A study on electron transport-driven proton translocation in Desulfovibrio desulfuricans

Proton translocation by washed cells of the sulfate-reducing bacterium Desulfovibrio desulfuricans strain Essex 6 was studied by means of pH and sulfide electrodes. Reversible extrusion of protons could be induced either by addition of electron acceptors to cells incubated under hydrogen, or by addition of hydrogen to cells incubated in the presence of an appropriate electron acceptor. Proton translocation was increased in the presence of ionophores that dissipate the membrane potential (thiocyanate, methyl triphenylphosphonium cation, but not valinomycin) and was sensitive to the uncoupler carbonylcyanide m-chlorophenylhydrazone (CCCP). Upon micromolar additions of H₂, usually sulfide was formed in stoichiometric amounts, and extrapolated H⁺/H₂ ratios were 1.8±0.5 with sulfate, 2.3±0.3 with sulfite and 0.5±0.1 with thiosulfate. In several experiments hydrogen pulses caused increased proton extrusion not associated with sulfide production. This was a hint that sulfite might be reduced via intermediates. In the absence of H₂S formation, extrapolated H⁺/H₂ ratios were 3.1±0.8 with sulfate, 3.4±1.1 with sulfite, 4.4±0.8 with thiosulfate and 6.3±1.2 with oxygen. Micromolar pulses of electron acceptors to cells incubated under H₂ caused less proton translocation than H₂ pulses in presence of excess of electron acceptor; extrapolated H⁺/H₂ ratios were 1.3±0.4 with sulfite, 3.3±0.9 with nitrite and 4.2±0.5 with oxygen. No proton translocation was observed after micromolar pulses of sulfate, thiosulfate or nitrate to cells incubated under hydrogen in the presence of thiocyanate. Inhibition experiments with CO and CuCl₂ revealed that the hydrogenase activity was localized in the intracellular space, and that no periplasmic hydrogenase was present. The results indicate that D. desulfuricans can generate a proton gradient by pumping protons across the cytoplasmic membrane.Abbreviations APS adenosine 5-phosphosulfate - CCCP carbonyl cyanide m-chlorophenylhydrazone - MTTP⁺ methyl triphenylphosphonium cation     

Palladium recovery by immobilized cells of Desulfovibrio desulfuricans using hydrogen as the electron donor in a novel electrobioreactor

Desulfovibrio desulfuricans reduces Pd(II) to Pd(0) at the expense of H₂. Mass transfer limits the rate under hydrogen in a static solution, while a bubble reactor was inefficient due to loss of H₂. A novel approach to the transfer of H₂ to the biomass utilized a biofilm on the surface of a Pd-Ag membrane that traps and transports atomic hydrogen (H), formed at the back-side electrochemically, for delivery to the immobilized biofilm to form a biocatalytic surface for reduction of Pd(II) and deposition of Pd(0). Separation of the primary electrolysis chamber from the biocatalytic chamber permits the use of different solutions and pH in each, and use of a low voltage for H₂ generation. Pd(0) recovery was efficient and fed by H₂ on demand to give a clean, economic system with no generation of secondary wastes. The system was tested against a precious metal processing waste where the continuous removal of Pd, Pt and Rh was up to 88%, 99% and 75%, respectively, at a flow residence time of 10–20 min at an input pH of 2.5 and a total metals concentration of approx. 5 mM. Biorecovered Pd(0) was a better chemical catalyst than its chemical counterpart in a test reaction which liberated H₂ from hypophosphite.     

Isolation and characterization of porins from <Emphasis Type="Italic">Desulfovibrio piger</Emphasis> and <Emphasis Type="Italic">Bilophila wadsworthia</Emphasis>: structure and gene sequencing

The outer membrane proteins of Desulfovibrio piger and Bilophila wadsworthia (Omp-DP and Omp-BW, respectively) and the genes encoding them (omp-DP and omp-BW) were isolated and characterized. Native Omp-DP and Omp-BW form a trimeric structure of approximately 120 kDa. These proteins disaggregated into monomers with a molecular weight of approximately 53 kDa after heating at 95°C for 10 min. The pore-forming abilities of these oligomeric proteins demonstrated that they form small nonspecific channels with an exclusion limit of 260–300 Da. The omp-DP and omp-BW genes were cloned and sequenced. Sequence analyses revealed an open reading frame of 1,512 bp for omp-DP and 1,440 bp for omp-BW. The mature Omp-DP protein consisted of 480 amino acids and had a calculated MW of 53,290 Da. The mature Omp-BW protein consisted of 456 amino acids and had a calculated MW of 50.050 Da. Alignment of Omp-DP with Omp-BW revealed 54% homology, whereas alignment with other known porins showed a low level of homology. Analysis of the secondary structures indicated that both proteins span the outer membrane 18 times with amphipathic β-strands. This research presents porins which were isolated and characterized for the first time from bacteria belonging to the Desulfovibrionaceae family. O. Avidan and E. Kaltageser have contributed equally to this work.     

