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Desulfovibrio vulgaris

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https://www.readbyqxmd.com/read/28550300/experimental-quantum-chemical-and-molecular-dynamic-simulations-studies-on-the-corrosion-inhibition-of-mild-steel-by-some-carbazole-derivatives
#1
Henry U Nwankwo, Lukman O Olasunkanmi, Eno E Ebenso
Five selected carbazole derivatives, namely carbazole, 3,6-dibromocarbazole, 2-hydroxycarbazole, 1,2,3,4-tetrahydrocarbazole and 9-(2-ethylhexyl)carbazole-3,6-dicarboxaldehyde were investigated for their inhibitive effects on Desulfovibrio vulgaris (D. vulgaris) induced corrosion of mild steel and in 1 M HCl medium using weight loss, potentiodynamic polarization and electrochemical impedance spectroscopy (EIS) techniques. The carbazole derivatives were found to be mixed type inhibitors with predominantly cathodic inhibitive effects for mild steel in 1 M HCl...
May 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28506671/modeling-of-flux-binding-and-substitution-of-urea-molecules-in-the-urea-transporter-dvut
#2
Hai-Tian Zhang, Zhe Wang, Tao Yu, Jian-Ping Sang, Xian-Wu Zou, Xiaoqin Zou
Urea transporters (UTs) are transmembrane proteins that transport urea molecules across cell membranes and play a crucial role in urea excretion and water balance. Modeling the functional characteristics of UTs helps us understand how their structures accomplish the functions at the atomic level, and facilitates future therapeutic design targeting the UTs. This study was based on the crystal structure of Desulfovibrio vulgaris urea transporter (dvUT). To model the binding behavior of urea molecules in dvUT, we constructed a cooperative binding model...
April 25, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28458201/reduction-of-adsorbed-as-v-on-nano-tio2-by-sulfate-reducing-bacteria
#3
Ting Luo, Li Ye, Cheng Ding, Jinlong Yan, Chuanyong Jing
Reduction of surface-bound arsenate [As(V)] and subsequent release into the aqueous phase contribute to elevated As in groundwater. However, this natural process is not fully understood, especially in the presence of sulfate-reducing bacteria (SRB). Gaining mechanistic insights into solid-As(V)-SRB interactions motivated our molecular level study on the fate of nano-TiO2 bound As(V) in the presence of Desulfovibrio vulgaris DP4, a strain of SRB, using incubation and in situ ATR-FTIR experiments. The incubation results clearly revealed the reduction of As(V), either adsorbed on nano-TiO2 or dissolved, in the presence of SRB...
November 15, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28436827/reductive-precipitation-of-sulfate-and-soluble-fe-iii-by-desulfovibrio-vulgaris-electron-donor-regulates-intracellular-electron-flow-and-nano-fes-crystallization
#4
Chen Zhou, Yun Zhou, Bruce E Rittmann
Fully understanding the metabolism of SRB provides fundamental guidelines for allowing the microorganisms to provide more beneficial services in water treatment and resource recovery. The electron-transfer pathway of sulfate respiration by Desulfovibrio vulgaris is well studied, but still partly unresolved. Here we provide deeper insight by comprehensively monitoring metabolite changes during D. vulgaris metabolism with two electron donors, lactate and pyruvate, in presence or absence of citrate-chelated soluble Fe(III) as an additional competing electron acceptor...
April 19, 2017: Water Research
https://www.readbyqxmd.com/read/28419704/robustness-of-a-model-microbial-community-emerges-from-population-structure-among-single-cells-of-a-clonal-population
#5
Anne W Thompson, Serdar Turkarslan, Christina E Arens, Adrián López García de Lomana, Arjun V Raman, David A Stahl, Nitin S Baliga
Microbial populations can withstand, overcome, and persist in the face of environmental fluctuation. Previously we demonstrated how conditional gene regulation in a fluctuating environment drives dilution of condition-specific transcripts, causing a population of Desulfovibrio vulgaris Hildenborough (DvH) to collapse after repeatedly transitioning from sulfate respiration to syntrophic conditions with the methanogen Methanococcus maripaludis. Failure of the DvH to successfully transition contributed to the collapse of this model community...
