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Desulfovibrio vulgaris

William D Leavitt, Sofia S Venceslau, Inês A C Pereira, David T Johnston, Alexander S Bradley
Dissimilatory sulfate reduction is the central microbial metabolism in global sulfur cycling. Understanding the importance of sulfate reduction to Earth's biogeochemical S cycle requires aggregating single-cell processes with geochemical signals. For sulfate reduction, these signals include the ratio of stable sulfur isotopes preserved in minerals, as well as the hydrogen isotope ratios and structures of microbial membrane lipids preserved in organic matter. In this study we cultivated the model sulfate reducer, Desulfovibrio vulgaris DSM 644(T), to investigate how these parameters were perturbed by changes in expression of the protein DsrC...
October 3, 2016: FEMS Microbiology Letters
Cristian Barca, David Ranava, Marielle Bauzan, Jean-Henry Ferrasse, Marie-Thérèse Giudici-Orticoni, Audrey Soric
Dark fermentation systems often show low H2 yields and unstable H2 production, as the result of the variability of microbial dynamics and metabolic pathways. Recent batch investigations have demonstrated that an artificial consortium of two anaerobic bacteria, Clostridium acetobutylicum and Desulfovibrio vulgaris Hildenborough, may redirect metabolic fluxes and improve H2 yields. This study aimed at evaluating the scale-up from batch to continuous H2 production in an up-flow anaerobic packed-bed reactor (APBR) continuously fed with a glucose-medium...
December 2016: Bioresource Technology
Ian T Cadby, Susan A Ibrahim, Matthew Faulkner, David J Lee, Douglas Browning, Stephen J Busby, Andrew L Lovering, Melanie R Stapleton, Jeffrey Green, Jeffrey A Cole
In silico analyses identified a Crp/Fnr family transcription factor (HcpR) in sulfate-reducing bacteria that controls expression of the hcp gene, which encodes the hybrid cluster protein and contributes to nitrosative stress responses. There is only one hcpR gene in the model sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, but two copies in Desulfovibrio desulfuricans 27774, which can use nitrate as an alternative electron acceptor to sulfate. Structures of the D. desulfuricans hcpR1, hcpR2 and hcp operons are reported...
September 27, 2016: Molecular Microbiology
Susana A L Lobo, Marco A M Videira, Isabel Pacheco, Mark N Wass, Martin J Warren, Miguel Teixeira, Pedro M Matias, Célia V Romão, Lígia M Saraiva
The sulphate-reducing bacteria of the Desulfovibrio genus make three distinct modified tetrapyrroles, haem, sirohaem and adenosylcobamide, where sirohydrochlorin acts as the last common biosynthetic intermediate along the branched tetrapyrrole pathway. Intriguingly, D. vulgaris encodes two sirohydrochlorin chelatases, CbiK(P) and CbiK(C) , that insert cobalt/iron into the tetrapyrrole macrocycle but are thought to be distinctly located in the periplasm and cytoplasm, respectively. Fusing GFP onto the C-terminus of CbiK(P) confirmed that the protein is transported to the periplasm...
August 3, 2016: Environmental Microbiology
N L Ritz, D M Lin, M R Wilson, L L Barton, H C Lin
BACKGROUND: Hydrogen sulfide (H2 S) serves as a mammalian cell-derived gaseous neurotransmitter. The intestines are exposed to a second source of this gas by sulfate-reducing bacteria (SRB). Bismuth subsalicylate binds H2 S rendering it insoluble. The aim of this study was to test the hypothesis that SRB may slow intestinal transit in a bismuth-reversible fashion. METHODS: Eighty mice were randomized to five groups consisting of Live SRB, Killed SRB, SRB+Bismuth, Bismuth, and Saline...
July 31, 2016: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
Hulin Tai, Liyang Xu, Seiya Inoue, Koji Nishikawa, Yoshiki Higuchi, Shun Hirota
The Ni-SIr state of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F was photoactivated to its Ni-SIa state by Ar(+) laser irradiation at 514.5 nm, whereas the Ni-SL state was light induced from a newly identified state, which was less active than any other identified state and existed in the "as-isolated" enzyme.
August 10, 2016: Physical Chemistry Chemical Physics: PCCP
Yingchao Li, Ru Jia, Hussain H Al-Mahamedh, Dake Xu, Tingyue Gu
Microbiologically influenced corrosion (MIC) is a major problem in the oil and gas industry as well as in many other industries. Current treatment methods rely mostly on pigging and biocide dosing. Biocide resistance is a growing concern. Thus, it is desirable to use biocide enhancers to improve the efficacy of existing biocides. D-Amino acids are naturally occurring. Our previous work demonstrated that some D-amino acids are biocide enhancers. Under a biocide stress of 50 ppm (w/w) hydroxymethyl phosphonium sulfate (THPS) biocide, 1 ppm D-tyrosine and 100 ppm D-methionine used separately successfully mitigated the Desulfovibrio vulgaris biofilm on carbon steel coupons...