Sulfate formation via ATP sulfurylase in thiosulfate- and sulfite-disproportionating bacteria

Disproportionation of thiosulfate or sulfite to sulfate plus sulfide was found in several sulfate-reducing bacteria. Out of nineteen strains tested, eight disproportionated thiosulfate, and four sulfite. Growth with thiosulfate or sulfite as the sole energy source was obtained with three strains (Desulfovibrio sulfodismutans and the strains Bra02 and NTA3); additionally, D. desulfuricans strain CSN grew with sulfite but not with thiosulfate, although thiosulfate was disproportionated. Two sulfur-reducing bacteria, four phototrophic sulfur-oxidizing bacteria (incubated in the dark), and Thiobacillus denitrificans did not disproportionate thiosulfate or sulfite. Desulfovibrio sulfodismutans and D. desulfuricans CSN formed sulfate from thiosulfate or sulfite even when simultaneously oxidizing hydrogen or ethanol, or in the presence of 50 mM sulfate. The capacities of sulfate reduction and of thiosulfate and sulfite disproportionation were constitutively present. Enzyme activities required for sulfate reduction (ATP sulfurylase, pyrophosphatase, APS reductase, sulfite reductase, thiosulfate reductase, as well as adenylate kinase and hydrogenase) were detected in sufficient activities to account for the growth rates observed. ADP sulfurylase and sulfite oxidoreductase activities were not detected. Disproportionation was sensitive to the uncoupler carbonylcyanide m-chlorophenylhydrazone (CCCP) but not to the ATPase inhibitor dicyclohexylcarbodiimide (DCCD). It is proposed that during thiosulfate and sulfite disproportionation sulfate is formed via APS reductase and ATP sulfurylase, but not by sulfite oxidoreductase. Reversed electron transport must be assumed to explain the reduction of thiosulfate and sulfite by the electrons derived from APS reductase.Abbreviations CCCP Carbonylcyanide m-chlorophenylhydrazone - DCCD N,N-dicyclohexylcarbodiimide - APS adenosine 5-phosphosulfate (adenylylsulfate)     

Dehalogenation of chlorinated aromatic compounds using a hybrid bioinorganic catalyst on cells of <Emphasis Type="Italic">Desulfovibrio desulfuricans</Emphasis>

A novel bioinorganic catalyst was obtained via reduction of Pd(II) to Pd⁰ on to the surface of cells of Desulfovibrio desulfuricans at the expense of H₂. Palladised biomass, supplied with formate or H₂ as an electron donor, catalysed the dehalogenation of 2-chlorophenol and polychlorinated biphenyls. In the example of 2,3,4,5-tetrachlorobiphenyl, the bioinorganic catalyst promoted a rate of chloride release of 9.33 ± 0.17 nmol min^–1 mg ^–1and only ~5% of this value was obtained using chemically reduced or commercially available Pd ⁰. In the case of 2,2,4,4,6,6-hexachlorobiphenyl the rate was more than four orders of magnitude faster than the degradation reported using a sulfidogenic culture. Negligible chloride release occurred from any of the chloroaromatic compounds using biomass alone, or from palladised biomass challenged with hexane carrier solvent only. Analysis of the spent solution showed that in addition to catalysis of reductive dehalogenation the new material was able to remove very effectively the organic residua, with neither any PCB nor any breakdown products identifiable by GC/MS.Revisions requested 8 September 2004; Revisions received 21 October 2004;     

Effects of tungstate on the growth of Desulfovibrio gigas NCIMB 9332 and other sulfate-reducing bacteria with ethanol as a substrate

