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Environmental Microbiology Jun 2021Sulfate-reducing bacteria (SRB) are widespread in human guts, yet their expansion has been linked to colonic diseases. We report the isolation, sequencing and...
Sulfate-reducing bacteria (SRB) are widespread in human guts, yet their expansion has been linked to colonic diseases. We report the isolation, sequencing and physiological characterization of strain QI0027 , a novel SRB species belonging to the class Desulfovibrionia. Metagenomic sequencing of stool samples from 45 Chinese individuals, and comparison with 1690 Desulfovibrionaceae metagenome-assembled genomes recovered from humans of diverse geographic locations, revealed the presence of QI0027 in 22 further individuals. QI0027 encoded nitrogen fixation genes and based on the acetylene reduction assay, actively fixed nitrogen. Transcriptomics revealed that QI0027 overexpressed 42 genes in nitrogen-limiting conditions compared to cultures supplemented with ammonia, including genes encoding nitrogenases, a urea uptake system and the urease complex. Reanalyses of 835 public stool metatranscriptomes showed that nitrogenase genes from Desulfovibrio bacteria were expressed in six samples suggesting that nitrogen fixation might be active in the gut environment. Although frequently thought of as a nutrient-rich environment, nitrogen fixation can occur in the human gut. Animals are often nitrogen limited and have evolved diverse strategies to capture biologically active nitrogen, ranging from amino acid transporters to stable associations with beneficial microbes that provide fixed nitrogen. QI0027 is the first Desulfovibrio human isolate for which nitrogen fixation has been demonstrated, suggesting that some sulfate-reducing bacteria could also play a role in the availability of nitrogen in the gut.
Topics: Animals; Bacteria; Desulfovibrio; Humans; Nitrogen Fixation; Nitrogenase; Oxidation-Reduction; Phylogeny; Sulfates
PubMed: 33876566
DOI: 10.1111/1462-2920.15538 -
Journal of Hazardous Materials Oct 2023This paper describes a unique molecular mechanism for the EPS-mediated synthesis of CdS QDs by sulfate-reducing bacteria (SRB) under carbon source-induced reinforcement....
This paper describes a unique molecular mechanism for the EPS-mediated synthesis of CdS QDs by sulfate-reducing bacteria (SRB) under carbon source-induced reinforcement. Under the induced by carbon sources (HCOONa, CHCOONa and CHO), there was a significant increase in EPS production of SRB, particularly in protein, and the capacity of Cd(II) adsorption was further enhanced. CdS QDs were extracellularly synthesized by adding S after Cd(II) adsorption. The results showed that CdS QDs were wrapped or adhered by EPS, and the most significant increase in Arg and Lys among basic amino acids in EPS after HCOONa-induced was 133.34% and 63.89%, respectively. This may serve as a biological template for QD synthesis, producing protein gels with a large number of microcavities and controlling the nucleation of CdS QDs. The highest yield of HCOONa-CdS was achieved after induction, with 23.59 g/g biomass per unit strain, which was 447.34% higher than that before induction and was at a high level in previous studies. The synthesized CdS QDs were uniform in size distribution and had higher luminescence activity and a larger specific surface area than those synthesized by the chemical synthesis route, provides a new idea for EPS treatment of heavy metal wastewater and metal biorecovery.
Topics: Cadmium; Desulfovibrio desulfuricans; Carbon; Metals, Heavy; Desulfovibrio
PubMed: 37499495
DOI: 10.1016/j.jhazmat.2023.132146 -
Research in Microbiology Jan 2018Mercury methylation and demethylation processes govern the fate of methylmercury in aquatic ecosystems. Under anoxic conditions, methylation activity is mainly of...