2016: Frontiers in Microbiology
Shu-Hong Gao, Jun Yuan Ho, Lu Fan, David J Richardson, Zhiguo Yuan, Philip L Bond
Hydrogen sulfide produced by sulfate-reducing bacteria (SRB) in sewers causes odor problems and asset deterioration due to the sulfide-induced concrete corrosion. Free nitrous acid (FNA) was recently demonstrated as a promising antimicrobial agent to alleviate hydrogen sulfide production in sewers. However, details of the antimicrobial mechanisms of FNA are largely unknown. Here, we report the multiple-targeted antimicrobial effects of FNA on the SRB Desulfovibrio vulgaris Hildenborough by determining the growth, physiological, and gene expression responses to FNA exposure...
September 15, 2016: Applied and Environmental Microbiology
Nadtanet Nunthaboot, Kiattisak Lugsanangarm, Somsak Pianwanit, Sirirat Kokpol, Fumio Tanaka, Takeshi Nakanishi, Masaya Kitamura
The structural and dynamical properties of five FMN binding protein (FBP) dimers, WT (wild type), E13K (Glu13 replaced by Lys), E13R (Glu13 replaced by Arg), E13T (Glu13 replaced by Thr) and E13Q (Glu13 replaced by Gln), were investigated using a method of molecular dynamics simulation (MDS). In crystal structures, subunit A (Sub A) and subunit B (Sub B) were almost completely equivalent in all of the five FBP dimers. However, the predicted MDS structures of the two subunits were not equivalent in solution, revealed by the distances and inter-planar angles between isoalloxazine (Iso) and aromatic amino acids (Trp32, Tyr35 and Trp106) as well as the hydrogen bonding pairs between Iso and nearby amino acids...
May 27, 2016: Computational Biology and Chemistry
Yang Zhang, Guangsheng Pei, Lei Chen, Weiwen Zhang
In this study, a comparative metabolomics approach combining gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) was applied first between planktonic cells and biofilms and then between pure cultures and biofilms of Desulfovibrio vulgaris. The results revealed that the overall metabolic level of the biofilm cells was down-regulated, especially for metabolites related to the central carbon metabolism, compared to the planktonic cells and the pure culture of D. vulgaris...
August 2016: Biofouling
Mónica Martins, Cláudia Mourato, Fabio O Morais-Silva, Claudina Rodrigues-Pousada, Gerrit Voordouw, Judy D Wall, Inês A C Pereira
The potential of sulfate-reducing bacteria (SRB) as biocatalysts for H2 production from formate was recently demonstrated, but the electron transfer pathways involved were not described. In the present work, we analyzed the H2 production capacity of five Desulfovibrio strains: Desulfovibrio vulgaris, Desulfovibrio desulfuricans, Desulfovibrio alaskensis, Desulfovibrio fructosivorans, and Desulfovibrio gigas. D. vulgaris showed the highest H2 productivity (865 mL Lmedium (-1)), and D. gigas the lowest one (374 mL Lmedium (-1) of H2)...
September 2016: Applied Microbiology and Biotechnology
Tobias Großkopf, Simone Zenobi, Mark Alston, Leighton Folkes, David Swarbreck, Orkun S Soyer
Syntrophies are metabolic cooperations, whereby two organisms co-metabolize a substrate in an interdependent manner. Many of the observed natural syntrophic interactions are mandatory in the absence of strong electron acceptors, such that one species in the syntrophy has to assume the role of electron sink for the other. While this presents an ecological setting for syntrophy to be beneficial, the potential genetic drivers of syntrophy remain unknown to date. Here, we show that the syntrophic sulfate-reducing species Desulfovibrio vulgaris displays a stable genetic polymorphism, where only a specific genotype is able to engage in syntrophy with the hydrogenotrophic methanogen Methanococcus maripaludis...
June 3, 2016: ISME Journal
Zhenhua Qi, Lei Chen, Weiwen Zhang
Sulfate-reducing bacteria (SRB) biofilm formed on metal surfaces can change the physicochemical properties of metals and cause metal corrosion. To enhance understanding of differential gene expression in Desulfovibrio vulgaris under planktonic and biofilm growth modes, a single-cell based RT-qPCR approach was applied to determine gene expression levels of 8 selected target genes in four sets of the 31 individual cells isolated from each growth condition (i.e., biofilm formed on a mild steel (SS) and planktonic cultures, exponential and stationary phases)...
2016: Frontiers in Microbiology
Maxim Shatsky, Ming Dong, Haichuan Liu, Lee Lisheng Yang, Megan Choi, Mary E Singer, Jil T Geller, Susan J Fisher, Steven C Hall, Terry C Hazen, Steven E Brenner, Gareth Butland, Jian Jin, H Ewa Witkowska, John-Marc Chandonia, Mark D Biggin
Identifying protein-protein interactions (PPIs) at an acceptable false discovery rate (FDR) is challenging. Previously we identified several hundred PPIs from affinity purification - mass spectrometry (AP-MS) data for the bacteria Escherichia coli and Desulfovibrio vulgaris These two interactomes have lower FDRs than any of the nine interactomes proposed previously for bacteria and are more enriched in PPIs validated by other data than the nine earlier interactomes. To more thoroughly determine the accuracy of ours or other interactomes and to discover further PPIs de novo, here we present a quantitative tagless method that employs iTRAQ MS to measure the copurification of endogenous proteins through orthogonal chromatography steps...
