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PloS One 2012Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint...
Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.
Topics: Base Sequence; DNA, Bacterial; Databases, Genetic; Desulfovibrio africanus; Desulfovibrio desulfuricans; Genome, Bacterial; Inverted Repeat Sequences; Molecular Sequence Annotation; Molecular Sequence Data; Polymerase Chain Reaction; Sequence Analysis, DNA
PubMed: 22859974
DOI: 10.1371/journal.pone.0041295 -
Applied and Environmental Microbiology Aug 2006Desulfovibrio vulgaris was cultivated in a defined medium, and biomass was sampled for approximately 70 h to characterize the shifts in gene expression as cells...
Desulfovibrio vulgaris was cultivated in a defined medium, and biomass was sampled for approximately 70 h to characterize the shifts in gene expression as cells transitioned from the exponential to the stationary phase during electron donor depletion. In addition to temporal transcriptomics, total protein, carbohydrate, lactate, acetate, and sulfate levels were measured. The microarray data were examined for statistically significant expression changes, hierarchical cluster analysis, and promoter element prediction and were validated by quantitative PCR. As the cells transitioned from the exponential phase to the stationary phase, a majority of the down-expressed genes were involved in translation and transcription, and this trend continued at the remaining times. There were general increases in relative expression for intracellular trafficking and secretion, ion transport, and coenzyme metabolism as the cells entered the stationary phase. As expected, the DNA replication machinery was down-expressed, and the expression of genes involved in DNA repair increased during the stationary phase. Genes involved in amino acid acquisition, carbohydrate metabolism, energy production, and cell envelope biogenesis did not exhibit uniform transcriptional responses. Interestingly, most phage-related genes were up-expressed at the onset of the stationary phase. This result suggested that nutrient depletion may affect community dynamics and DNA transfer mechanisms of sulfate-reducing bacteria via the phage cycle. The putative feoAB system (in addition to other presumptive iron metabolism genes) was significantly up-expressed, and this suggested the possible importance of Fe2+ acquisition under metal-reducing conditions. The expression of a large subset of carbohydrate-related genes was altered, and the total cellular carbohydrate levels declined during the growth phase transition. Interestingly, the D. vulgaris genome does not contain a putative rpoS gene, a common attribute of the delta-Proteobacteria genomes sequenced to date, and the transcription profiles of other putative rpo genes were not significantly altered. Our results indicated that in addition to expected changes (e.g., energy conversion, protein turnover, translation, transcription, and DNA replication and repair), genes related to phage, stress response, carbohydrate flux, the outer envelope, and iron homeostasis played important roles as D. vulgaris cells experienced electron donor depletion.
Topics: Bacterial Proteins; Culture Media; Desulfovibrio vulgaris; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Heat-Shock Response; Iron; Lactates; Proteome; Sulfates; Transcription, Genetic
PubMed: 16885312
DOI: 10.1128/AEM.00284-06 -
Chemosphere Nov 2021Sulfate-reducing bacteria (SRB) are key players in many passive and active systems dedicated to the treatment of hydrometallurgical leachates. One of the main factors...
Biostimulation of sulfate-reducing bacteria used for treatment of hydrometallurgical waste by secondary metabolites of urea decomposition by Ochrobactrum sp. POC9: From genome to microbiome analysis.
Sulfate-reducing bacteria (SRB) are key players in many passive and active systems dedicated to the treatment of hydrometallurgical leachates. One of the main factors reducing the efficiency and activity of SRB is the low pH and poor nutrients in leachates. We propose an innovative solution utilizing biogenic ammonia (B-NH), produced by urea degrading bacteria, as a pretreatment agent for increasing the pH of the leachate and spontaneously stimulating SRB activity via bacterial secondary metabolites. The selected strain, Ochrobactrum sp. POC9, generated 984.7 mg/L of ammonia in 24 h and promotes an effective neutralization of B-NH. The inferred metabolic traits indicated that the Ochrobactrum sp. POC9 can synthesize a group of vitamins B, and the production of various organic metabolites was confirmed by GC-MS analysis. These metabolites comprise alcohols, organic acids, and unsaturated hydrocarbons that may stimulate biological sulfate reduction. With the pretreatment of B-NH, sulfate removal efficiency reached ~92.3% after 14 days of incubation, whereas SRB cell count and abundance were boosted (~10 cell counts and 88 OTUs of SRB) compared to synthetic ammonia (S-NH) (~10 cell counts and 40 OTUs of SRB). The dominant SRB is Desulfovibrio in both S-NH and B-NH pretreated leachate, however, it belonged to two different clades. By reconstructing the ecological network, we found that B-NH not only directly increases SRB performance but also promotes other strains with positive correlations with SRB.
