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New Biotechnology Dec 2022A range of Desulfovibrio spp. can reduce metal ions to form metallic nanoparticles that remain attached to their surfaces. The bioreduction of palladium (Pd) has been...
A range of Desulfovibrio spp. can reduce metal ions to form metallic nanoparticles that remain attached to their surfaces. The bioreduction of palladium (Pd) has been given considerable attention due to its extensive use in areas of catalysis and electronics and other technological domains. In this study we report, for the first time, evidence for Pd(II) reduction by the highly corrosive Desulfovibrio ferrophilus IS5 strain to form surface attached Pd nanoparticles, as well as rapid formation of Pd(0) coated microbial nanowires. These filaments reached up to 8 µm in length and led to the formation of a tightly bound group of interconnected cells with enhanced ability to attach to a low carbon steel surface. Moreover, when supplied with high concentrations of Pd (≥ 100 mmol Pd(II) g dry cells), both Desulfovibrio desulfuricans and D. ferrophilus IS5 formed bacteria/Pd hybrid porous microstructures comprising millions of cells. These three-dimensional structures reached up to 3 mm in diameter with a dose of 1200 mmol Pd(II) g dry cells. Under suitable hydrodynamic conditions during reduction, two-dimensional nanosheets of Pd metal were formed that were up to several cm in length. Lower dosing of Pd(II) for promoting rapid synthesis of metal coated nanowires and enhanced attachment of cells onto metal surfaces could improve the efficiency of various biotechnological applications such as microbial fuel cells. Formation of biologically stimulated Pd microstructures could lead to a novel way to produce metal scaffolds or nanosheets for a wide variety of applications.
Topics: Palladium; Desulfovibrio desulfuricans; Desulfovibrio; Catalysis
PubMed: 36396027
DOI: 10.1016/j.nbt.2022.11.001 -
Journal of Bacteriology Mar 2013Mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers linked by interspecies electron transfer...
Mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers linked by interspecies electron transfer in syntrophic consortia that may include sulfate-reducing species (e.g., Desulfovibrio). Physiological differences and various gene repertoires implicated in syntrophic metabolism among Desulfovibrio species suggest considerable variation in the biochemical basis of syntrophy. In this study, comparative transcriptional and mutant analyses of Desulfovibrio alaskensis strain G20 and Desulfovibrio vulgaris strain Hildenborough growing syntrophically with Methanococcus maripaludis on lactate were used to develop new and revised models for their alternative electron transfer and energy conservation systems. Lactate oxidation by strain G20 generates a reduced thiol-disulfide redox pair(s) and ferredoxin that are energetically coupled to H(+)/CO(2) reduction by periplasmic formate dehydrogenase and hydrogenase via a flavin-based reverse electron bifurcation process (electron confurcation) and a menaquinone (MQ) redox loop-mediated reverse electron flow involving the membrane-bound Qmo and Qrc complexes. In contrast, strain Hildenborough uses a larger number of cytoplasmic and periplasmic proteins linked in three intertwining pathways to couple H(+) reduction to lactate oxidation. The faster growth of strain G20 in coculture is associated with a kinetic advantage conferred by the Qmo-MQ-Qrc loop as an electron transfer system that permits higher lactate oxidation rates under elevated hydrogen levels (thereby enhancing methanogenic growth) and use of formate as the main electron-exchange mediator (>70% electron flux), as opposed to the primarily hydrogen-based exchange by strain Hildenborough. This study further demonstrates the absence of a conserved gene core in Desulfovibrio that would determine the ability for a syntrophic lifestyle.