June 2016: Molecular & Cellular Proteomics: MCP
Maxim Shatsky, Simon Allen, Barbara L Gold, Nancy L Liu, Thomas R Juba, Sonia A Reveco, Dwayne A Elias, Ramadevi Prathapam, Jennifer He, Wenhong Yang, Evelin D Szakal, Haichuan Liu, Mary E Singer, Jil T Geller, Bonita R Lam, Avneesh Saini, Valentine V Trotter, Steven C Hall, Susan J Fisher, Steven E Brenner, Swapnil R Chhabra, Terry C Hazen, Judy D Wall, H Ewa Witkowska, Mark D Biggin, John-Marc Chandonia, Gareth Butland
Numerous affinity purification-mass spectrometry (AP-MS) and yeast two-hybrid screens have each defined thousands of pairwise protein-protein interactions (PPIs), most of which are between functionally unrelated proteins. The accuracy of these networks, however, is under debate. Here, we present an AP-MS survey of the bacterium Desulfovibrio vulgaris together with a critical reanalysis of nine published bacterial yeast two-hybrid and AP-MS screens. We have identified 459 high confidence PPIs from D. vulgaris and 391 from Escherichia coli Compared with the nine published interactomes, our two networks are smaller, are much less highly connected, and have significantly lower false discovery rates...
May 2016: Molecular & Cellular Proteomics: MCP
Sabine Koch, Dirk Benndorf, Karen Fronk, Udo Reichl, Steffen Klamt
BACKGROUND: Microbial communities are ubiquitous in nature and play a major role in ecology, medicine, and various industrial processes. In this study, we used stoichiometric metabolic modeling to investigate a community of three species, Desulfovibrio vulgaris, Methanococcus maripaludis, and Methanosarcina barkeri, which are involved in acetogenesis and methanogenesis in anaerobic digestion for biogas production. RESULTS: We first constructed and validated stoichiometric models of the core metabolism of the three species which were then assembled to community models...
2016: Biotechnology for Biofuels
G Y Fisunov, D V Evsyutina, A A Arzamasov, I O Butenko, V M Govorun
The development of high-throughput technologies is increasingly resulting in identification of numerous cases of low correlation between mRNA and the protein level in cells. These controversial observations were made on various bacteria, such as E. coli, Desulfovibrio vulgaris, and Lactococcus lactis. Thus, it is important to develop technologies, including high-throughput techniques, aimed at studying gene expression regulation at the level of translation. In the current study, we performed proteomic profiling of M...
October 2015: Acta Naturae
Y Li, P Zhang, W Cai, J S Rosenblatt, I I Raad, D Xu, T Gu
Microbiologically influenced corrosion (MIC), also known as biocorrosion, is caused by corrosive biofilms. MIC is a growing problem, especially in the oil and gas industry. Among various corrosive microbes, sulfate reducing bacteria (SRB) are often the leading culprit. Biofilm mitigation is the key to MIC mitigation. Biocide applications against biofilms promote resistance over time. Thus, it is imperative to develop new biodegradable and cost-effective biocides for large-scale field applications. Using the corrosive Desulfovibrio vulgaris (an SRB) biofilm as a model biofilm, this work demonstrated that a cocktail of glyceryl trinitrate (GTN) and caprylic acid (CA) was very effective for biofilm prevention and mitigation of established biofilms on C1018 carbon steel coupons...
February 2016: World Journal of Microbiology & Biotechnology
Mónica Martins, Cláudia Mourato, Inês A C Pereira
Formate is recognized as a superior substrate for biological H2 production by several bacteria. However, the growth of a single organism coupled to this energetic pathway has not been shown in mesophilic conditions. In the present study, a bioreactor with gas sparging was used, where we observed for the first time that H2 production from formate can be coupled with growth of the model sulfate-reducing bacterium Desulfovibrio vulgaris in the absence of sulfate or a syntrophic partner. In these conditions, D...
December 15, 2015: Environmental Science & Technology
Meriem Merrouch, Jessica Hadj-Saïd, Lilith Domnik, Holger Dobbek, Christophe Léger, Sébastien Dementin, Vincent Fourmond
Ni-containing CO dehydrogenases (CODHs) are very efficient metalloenzymes that catalyze the conversion between CO2 and CO. They are a source of inspiration for designing CO2-reduction catalysts and can also find direct use in biotechnology. They are deemed extremely sensitive to O2, but very little is known about this aspect of their reactivity. We investigated the reaction with O2 of Carboxydothermus hydrogenoformans (Ch) CODH II and the homologous, recently characterized CODH from Desulfovibrio vulgaris (Dv) through protein film voltammetry and solution assays (in the oxidative direction)...
December 21, 2015: Chemistry: a European Journal
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