Topics: Bacteria; Desulfovibrio; Microbiota; Ochrobactrum; Sulfates; Urea
PubMed: 34118631
DOI: 10.1016/j.chemosphere.2021.131064 -
FEMS Microbiology Ecology Apr 2024Phytoplankton blooms fuel marine food webs with labile dissolved carbon and also lead to the formation of particulate organic matter composed of living and dead algal...
Phytoplankton blooms fuel marine food webs with labile dissolved carbon and also lead to the formation of particulate organic matter composed of living and dead algal cells. These particles contribute to carbon sequestration and are sites of intense algal-bacterial interactions, providing diverse niches for microbes to thrive. We analyzed 16S and 18S ribosomal RNA gene amplicon sequences obtained from 51 time points and metaproteomes from 3 time points during a spring phytoplankton bloom in a shallow location (6-10 m depth) in the North Sea. Particulate fractions larger than 10 µm diameter were collected at near daily intervals between early March and late May in 2018. Network analysis identified two major modules representing bacteria co-occurring with diatoms and with dinoflagellates, respectively. The diatom network module included known sulfate-reducing Desulfobacterota as well as potentially sulfur-oxidizing Ectothiorhodospiraceae. Metaproteome analyses confirmed presence of key enzymes involved in dissimilatory sulfate reduction, a process known to occur in sinking particles at greater depths and in sediments. Our results indicate the presence of sufficiently anoxic niches in the particle fraction of an active phytoplankton bloom to sustain sulfate reduction, and an important role of benthic-pelagic coupling for microbiomes in shallow environments. Our findings may have implications for the understanding of algal-bacterial interactions and carbon export during blooms in shallow-water coastal areas.
Topics: Diatoms; Phytoplankton; Bacteria; Microbiota; Desulfovibrio; Carbon
PubMed: 38490736
DOI: 10.1093/femsec/fiae037 -
Journal of Bacteriology Jul 1990The different nutritional properties of several Desulfovibrio desulfuricans strains suggest that either the strains are misclassified or there is a high degree of...
The different nutritional properties of several Desulfovibrio desulfuricans strains suggest that either the strains are misclassified or there is a high degree of phenotypic diversity within the genus Desulfovibrio. The results of partial 16S rRNA and 23S rRNA sequence determinations demonstrated that Desulfovibrio desulfuricans ATCC 27774 and "Desulfovibrio multispirans" are closely related to the type strain (strain Essex 6) and that strains ATCC 7757, Norway 4, and El Agheila Z are not. Therefore, these latter three strains of Desulfovibrio desulfuricans are apparently misclassified. A comparative analysis of nearly complete 16S rRNA sequences in which we used a least-squares analysis method for evolutionary distances, an unweighted pair group method, a signature analysis method, and maximum parsimony was undertaken to further investigate the phylogeny of Desulfovibrio species. The species analyzed were resolved into two branches with origins deep within the delta subdivision of the purple photosynthetic bacteria. One branch contained five deep lineages, which were represented by (i) Desulfovibrio salexigens and Desulfovibrio desulfuricans El Agheila Z; (ii) Desulfovibrio africanus; (iii) Desulfovibrio desulfuricans ATCC 27774, Desulfomonas pigra, and Desulfovibrio vulgaris; (iv) Desulfovibrio gigas; and (v) Desulfomicrobium baculatus (Desulfovibrio baculatus) and Desulfovibrio desulfuricans Norway 4. A correlation between 16S rRNA sequence similarity and percentage of DNA relatedness showed that these five deep lineages are related at levels below the minimum genus level suggested by Johnson (in Bergey's Manual of Systematic Bacteriology, vol. 1, 1984). We propose that this branch should be grouped into a single family, the Desulfovibrionaceae. The other branch includes other genera of sulfate-reducing bacteria (e.g., Desulfobacter and Desulfococcus) and contains Desulfovibrio sapovorans and Desulfovibrio baarsii as separate, distantly related lineages.