Mercury methylation and demethylation processes govern the fate of methylmercury in aquatic ecosystems. Under anoxic conditions, methylation activity is mainly of biological origin and is often the result of sulfate-reducing bacteria. In this study, the use of a luminescent biosensor for screening methylmercury production was validated by exposing the reporter strain to methylating or non-methylating Desulfovibrio strains. The sensitivity of the biosensor to methylmercury was shown to depend on sulfate-reducing bacterial growth conditions. Bioluminescence was measured using 1-10 mM of sulfides. As the sulfide level increased, luminescence decreased by 40-70%, respectively. Nevertheless, assuming an average of 5 mM of sulfide produced during sulfate-reducing growth, a mercury methylation potential of over 4% was detected when using 185 nM of inorganic mercury. Due to technical limitations, mercury speciation has, to date, only been investigated in a small number of bacterial strains, and no consistent phylogenetic distribution has been identified. Here, the biosensor was further used to assess the Hg methylation capacities of an additional 21 strains related to the Desulfobulbaceae. Seven of them were identified as methylmercury producers. Cultivation procedures combined with bacterial biosensors could provide innovative tools to identify new methylator clades amongst the prokaryotes.
Topics: Biosensing Techniques; Desulfovibrio; Geologic Sediments; Mercury; Methylation; Phylogeny; Sulfates; Sulfides
PubMed: 28951230
DOI: 10.1016/j.resmic.2017.09.005 -
Biomolecules Jun 2020A comparative study of the kinetic characteristics (specific activity, initial and maximum rate, and affinity for substrates) of key enzymes of assimilatory sulfate...
A comparative study of the kinetic characteristics (specific activity, initial and maximum rate, and affinity for substrates) of key enzymes of assimilatory sulfate reduction (APS reductase and dissimilatory sulfite reductase) in cell-free extracts of sulphate-reducing bacteria (SRB) from various biotopes was performed. The material for the study represented different strains of SRB from various ecotopes. Microbiological (isolation and cultivation), biochemical (free cell extract preparation) and chemical (enzyme activity determination) methods served in defining kinetic characteristics of SRB enzymes. The determined affinity data for substrates (i.e., sulfite) were 10 times higher for SRB strains isolated from environmental (soil) ecotopes than for strains from the human intestine. The maximum rate of APS reductase reached 0.282-0.862 µmol/min×mg of protein that is only 10 to 28% higher than similar initial values. The maximum rate of sulfite reductase for corrosive relevant collection strains and SRB strains isolated from heating systems were increased by 3 to 10 times. A completely different picture was found for the intestinal SRB V in the strains Desulfovibrio piger Vib-7 (0.67 µmol/min × mg protein) and Desulfomicrobium orale Rod-9 (0.45 µmol/min × mg protein). The determinant in the cluster distribution of SRB strains is the activity of the terminal enzyme of dissimilatory sulfate reduction-sulfite reductase, but not APS reductase. The data obtained from the activity of sulfate reduction enzymes indicated the adaptive plasticity of SRB strains that is manifested in the change in enzymatic activity.
Topics: Adenosine Phosphosulfate; Biodegradation, Environmental; Desulfovibrio desulfuricans; Desulfovibrio vulgaris; Hydrogen Sulfide; Oxidoreductases Acting on Sulfur Group Donors
PubMed: 32560561
DOI: 10.3390/biom10060921 -
Environmental Microbiology Apr 2019Hydrogen sulfide produced by sulfate-reducing microorganisms (SRM) poses significant health and economic risks, particularly during oil recovery. Previous studies...
Hydrogen sulfide produced by sulfate-reducing microorganisms (SRM) poses significant health and economic risks, particularly during oil recovery. Previous studies identified perchlorate as a specific inhibitor of SRM. However, constant inhibitor addition to natural systems results in new selective pressures. Consequently, we investigated the ability of Desulfovibrio alaskensis G20 to evolve perchlorate resistance. Serial transfers in increasing concentrations of perchlorate led to robust growth in the presence of 100 mM inhibitor. Isolated adapted strains demonstrated a threefold increase in perchlorate resistance compared to the wild-type ancestor. Whole genome sequencing revealed a single base substitution in Dde_2265, the sulfate adenylyltransferase (sat). We purified and biochemically characterized the Sat from both wild-type and adapted strains, and showed that the adapted Sat was approximately threefold more resistant to perchlorate inhibition, mirroring whole cell results. The ability of this mutation to confer resistance across other inhibitors of sulfidogenesis was also assayed. The generalizability of this mutation was confirmed in multiple evolving G20 cultures and in another SRM, D. vulgaris Hildenborough. This work demonstrates that a single nucleotide polymorphism in Sat can have a significant impact on developing perchlorate resistance and emphasizes the value of adaptive laboratory evolution for understanding microbial responses to environmental perturbations.
