no detectable amplification products. These results were confirmed by hybridization of amplified DNA to radiolabeled probes specific for each product. DNA sequencing of a 145-bp polymerase chain reaction fragment from strains NCIMB 8302, 8303, 11779, and DSM 2119 revealed complete sequence homology between these strains, whereas slight differences were seen with strain NCIMB 8456. Amino acid sequencing of the first 20 residues of cytochrome c3 purified from strains NCIMB 8456 and 8303 also showed differences in the two proteins. In contrast to the results obtained with strain NCIMB 8456, limited homology was observed between the first 20 amino acid residues of cytochrome c3 from strain DSM 1744 and strain NCIMB 8303.