Topics: Base Sequence; Biological Evolution; Culture Media; Desulfovibrio; Molecular Sequence Data; Oligonucleotide Probes; Phylogeny; RNA, Ribosomal; RNA, Ribosomal, 16S
PubMed: 2361938
DOI: 10.1128/jb.172.7.3609-3619.1990 -
Microbiology (Reading, England) Aug 2017Desulfovibrio sp. A2 is a novel Gram-negative sulfate-reducing bacterium that was isolated from sediments of the Norilsk mining/smelting area in Russia. The organism...
Desulfovibrio sp. A2 is a novel Gram-negative sulfate-reducing bacterium that was isolated from sediments of the Norilsk mining/smelting area in Russia. The organism possesses a monocistronic operon encoding a 71 kDa periplasmic multicopperoxidase, which we call DA2_CueO. Histidine-tagged DA2_CueO expressed from a plasmid in Escherichia coli and purified by Ni-NTA affinity chromatography oxidizes Cu+ and Fe2+, and exhibits phenol oxidase activity with 2,2-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid), 2,3-dihydroxybenzoic acid and 2,6-dimethoxyphenol as substrates, using O2 as the oxidant. When expressed in an E. coli cueO knock-out strain, DA2_CueO exhibits phenol oxidase activity in vivo and enhances the copper tolerance of the strain. These findings indicate that the DA2_CueO gene of Desulfovibrio sp. A2 encodes a multicopperoxidase with a role in metal ion resistance. The enzyme displays some novel structural features, which are discussed.
Topics: Bacterial Proteins; Copper; Desulfovibrio; Ferrous Compounds; Geologic Sediments; Oxidoreductases; Phenol
PubMed: 28749328
DOI: 10.1099/mic.0.000509 -
Applied and Environmental Microbiology Feb 2000To explore the physiological role of tetraheme cytochrome c(3) in the sulfate-reducing bacterium Desulfovibrio desulfuricans G20, the gene encoding the preapoprotein was...
To explore the physiological role of tetraheme cytochrome c(3) in the sulfate-reducing bacterium Desulfovibrio desulfuricans G20, the gene encoding the preapoprotein was cloned, sequenced, and mutated by plasmid insertion. The physical analysis of the DNA from the strain carrying the integrated plasmid showed that the insertion was successful. The growth rate of the mutant on lactate with sulfate was comparable to that of the wild type; however, mutant cultures did not achieve the same cell densities. Pyruvate, the oxidation product of lactate, served as a poor electron source for the mutant. Unexpectedly, the mutant was able to grow on hydrogen-sulfate medium. These data support a role for tetraheme cytochrome c(3) in the electron transport pathway from pyruvate to sulfate or sulfite in D. desulfuricans G20.
Topics: Amino Acid Sequence; Base Sequence; Cloning, Molecular; Conjugation, Genetic; Cytochrome c Group; Desulfovibrio; Molecular Sequence Data; Mutation; Periplasm; Plasmids; Reverse Transcriptase Polymerase Chain Reaction; Sequence Analysis, DNA; Transcription, Genetic
PubMed: 10653734
DOI: 10.1128/AEM.66.2.671-677.2000 -
PloS One 2019The central carbon/lactate utilization pathway in the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough, is encoded by the highly conserved operon...
The central carbon/lactate utilization pathway in the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough, is encoded by the highly conserved operon DVU3025-3033. Our earlier in vitro genome-wide study had suggested a network of four two-component system regulators that target this large operon; however, how these four regulators control this operon was not known. Here, we probe the regulation of the lactate utilization operon with mutant strains and DNA-protein binding assays. We show that the LurR response regulator is required for optimal growth and complete lactate utilization, and that it activates the DVU3025-3033 lactate oxidation operon as well as DVU2451, a lactate permease gene, in the presence of lactate. We show by electrophoretic mobility shift assays that LurR binds to three sites in the upstream region of DVU3025, the first gene of the operon. NrfR, a response regulator that is activated under nitrite stress, and LurR share similar binding site motifs and bind the same sites upstream of DVU3025. The DVU3025 promoter also has a binding site motif (Pho box) that is bound by PhoB, a two-component response regulator activated under phosphate limitation. The lactate utilization operon, the regulator LurR, and LurR binding sites are conserved across the order Desulfovibrionales whereas possible modulation of the lactate utilization genes by additional regulators such as NrfR and PhoB appears to be limited to D. vulgaris.