April 17, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28365342/a-continuous-system-for-biocatalytic-hydrogenation-of-co2-to-formate
#6
Cláudia Mourato, Mónica Martins, Sofia M da Silva, Inês A C Pereira
In this work a novel bioprocess for hydrogenation of CO2 to formate was developed, using whole cell catalysis by a sulfate-reducing bacterium. Three Desulfovibrio species were tested (D. vulgaris Hildenborough, D. alaskensis G20, and D. desulfuricans ATCC 27774), of which D. desulfuricans showed the highest activity, producing 12mM of formate in batch, with a production rate of 0.09mMh(-1). Gene expression analysis indicated that among the three formate dehydrogenases and five hydrogenases, the cytoplasmic FdhAB and the periplasmic [FeFe] HydAB are the main enzymes expressed in D...
July 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28320772/mechanism-for-microbial-population-collapse-in-a-fluctuating-resource-environment
#7
Serdar Turkarslan, Arjun V Raman, Anne W Thompson, Christina E Arens, Mark A Gillespie, Frederick von Netzer, Kristina L Hillesland, Sergey Stolyar, Adrian López García de Lomana, David J Reiss, Drew Gorman-Lewis, Grant M Zane, Jeffrey A Ranish, Judy D Wall, David A Stahl, Nitin S Baliga
Managing trade-offs through gene regulation is believed to confer resilience to a microbial community in a fluctuating resource environment. To investigate this hypothesis, we imposed a fluctuating environment that required the sulfate-reducer Desulfovibrio vulgaris to undergo repeated ecologically relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen-consuming Methanococcus maripaludis Strikingly, the microbial community became progressively less proficient at restoring the environmentally relevant physiological state after each perturbation and most cultures collapsed within 3-7 shifts...
March 20, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28319099/the-direct-role-of-selenocysteine-in-nifese-hydrogenase-maturation-and-catalysis
#8
Marta C Marques, Cristina Tapia, Oscar Gutiérrez-Sanz, Ana Raquel Ramos, Kimberly L Keller, Judy D Wall, Antonio L De Lacey, Pedro M Matias, Inês A C Pereira
Hydrogenases are highly active enzymes for hydrogen production and oxidation. [NiFeSe] hydrogenases, in which selenocysteine is a ligand to the active site Ni, have high catalytic activity and a bias for H2 production. In contrast to [NiFe] hydrogenases, they display reduced H2 inhibition and are rapidly reactivated after contact with oxygen. Here we report an expression system for production of recombinant [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough and study of a selenocysteine-to-cysteine variant (Sec489Cys) in which, for the first time, a [NiFeSe] hydrogenase was converted to a [NiFe] type...
May 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28192203/electrostatic-roles-in-electron-transfer-from-nife-hydrogenase-to-cytochrome-c3-from-desulfovibrio-vulgaris-miyazaki-f
#9
Yu Sugimoto, Yuki Kitazumi, Osamu Shirai, Koji Nishikawa, Yoshiki Higuchi, Masahiro Yamamoto, Kenji Kano
Electrostatic interactions between proteins are key factors that govern the association and reaction rate. We spectroscopically determine the second-order reaction rate constant (k) of electron transfer from [NiFe] hydrogenase (H2ase) to cytochrome (cyt) c3 at various ionic strengths (I). The k value decreases with I. To analyze the results, we develop a semi-analytical formula for I dependence of k based on the assumptions that molecules are spherical and the reaction proceeds via a transition state. Fitting of the formula to the experimental data reveals that the interaction occurs in limited regions with opposite charges and with radii much smaller than those estimated from crystal structures...
May 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28159790/effects-of-sulfate-reduction-on-trichloroethene-dechlorination-by-dehalococcoides-containing-microbial-communities
#10
Xinwei Mao, Alexandra Polasko, Lisa Alvarez-Cohen
In order to elucidate interactions between sulfate reduction and dechlorination, we systematically evaluated the effects of different concentrations of sulfate and sulfide on reductive dechlorination by isolates, constructed consortia, and enrichments containing Dehalococcoides sp. Sulfate (up to 5 mM) did not inhibit the growth or metabolism of pure cultures of the dechlorinator Dehalococcoides mccartyi 195, the sulfate reducer Desulfovibrio vulgaris Hildenborough, or the syntroph Syntrophomonas wolfei In contrast, sulfide at 5 mM exhibited inhibitory effects on growth of the sulfate reducer and the syntroph, as well as on both dechlorination and growth rates of D...