Topics: Adaptation, Physiological; Desulfovibrio; Desulfovibrio vulgaris; Drug Resistance, Bacterial; Hydrogen Sulfide; Mutation; Oxidation-Reduction; Perchlorates; Polymorphism, Single Nucleotide; Sulfates; Whole Genome Sequencing
PubMed: 30807684
DOI: 10.1111/1462-2920.14570 -
Bioelectrochemistry (Amsterdam,... Feb 2023Desulfovibrio vulgaris biofilm was pre-grown on Ti coupons for 7 d and then the biofilm covered coupons were incubated again with fresh culture media with 10 %...
Desulfovibrio vulgaris biofilm was pre-grown on Ti coupons for 7 d and then the biofilm covered coupons were incubated again with fresh culture media with 10 % (reduced) and 100 % (normal) carbon source levels, respectively. After the pre-growth, sessile D. vulgaris cell count reached 10 cells/cm. The sessile cell counts were 2 × 10 and 4.2 × 10 cells/cm for 10 % and 100 % carbon sources, respectively after the subsequent 7 d starvation test. The maximum pit depth after the 7 d pre-growth was 4.7 µm. After the additional 7 d of the starvation test, the maximum pit depth increased to 5.1 µm for 100 % carbon source vs 6.2 µm for 10 % carbon source. Corrosion current density (i) from potentiodynamic polarization data at the end of the 7 d starvation test for 10 % carbon source was more than 3 times of that for 100 % carbon source, despite a reduced sessile cell count with 10 % carbon source. The polarization resistance (R) started to decrease within minutes after 20 ppm (w/w) riboflavin (electron mediator) injection. The carbon starvation data and riboflavin corrosion acceleration data both suggested that D. vulgaris utilized elemental Ti as an electron source to replace carbon source as the electron donor during carbon source starvation.
Topics: Corrosion; Desulfovibrio vulgaris; Titanium; Carbon; Biofilms; Riboflavin; Steel; Desulfovibrio
PubMed: 36274516
DOI: 10.1016/j.bioelechem.2022.108307 -
Archives of Microbiology Sep 1996The enrichment and isolation in pure culture of a bacterium, identified as a strain of Desulfovibrio, able to release and reduce the sulfur of isethionate...
The enrichment and isolation in pure culture of a bacterium, identified as a strain of Desulfovibrio, able to release and reduce the sulfur of isethionate (2-hydroxyethanesulfonate) and other sulfonates to support anaerobic respiratory growth, is described. The sulfonate moiety was the source of sulfur that served as the terminal electron acceptor, while the carbon skeleton of isethionate functioned as an accessory electron donor for the reduction of sulfite. Cysteate (alanine-3-sulfonate) and sulfoacetaldehyde (acetaldehyde-2-sulfonate) could also be used for anaerobic respiration, but many other sulfonates could not. A survey of known sulfate-reducing bacteria revealed that some, but not all, strains tested could utilize the sulfur of some sulfonates as terminal electron acceptor. Isethionate-grown cells of Desulfovibrio strain IC1 reduced sulfonate-sulfur in preference to that of sulfate; however, sulfate-grown cells reduced sulfate-sulfur in preference to that of sulfonate.