Topics: Bacterial Proteins; Desulfovibrio vulgaris; Genome-Wide Association Study; Lactic Acid; Nucleotide Motifs; Operon; Oxidation-Reduction; Response Elements; Species Specificity; Transcription Factors
PubMed: 30964892
DOI: 10.1371/journal.pone.0214960 -
Journal of Bacteriology Jun 2013Desulfovibrio species are Gram-negative anaerobic sulfate-reducing bacteria that colonize the human gut. Recently, Desulfovibrio spp. have been implicated in...
Desulfovibrio species are Gram-negative anaerobic sulfate-reducing bacteria that colonize the human gut. Recently, Desulfovibrio spp. have been implicated in gastrointestinal diseases and shown to stimulate the epithelial immune response, leading to increased production of inflammatory cytokines by macrophages. Activated macrophages are key cells of the immune system that impose nitrosative stress during phagocytosis. Hence, we have analyzed the in vitro and in vivo responses of Desulfovibrio vulgaris Hildenborough to nitric oxide (NO) and the role of the hybrid cluster proteins (HCP1 and HCP2) and rubredoxin oxygen oxidoreductases (ROO1 and ROO2) in NO protection. Among the four genes, hcp2 was the gene most highly induced by NO, and the hcp2 transposon mutant exhibited the lowest viability under conditions of NO stress. Studies in murine macrophages revealed that D. vulgaris survives incubation with these phagocytes and triggers NO production at levels similar to those stimulated by the cytokine gamma interferon (IFN-γ). Furthermore, D. vulgaris hcp and roo mutants exhibited reduced viability when incubated with macrophages, revealing that these gene products contribute to the survival of D. vulgaris during macrophage infection.
Topics: Animals; Bacterial Proteins; Cell Line; Desulfovibrio vulgaris; Desulfovibrionaceae Infections; Gene Expression Regulation, Bacterial; Humans; Iron-Sulfur Proteins; Macrophages; Mice; Microbial Sensitivity Tests; Microbial Viability; Mutagenesis, Insertional; NADH, NADPH Oxidoreductases; Nitric Oxide; Nitrites; Oxidative Stress; Phenotype; Stress, Physiological
PubMed: 23564166
DOI: 10.1128/JB.00074-13 -
Biodegradation 1998Eleven pure strains of sulfate-reducing bacteria have been isolated from lab-scale bioreactors or gypsum disposal sites, all featuring relatively high concentrations of... (Comparative Study)
Comparative Study
Eleven pure strains of sulfate-reducing bacteria have been isolated from lab-scale bioreactors or gypsum disposal sites, all featuring relatively high concentrations of sulfate, and from natural environments in order to produce sulfide from gypsum using hydrogen as energy source. The properties of the eleven strains have been investigated and compared to these of three collection strains i.e. Desulfovibrio desulfuricans and Dv. vulgaris and Desulfotomaculum orientis. Particular attention was paid to the volumetric and specific sulfide production rate and to the hydrogen sulfide inhibition level. By comparison to the three collection strains, a 75% higher production rate and a hydrogen sulfide inhibition level about twice as high i.e. 25.1 mM have been achieved with strains isolated from sulfate-rich environments. The strain selection, particularly from sulfate-rich environments, should be considered as an optimization factor for the sulfate reduction processes.
Topics: Biodegradation, Environmental; Bioreactors; Calcium Sulfate; Chemical Industry; Culture Media; Desulfovibrio; Kinetics; Nephelometry and Turbidimetry; Oxidation-Reduction; Species Specificity; Sulfates; Sulfides; Sulfur-Reducing Bacteria
PubMed: 10022071
DOI: 10.1023/a:1008382102417