Growth of Desulfovibrio gigas NCIMB 9332 in mineral, vitamin-supplemented media with ethanol as substrate was strongly stimulated by the addition of tungstate (optimal level approximately 10^-7 M). At suboptimal tungstate concentrations, up to 1.0 mM acetaldehyde was detected in the culture supernatant and growth was slow. Omission of both tungstate and molybdate from the media prevented growth and ethanol utilization. Tungstate-deprived cultures that were grown on lactate had much lower aldehyde dehydrogenase (benzylviologen as acceptor; BV-AIDH) levels than tungstate-supplemented cultures. These data suggest that tungstate is required for the synthesis of active BV-AIDH. The characteristics of the enzyme activities in cell-free extracts show that the BV-AIDH activity present in tungstate-supplemented cultures is not due to the recently characterized molybdenum-containing aldehyde dehydrogenase of D. gigas. Out of 13 other strains of ethanol-oxidizing, gram-negative, sulfate-reducing bacteria tested, most strains grew well with either tungstate or molybdate supplementation. In contrast to a recent report, good growth on ethanol of two D. baculatus (Desulfomicrobium) strains (DSM 1741 and DSM 1743) was observed.Abbreviations BV-AIDH Benzylviologen-linked aldehyde dehydrogenase - DCPIP-AIDH 2,6-dichlorophenolindophenol-linked aldehyde dehydrogenase - DTT dithiothreitol     

Contribution of the [Fe<Superscript>II</Superscript>(SCys)<Subscript>4</Subscript>] site to the thermostability of rubredoxins

The thermostabilities of Fe²⁺ ligation in rubredoxins (Rds) from the hyperthermophile Pyrococcus furiosus (Pf) and the mesophiles Clostridium pasteurianum (Cp) and Desulfovibrio vulgaris (Dv) were compared. Residue 44 forms an NH...S(Cys) hydrogen bond to one of the cysteine ligands to the [Fe(SCys)₄] site, and substitutions at this location affect the redox properties of the [Fe(SCys)₄] site. Both Pf Rd and Dv Rd have an alanine residue at position 44, whereas Cp Fd has a valine residue. Wild-type proteins were examined along with V44A and A44V exchange mutants of Cp and Pf Rds, respectively, in order to assess the effects of the residue at position 44 on the stability of the [Fe(SCys)₄] site. Stability of iron ligation was measured by temperature-ramp and fixed-temperature time course experiments, monitoring iron release in both the absence and presence of more thiophilic metals (Zn²⁺, Cd²⁺) and over a range of pH values. The thermostability of the polypeptide fold was concomitantly measured by fluorescence, circular dichroism, and ¹H NMR spectroscopies. The A44V mutation strongly lowered the stability of the [Fe^II(SCys)₄] site in Pf Rd, whereas the converse V44A mutation of Cp Rd significantly raised the stability of the [Fe^II(SCys)₄] site, but not to the levels measured for wild-type Dv Rd. The region around residue 44 is thus a significant contributor to stability of iron coordination in reduced Rds. This region, however, made only a minor contribution to the thermostability of the protein folding, which was found to be higher for hyperthermophilic versus mesophilic Rds, and largely independent of the residue at position 44. These results, together with our previous studies, show that localized charge density, solvent accessibility, and iron site/backbone interactions control the thermostability of the [Fe(SCys)₄] site. The iron site thermostability does make a minor contribution to the overall Rd thermostability. From a mechanistic standpoint, we also found that attack of displacing ions (H⁺, Cd²⁺) on the Cys42 sulfur ligand at the [Fe(SCys)₄] site occurs through the V8 side and not the V44 side of the iron site.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00775-004-0525-4Abbreviations BPS bathophenanthroline sulfonate, sodium salt - Cp Rd (Pf Rd, Dv Rd) recombinant rubredoxin from Clostridium pasteurianum (Pyrococcus furiosus, Desulfovibrio vulgaris) - HEPES hydroxyethylpiperazineethanesulfonic acid - MES morpholinoethanesulfonic acid - Tris tris(hydroxymethyl)aminomethane - wt wild-type - ZnRd recombinant rubredoxin containing a [Zn(SCys)₄] site     

Activity of nitrate reductase in <Emphasis Type="Italic">Desulfovibrio vulgaris</Emphasis> VKM 1388

Evidence was obtained of the inhibitory effect of nitrate on the metabolism of Desulfovibrio vulgaris 1388. Nitrate is reduced only at low concentrations and in the presence of sulfate in the medium. Genetic data suggest that the genome of D. vulgaris 1388 contains the information about the γ subunit and possibly the NarG catalytic subunit of the membrane-bound nitrate reductase.     

Bactéries fermentatives,sulfato-réductrices et phototrophes sulfureuses en cultures mixtes

Résumé Dans les cultures mixtes, la fermentation du glucose par Escherichia coli fournit des sources de carbone et d'électrons au Desulfovibrio desulfuricans qui est à l'origine de la formation des substrats utilisables par la souche de Chlorobium.