Topics: Anaerobiosis; Desulfovibrio; Molecular Sequence Data; RNA; Sulfonic Acids
PubMed: 8703197
DOI: 10.1007/s002030050376 -
Cellular and Molecular Biology... Sep 2021The study presented here aimed to assess the ability of Desulfovibrio fairfieldensis bacteria to adhere to and form biofilm on the structure of titanium used in...
The study presented here aimed to assess the ability of Desulfovibrio fairfieldensis bacteria to adhere to and form biofilm on the structure of titanium used in implants. D. fairfieldensis was found in the periodontal pockets in the oral environment, indicating that these bacteria can colonize the implant-bone interface and consequently cause bone infection and implant corrosion. Plates of implantable titanium, of which surfaces were characterized by scanning electronic microscopy and Raman spectroscopy, were immersed in several suspensions of D. fairfieldensis cells containing potassium nitrate on the one hand, and artificial saliva or a sulfato-reducing bacterial culture medium on the other hand. Following various incubation timepoints bacteria were counted in different media to determine their doubling time and titanium samples are checked for and determination of the total number of adhered bacteria and biofilm formation. Adhesion of D. fairfieldensis on titanium occurs at rates ranging from 2.105 to 4.6.106 bacteria h-1cm-2 in the first 18 h of incubation on both native and implantable titanium samples. Following that time, the increase in cell numbers per h and cm2 is attributed to growth in adhered bacteria. After 30 days of incubation in a nutrient-rich medium, dense biofilms are observed forming on the implant surface where bacteria became embedded in a layer of polymers D. fairfieldensis is able of adhering to an implantable titanium surface in order to form a biofilm. Further studies are still necessary, however, to assess whether this adhesion still occurs in an environment containing saliva or serum proteins that may alter the implant surface.
Topics: Bacterial Adhesion; Biofilms; Dental Implants; Desulfovibrio; Desulfovibrio desulfuricans; Humans; Microscopy, Electron, Scanning; Phylogeny; Pilot Projects; Porphyromonas; RNA, Ribosomal, 16S; Titanium
PubMed: 34817338
DOI: 10.14715/cmb/2021.67.2.9 -
PloS One 2021Magnetotactic bacteria (MTB) synthesize magnetosomes composed of membrane-enveloped magnetite (Fe3O4) and/or greigite (Fe3S4) nanoparticles in the cells. It is known...
Magnetotactic bacteria (MTB) synthesize magnetosomes composed of membrane-enveloped magnetite (Fe3O4) and/or greigite (Fe3S4) nanoparticles in the cells. It is known that the magnetotactic Deltaproteobacteria are ubiquitous and inhabit worldwide in the sediments of freshwater and marine environments. Mostly known MTB belonging to the Deltaproteobacteria are dissimilatory sulfate-reducing bacteria that biomineralize bullet-shaped magnetite nanoparticles, but only a few axenic cultures have been obtained so far. Here, we report the isolation, cultivation and characterization of a dissimilatory sulfate-reducing magnetotactic bacterium, which we designate "strain FSS-1". We found that the strain FSS-1 is a strict anaerobe and uses casamino acids as electron donors and sulfate as an electron acceptor to reduce sulfate to hydrogen sulfide. The strain FSS-1 produced bullet-shaped magnetite nanoparticles in the cells and responded to external magnetic fields. On the basis of 16S rRNA gene sequence analysis, the strain FSS-1 is a member of the genus Desulfovibrio, showing a 96.7% sequence similarity to Desulfovibrio putealis strain B7-43T. Futhermore, the magnetosome gene cluster of strain FSS-1 was different from that of Desulfovibrio magneticus strain RS-1. Thus, the strain FSS-1 is considered to be a novel sulfate-reducing magnetotactic bacterium belonging to the genus Desulfovibrio.
Topics: Desulfovibrio; Ferrosoferric Oxide; Magnetite Nanoparticles; RNA, Bacterial; RNA, Ribosomal, 16S
PubMed: 33705469
DOI: 10.1371/journal.pone.0248313 -
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