Topics: Desulfovibrio; Electron Transport; Energy Metabolism; Ferredoxins; Formate Dehydrogenases; Genetic Variation; Genome, Bacterial; Hydrogen; Lactic Acid; Methanococcus; Mutation; Periplasmic Proteins; Phenotype; Transcription, Genetic; Vitamin K 2
PubMed: 23264581
DOI: 10.1128/JB.01959-12 -
Journal of Clinical Microbiology Aug 2005Seventeen human clinical isolates representing four species of Desulfovibrio were characterized using 16S rRNA gene sequences and tests for catalase, indole, nitrate,... (Comparative Study)
Comparative Study
Seventeen human clinical isolates representing four species of Desulfovibrio were characterized using 16S rRNA gene sequences and tests for catalase, indole, nitrate, bile, urease, formate-fumarate stimulation, desulfoviridin, motility, and hydrogen sulfide production, plus susceptibility to antimicrobial agents. Eighty additional strains representing 10 phenotypically similar genera (Bilophila, Selenomonas, Capnocytophaga, Campylobacter, Bacteroides, Sutterella, Anaerobiospirillum, Dialister, Veillonella, and Mobiluncus) were included for comparison. All Desulfovibrio species produced H2S and were desulfoviridin positive, and all Desulfovibrio species except D. piger were motile. The four Desulfovibrio species could be distinguished from each other using tests for catalase, indole, nitrate, urease, and growth on bile, with the following results (positive [+], negative [-], growth [G], and no growth [NG]): for D. piger, -, -, -, -, and G, respectively; for D. fairfieldensis, +, -, +, -, and G, respectively; for D. desulfuricans, -, -, +, +, and NG, respectively; and for D. vulgaris, -, +, -, -, and G, respectively. Resistance to the 10-microg colistin disk separated the Desulfovibrio species from most of the other genera, which were usually susceptible. These simple tests were useful for characterizing the Desulfovibrio species and differentiating them from other phenotypically similar genera.
Topics: Desulfovibrio; Humans; Microbial Sensitivity Tests; Phenotype
PubMed: 16081948
DOI: 10.1128/JCM.43.8.4041-4045.2005 -
Analytical Chemistry Jan 2015An autonomous metabolomic workflow combining mass spectrometry analysis with tandem mass spectrometry data acquisition was designed to allow for simultaneous data...
An autonomous metabolomic workflow combining mass spectrometry analysis with tandem mass spectrometry data acquisition was designed to allow for simultaneous data processing and metabolite characterization. Although previously tandem mass spectrometry data have been generated on the fly, the experiments described herein combine this technology with the bioinformatic resources of XCMS and METLIN. As a result of this unique integration, we can analyze large profiling datasets and simultaneously obtain structural identifications. Validation of the workflow on bacterial samples allowed the profiling on the order of a thousand metabolite features with simultaneous tandem mass spectra data acquisition. The tandem mass spectrometry data acquisition enabled automatic search and matching against the METLIN tandem mass spectrometry database, shortening the current workflow from days to hours. Overall, the autonomous approach to untargeted metabolomics provides an efficient means of metabolomic profiling, and will ultimately allow the more rapid integration of comparative analyses, metabolite identification, and data analysis at a systems biology level.
Topics: Chromatography, Liquid; Computational Biology; Databases, Factual; Desulfovibrio vulgaris; Electronic Data Processing; Metabolomics; Software; Tandem Mass Spectrometry
PubMed: 25496351
DOI: 10.1021/ac5025649 -
PloS One 2013Gut microbiota has diverse ecological and evolutionary effects on its hosts. However, the ways in which it responds to environmental heterogeneity and host physiology...
Gut microbiota has diverse ecological and evolutionary effects on its hosts. However, the ways in which it responds to environmental heterogeneity and host physiology remain poorly understood. To this end, we surveyed intestinal microbiota of Holotrichia parallela larvae at different instars and from different geographic regions. Bacterial 16S rRNA gene clone libraries were constructed and clones were subsequently screened by DGGE and sequenced. Firmicutes and Proteobacteria were the major phyla, and bacteria belonging to Ruminococcaceae, Lachnospiraceae, Enterobacteriaceae, Desulfovibrionaceae and Rhodocyclaceae families were commonly found in all natural populations. However, bacterial diversity (Chao1 and Shannon indices) and community structure varied across host populations, and the observed variation can be explained by soil pH, organic carbon and total nitrogen, and the climate factors (e.g., mean annual temperature) of the locations where the populations were sampled. Furthermore, increases in the species richness and diversity of gut microbiota were observed during larval growth. Bacteroidetes comprised the dominant group in the first instar; however, Firmicutes composed the majority of the hindgut microbiota during the second and third instars. Our results suggest that the gut's bacterial community changes in response to environmental heterogeneity and host's physiology, possibly to meet the host's ecological needs or physiological demands.
Topics: Animals; China; Climate; Coleoptera; Desulfovibrio; Digestive System; Enterobacteriaceae; Gene Library; Larva; Metagenome; Phylogeny; Phylogeography; Proteobacteria; RNA, Ribosomal, 16S; Ruminococcus; Symbiosis; Temperature
PubMed: 23437336
DOI: 10.1371/journal.pone.0057169 -
Proceedings of the National Academy of... Feb 2010Mutualistic interactions are taxonomically and functionally diverse. Despite their ubiquity, however, the basic ecological and evolutionary processes underlying their...