---

Mixed cultures of heterotrophic, sulfate-reducing and sulfur phototrophic bacteria

In mixed cultures, carbon and electron sources for Desulfovibrio desulfuricans are excreted by Escherichia coli from glucose fermentation. Desulfovibrio produces substrates for Chlorobium strain.

     

Gas phase H<Subscript>2</Subscript>S product recovery in a packed bed bioreactor with immobilized sulfate-reducing bacteria

An N₂ strip gas was used in a packed bed sulfate-reducing bioreactor to recover the dissolved sulfide product and improve sulfate conversion. The highest volumetric productivity obtained was 261 mol H₂S m⁻³ d⁻¹. Lowering the initial pH of the medium from 7 to 6 increased the H₂S content of the strip gas from 3.6 to 5.8 mol%. The ratio of strip gas to liquid flow rates (G/L) was found be to a suitable basis for scaling the process. Calculations indicated that modest G/L values (<10²) were required to recover the residual dissolved sulfide in a downstream stripping column.     

Two-Component Signal Transduction Systems of Desulfovibrio vulgaris: Structural and Phylogenetic Analysis and Deduction of Putative Cognate Pairs

A large number of two-component signal transduction systems (TCSTS) including 59 putative sensory histidine kinases (HK) and 55 response regulators (RR) were identified from the Desulfovibrio vulgaris genome. In this study, the structural and phylogenetic analyses of all putative TCSTSs in D. vulgaris were performed. The results showed that D. vulgaris contained 21 hybrid-type HKs, implying that multiple-step phosphorelay may be a common signal transduction mechanism in D. vulgaris. Despite the low sequence similarity that restricted the resolution of the phylogenetic analyses, most TCSTS components of D. vulgaris were found clustered into several subfamilies previously recognized in Escherichia coli and Bacillus subtilis. An attempt was made in this investigation to identify the possible cognate HK-RR pairs not linked on the chromosome in D. vulgaris based on similar expression patterns in response to various environmental and genetic changes. Expression levels of all HK and RR genes were measured using whole-genome microarrays. Five groups of HK-RR genes not linked on the chromosome were identified as possible cognate pairs in D. vulgaris. The results provided a preliminary list of possible cognate HK-RR pairs and constitute a basis for further exploration of interaction and physiological function of TCSTSs in D. vulgaris. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Gail Simmons]     

Antioxidative enzymes of sulfate-reducing bacterium desulfovibrio desulfuricans: superoxide dismutase and peroxidases

Extracts of Desulfovibrio desulfuricans B-1388 cells grown under anaerobic conditions displayed superoxide dismutase activity. The maximal activity was found during the stationary growth phase. The enzyme was virtually completely located in the periplasm fraction. D. desulfuricans B-1388 lacked catalase activity but contained active NADH- and NADPH-peroxidases. The activity of NADH-peroxidase depended on the physiological state of the culture. On changing the growth conditions (the presence of 5% CO in the gaseous phase), the activity of superoxide dismutase decreased.     

Palladium and gold removal and recovery from precious metal solutions and electronic scrap leachates by Desulfovibrio desulfuricans

Biomass of Desulfovibrio desulfuricans was used to recover Au(III) as Au(0) from test solutions and from waste electronic scrap leachate. Au(0) was precipitated extracellularly by a different mechanism from the biodeposition of Pd(0). The presence of Cu²⁺ (∼2000 mg/l) in the leachate inhibited the hydrogenase-mediated removal of Pd(II) but pre-palladisation of the cells in the absence of added Cu²⁺ facilitated removal of Pd(II) from the leachate and more than 95% of the Pd(II) was removed autocatalytically from a test solution supplemented with Cu(II) and Pd(II). Metal recovery was demonstrated in a gas-lift electrobioreactor with electrochemically generated hydrogen, followed by precipitation of recovered metal under gravity. A 3-stage bioseparation process for the recovery of Au(III), Pd(II) and Cu(II) is proposed.Victoria S. Baxter-Plant – Deceased     

Anaerobic degradation of 1,3-propanediol by sulfate-reducing and by fermenting bacteria