April 15, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27873195/community-structure-of-a-sulfate-reducing-consortium-in-lead-contaminated-wastewater-treatment-process
#11
Yen T Nguyen, Hoa T Q Kieu, Stephanie West, Yen T Dang, Harald Horn
This study evaluated the capacity to remove lead by an indigenous consortium of five sulfate-reducing bacteria (SRB): Desulfobacterium autotrophicum, Desulfomicrobium salsugmis, Desulfomicrobium escambiense, Desulfovibrio vulgaris, and Desulfovibrio carbinolicus, using continuous moving bed biofilm reactor systems. Four continuous moving bed biofilm reactors (referred as R1-R4) were run in parallel for 40 days at lead loading rates of 0, 20, 30 and 40 mg l(-1) day(-1), respectively. The impact of lead on community structure of the SRB consortium was investigated by dsrB gene-based denaturing gradient gel electrophoresis (dsrB-based DGGE), fluorescence in situ hybridization (FISH) and chemical analysis...
January 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/27817891/biogenic-platinum-and-palladium-nanoparticles-as-new-catalysts-for-the-removal-of-pharmaceutical-compounds
#12
Mónica Martins, Cláudia Mourato, Sandra Sanches, João Paulo Noronha, M T Barreto Crespo, Inês A C Pereira
Pharmaceutical products (PhP) are one of the most alarming emergent pollutants in the environment. Therefore, it is of extreme importance to investigate efficient PhP removal processes. Biologic synthesis of platinum nanoparticles (Bio-Pt) has been reported, but their catalytic activity was never investigated. In this work, we explored the potential of cell-supported platinum (Bio-Pt) and palladium (Bio-Pd) nanoparticles synthesized with Desulfovibrio vulgaris as biocatalysts for removal of four PhP: ciprofloxacin, sulfamethoxazole, ibuprofen and 17β-estradiol...
January 1, 2017: Water Research
https://www.readbyqxmd.com/read/27702753/fractionation-of-sulfur-and-hydrogen-isotopes-in-desulfovibrio-vulgaris-with-perturbed-dsrc-expression
#13
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
https://www.readbyqxmd.com/read/27686721/fermentative-hydrogen-production-in-an-up-flow-anaerobic-biofilm-reactor-inoculated-with-a-co-culture-of-clostridium-acetobutylicum-and-desulfovibrio-vulgaris
#14
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
https://www.readbyqxmd.com/read/27671526/regulation-sensory-domains-and-roles-of-two-desulfovibrio-desulfuricans-atcc27774-crp-family-transcription-factors-hcpr1-and-hcpr2-in-response-to-nitrosative-stress
#15
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...
December 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/27486032/desulfovibrio-vulgaris-cbik-p-cobaltochelatase-evolution-of-a-haem-binding-protein-orchestrated-by-the-incorporation-of-two-histidine-residues
#16
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 sulfate-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
https://www.readbyqxmd.com/read/27477318/sulfate-reducing-bacteria-slow-intestinal-transit-in-a-bismuth-reversible-fashion-in-mice
#17
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...
January 2017: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
https://www.readbyqxmd.com/read/27456760/photoactivation-of-the-ni-sir-state-to-the-ni-sia-state-in-nife-hydrogenase-ft-ir-study-on-the-light-reactivity-of-the-ready-ni-sir-state-and-as-isolated-enzyme-revisited
#18
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
https://www.readbyqxmd.com/read/27379039/enhanced-biocide-mitigation-of-field-biofilm-consortia-by-a-mixture-of-d-amino-acids
#19
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
https://www.readbyqxmd.com/read/27371588/antimicrobial-effects-of-free-nitrous-acid-on-desulfovibrio-vulgaris-implications-for-sulfide-induced-corrosion-of-concrete
#20
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
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