Mutualistic interactions are taxonomically and functionally diverse. Despite their ubiquity, however, the basic ecological and evolutionary processes underlying their origin and maintenance are poorly understood. A major reason for this is the lack of an experimentally tractable model system. We examine the evolution of an experimentally imposed obligate mutualism between sulfate-reducing and methanogenic microorganisms that have no known history of previous interaction. Twenty-four independent pairings (cocultures) of the bacterium Desulfovibrio vulgaris and the archaeon Methanococcus maripaludis were established and followed for 300 community doublings in two environments, one allowing for the development of a heterogeneous distribution of resources and the other not. Evolved cocultures grew up to 80% faster and were up to 30% more productive (biomass yield per mole of substrate) than the ancestors. The evolutionary process was marked by periods of significant instability leading to extinction of two of the cocultures, but it resulted in more stable, efficient, and productive mutualisms for most replicated pairings. Comparisons of evolved cocultures with those assembled from one evolved mutualist and one ancestral mutualist showed that evolution of both species contributed to improved productivity. Surprisingly, however, overall improvements in growth rate and yield were less than the sum of the individual contributions, suggesting antagonistic interactions between mutations from the coevolved populations. Physical constraints on the transfer of metabolites in the evolution environment affected the evolution of M. maripaludis, but not of D. vulgaris. Together, these results demonstrate that challenges can imperil nascent obligate mutualisms and demonstrate the evolutionary responses that enable their persistence and future evolution.
Topics: Adaptation, Biological; Biological Evolution; Coculture Techniques; Desulfovibrio vulgaris; Directed Molecular Evolution; Ecosystem; Methane; Methanococcus; Mutation; Species Specificity; Sulfates
PubMed: 20133857
DOI: 10.1073/pnas.0908456107 -
Revista Argentina de Microbiologia 2022Desulfovibrio spp. are strict anaerobes that are ubiquitous in nature. They can reside in the human or animal gastrointestinal tract and, as they are also environmental...
Desulfovibrio spp. are strict anaerobes that are ubiquitous in nature. They can reside in the human or animal gastrointestinal tract and, as they are also environmental bacteria, may be present in soil and water. They can persist asymptomatically in the intestine or behave as opportunistic pathogens associated with primary bacteremia and intraabdominal infections. Several Desulfovibrio spp. infections may be underestimated due to their slow growth rate and because many laboratories do not routinely perform anaerobic cultures. Simple tests such as motility detection on a fresh subculture, Gram stain to confirm cell morphology, presence of HS in SIM agar and production of a red fluorescence in alkaline pH under UV light would be indicative of Desulfovibrio spp. Here we report the case of Desulfovibrio desulfuricans bacteremia in a woman with clinical picture of abdominal sepsis due to gangrenous appendicitis with multiple organ failure.
Topics: Female; Humans; Desulfovibrio desulfuricans; Bacteremia; Intraabdominal Infections
PubMed: 35688718
DOI: 10.1016/j.ram.2022.05.002 -
Proceedings of the National Academy of... Feb 2019Hydrogen sulfide (HS) production in the intestinal microbiota has many contributions to human health and disease. An important source of HS in the human gut is anaerobic...
Hydrogen sulfide (HS) production in the intestinal microbiota has many contributions to human health and disease. An important source of HS in the human gut is anaerobic respiration of sulfite released from the abundant dietary and host-derived organic sulfonate substrate in the gut, taurine (2-aminoethanesulfonate). However, the enzymes that allow intestinal bacteria to access sulfite from taurine have not yet been identified. Here we decipher the complete taurine desulfonation pathway in 3.1.6 using differential proteomics, in vitro reconstruction with heterologously produced enzymes, and identification of critical intermediates. An initial deamination of taurine to sulfoacetaldehyde by a known taurine:pyruvate aminotransferase is followed, unexpectedly, by reduction of sulfoacetaldehyde to isethionate (2-hydroxyethanesulfonate) by an NADH-dependent reductase. Isethionate is then cleaved to sulfite and acetaldehyde by a previously uncharacterized glycyl radical enzyme (GRE), isethionate sulfite-lyase (IslA). The acetaldehyde produced is oxidized to acetyl-CoA by a dehydrogenase, and the sulfite is reduced to HS by dissimilatory sulfite reductase. This unique GRE is also found in DSM642 and G20, which use isethionate but not taurine; corresponding knockout mutants of G20 did not grow with isethionate as the terminal electron acceptor. In conclusion, the novel radical-based C-S bond-cleavage reaction catalyzed by IslA diversifies the known repertoire of GRE superfamily enzymes and enables the energy metabolism of This GRE is widely distributed in gut bacterial genomes and may represent a novel target for control of intestinal HS production.