Three strains of strictly anaerobic Gram-negative, non-sporeforming, motile bacteria were enriched and isolated from freshwater sediments with 1,3-propanediol as sole energy and carbon source. Strain OttPdl was a sulfate-reducing bacterium which grew also with lactate, ethanol, propanol, butanol, 1,4-butanediol, formate or hydrogen plus CO₂, the latter only in the presence of acetate. In the absence of sulfate, most of these substrates were fermented to the respective fatty acids in syntrophic cooperation with Methanospirillum hungatei. Sulfur, thiosulfate, or sulfite were reduced, nitrate not. The other two isolates degraded propanediol only in coculture with Methanospirillum hungatei. Strain OttGlycl grew in pure culture with acetoin and with glycerol in the presence of acetate. Strain WoAcl grew in pure culture only with acetoin. Both strains did not grow with other substrates, and did not reduce nitrate, sulfate, sulfur, thiosulfate or sulfite. The isolates were affiliated with the genera Desulfovibrio and Pelobacter. The pathways of propanediol degradation and the ecological importance of this process are discussed.     

Sulphate respiration from hydrogen in Desulfovibrio bacteria: a structural biology overview

Sulphate-reducing organisms are widespread in anaerobic enviroments, including the gastrointestinal tract of man and other animals. The study of these bacteria has attracted much attention over the years, due also to the fact that they can have important implications in industry (in biocorrosion and souring of oil and gas deposits), health (in inflamatory bowel diseases) and the environment (bioremediation). The characterization of the various components of the electron transport chain associated with the hydrogen metabolism in Desulfovibrio has generated a large and comprehensive list of studies. This review summarizes the more relevant aspects of the current information available on the structural data of various molecules associated with hydrogen metabolism, namely hydrogenases and cytochromes. The transmembrane redox complexes known to date are also described and discussed. Redox-Bohr and cooperativity effects, observed in a few cytochromes, and believed to be important for their functional role, are discussed. Kinetic studies performed with these redox proteins, showing clues to their functional inter-relationship, are also addressed. These provide the groundwork for the application of a variety of molecular modelling approaches to understanding electron transfer and protein interactions among redox partners, leading to the characterization of several transient periplasmic complexes. In contrast to the detailed understanding of the periplasmic hydrogen oxidation process, very little is known about the cytoplasmic side of the respiratory electron transfer chain, in terms of molecular components (with exception of the terminal reductases), their structure and the protein–protein interactions involved in sulphate reduction. Therefore, a thorough understanding of the sulphate respiratory chain in Desulfovibrio remains a challenging task.     

From bio-mineralisation to fuel cells: biomanufacture of Pt and Pd nanocrystals for fuel cell electrode catalyst

Biosynthesis of nano-scale platinum and palladium was achieved via enzymatically-mediated deposition of metal ions from solution. The bio-accumulated Pt(0) and Pd(0) crystals were dried, applied onto carbon paper and tested as anodes in a polymer electrolyte membrane (PEM) fuel cell for power production. Up to 100% and 81% of the maximum power generation was achieved by the bio-Pt and bio-Pd catalysts, respectively, compared to commercial fuel cell grade Pt catalyst. Hence, biomineralisation could pave the way for economical production of fuel cell catalysts since previous studies have shown that precious metals can be biorecovered from wastes into catalytically active bionanomaterials.     

Several new substrates for Desulfovibrio vulgaris strain Marburg and a spontaneous mutant from it

The ability of Desulfovibrio vulgaris strain Marburg (DSM 2119) to oxidize alcohols was surveyed in the presence and absence of hydrogen-scavenging anaerobes, Acetobacterium woodii and Methanospirillum hungatei. In the presence of sulfate, D. vulgaris grew not only on ethanol, 1-propanol, and 1-butanol, but also on isobutanol, 1-pentanol, ethyleneglycol, and 1,3-propanediol. Metabolism of these alcohols was simple oxidation to the corresponding acids, except with the last two substrates: ethyleneglycol was oxidized to glycolate plus acetate, 1,3-propanediol to 3-hydroxypropionate plus acetate. Experimental evidence was obtained, suggesting that 2-methoxyethanol was not utilized by all the cells of strain marburg, but by a spontaneous mutant. 2-Methoxyethanol was oxidized to methoxyacetate by the mutant. Co-culture of strain Marburg plus A. woodii grew on ethanol, 1-propanol, 1-butanol, and 1,3-propanediol in the absence of sulfate. Co-culture of strain Marburg plus M. hungatei grew on ethanol, 1-propanol, and 1-butanol, but not on ethyleneglycol and 1,3-propanediol, Co-culture of the mutant plus A. woodii or M. hungatei did not grow on 2-methoxyethanol.