Topics: Alcohol Oxidoreductases; Anaerobiosis; Bilophila; Gastrointestinal Microbiome; Humans; Hydrogen Sulfide; Oxidation-Reduction; Proteomics; Taurine
PubMed: 30718429
DOI: 10.1073/pnas.1815661116 -
Applied and Environmental Microbiology Feb 2014To understand the energy conversion activities of the anaerobic sulfate-reducing bacteria, it is necessary to identify the components involved in electron flow. The...
To understand the energy conversion activities of the anaerobic sulfate-reducing bacteria, it is necessary to identify the components involved in electron flow. The importance of the abundant type I tetraheme cytochrome c3 (TpIc3) as an electron carrier during sulfate respiration was questioned by the previous isolation of a null mutation in the gene encoding TpIc3, cycA, in Desulfovibrio alaskensis G20. Whereas respiratory growth of the CycA mutant with lactate and sulfate was little affected, growth with pyruvate and sulfate was significantly impaired. We have explored the phenotype of the CycA mutant through physiological tests and transcriptomic and proteomic analyses. Data reported here show that electrons from pyruvate oxidation do not reach adenylyl sulfate reductase, the enzyme catalyzing the first redox reaction during sulfate reduction, in the absence of either CycA or the type I cytochrome c3:menaquinone oxidoreductase transmembrane complex, QrcABCD. In contrast to the wild type, the CycA and QrcA mutants did not grow with H2 or formate and sulfate as the electron acceptor. Transcriptomic and proteomic analyses of the CycA mutant showed that transcripts and enzymes for the pathway from pyruvate to succinate were strongly decreased in the CycA mutant regardless of the growth mode. Neither the CycA nor the QrcA mutant grew on fumarate alone, consistent with the omics results and a redox regulation of gene expression. We conclude that TpIc3 and the Qrc complex are D. alaskensis components essential for the transfer of electrons released in the periplasm to reach the cytoplasmic adenylyl sulfate reductase and present a model that may explain the CycA phenotype through confurcation of electrons.
Topics: Desulfovibrio; Electron Transport; Gene Deletion; Lactates; Metabolic Networks and Pathways; Models, Biological; Oxidation-Reduction; Proteome; Pyruvic Acid; Sulfates; Transcriptome
PubMed: 24242254
DOI: 10.1128/AEM.02963-13 -
Journal of Bacteriology Sep 2009Interspecies hydrogen transfer between organisms producing and consuming hydrogen promotes the decomposition of organic matter in most anoxic environments. Although...
Interspecies hydrogen transfer between organisms producing and consuming hydrogen promotes the decomposition of organic matter in most anoxic environments. Although syntrophic coupling between hydrogen producers and consumers is a major feature of the carbon cycle, mechanisms for energy recovery at the extremely low free energies of reactions typical of these anaerobic communities have not been established. In this study, comparative transcriptional analysis of a model sulfate-reducing microbe, Desulfovibrio vulgaris Hildenborough, suggested the use of alternative electron transfer systems dependent on growth modality. During syntrophic growth on lactate with a hydrogenotrophic methanogen, numerous genes involved in electron transfer and energy generation were upregulated in D. vulgaris compared with their expression in sulfate-limited monocultures. In particular, genes coding for the putative membrane-bound Coo hydrogenase, two periplasmic hydrogenases (Hyd and Hyn), and the well-characterized high-molecular-weight cytochrome (Hmc) were among the most highly expressed and upregulated genes. Additionally, a predicted operon containing genes involved in lactate transport and oxidation exhibited upregulation, further suggesting an alternative pathway for electrons derived from lactate oxidation during syntrophic growth. Mutations in a subset of genes coding for Coo, Hmc, Hyd, and Hyn impaired or severely limited syntrophic growth but had little effect on growth via sulfate respiration. These results demonstrate that syntrophic growth and sulfate respiration use largely independent energy generation pathways and imply that to understand microbial processes that sustain nutrient cycling, lifestyles not captured in pure culture must be considered.
Topics: Bacterial Proteins; Biomass; Culture Media; Desulfovibrio vulgaris; Electron Transport; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Hydrogen; Lactic Acid; Methanococcus; Mutation; Oxidation-Reduction; Sulfates
PubMed: 19581361
DOI: 10.1128/JB.00356-09