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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 -
Scientific Reports Nov 2018The marine bacterial strain Desulfovibrio ferrophilus IS5, known for its lithotrophic growth ability to use metallic iron as a sole electron donor and for causing...
The marine bacterial strain Desulfovibrio ferrophilus IS5, known for its lithotrophic growth ability to use metallic iron as a sole electron donor and for causing corrosion of steel, was used in the current study. Four commonly used biocides in the oil and gas industry, namely tetrakis(hydroxymethyl) phosphonium sulfate (THPS), glutaraldehyde (GLUT), benzalkonium chloride (BAC), and GLUT/BAC were selected to study their efficacy in controlling carbon steel corrosion in the presence of this strain. Incubations containing strain IS5 and low carbon steel coupons were prepared in the presence and absence of the four biocides, and these were monitored using both electrochemical methods (electrochemical impedance spectroscopy, linear polarization resistance and potentiodynamic polarization) and surface analyses (scanning electron microscopy, confocal measurements, optical microscopy, and profilometry) to assess the biofilm/metal interactions. When THPS, BAC, and GLUT/BAC treatments were applied, minimal corrosion was measured by all methods. In contrast, severe pitting was observed in the presence of 50 ppm GLUT, similar to what was observed when D. ferrophilus IS5 was incubated in the absence of biocide, suggesting that GLUT alone may not be effective in controlling MIC in marine environments. This study also showed that the use of non-destructive electrochemical methods is effective for screening for real time biocide selection and monitoring of the impact of chemicals post-dosage in oil and gas operations.
Topics: Benzalkonium Compounds; Biofilms; Corrosion; Desulfovibrio; Desulfovibrionaceae Infections; Disinfectants; Glutaral; Steel; Sulfates
PubMed: 30413730
DOI: 10.1038/s41598-018-34789-7 -
PloS One 2016The prevalence of lipids devoid of phosphorus suggests that the availability of phosphorus limits microbial growth and activity in many anoxic, stratified environments....
The prevalence of lipids devoid of phosphorus suggests that the availability of phosphorus limits microbial growth and activity in many anoxic, stratified environments. To better understand the response of anaerobic bacteria to phosphate limitation and starvation, this study combines microscopic and lipid analyses with the measurements of fitness of pooled barcoded transposon mutants of the model sulfate reducing bacterium Desulfovibrio alaskensis G20. Phosphate-limited G20 has lower growth rates and replaces more than 90% of its membrane phospholipids by a mixture of monoglycosyl diacylglycerol (MGDG), glycuronic acid diacylglycerol (GADG) and ornithine lipids, lacks polyphosphate granules, and synthesizes other cellular inclusions. Analyses of pooled and individual mutants reveal the importance of the high-affinity phosphate transport system (the Pst system), PhoR, and glycolipid and ornithine lipid synthases during phosphate limitation. The phosphate-dependent synthesis of MGDG in G20 and the widespread occurrence of the MGDG/GADG synthase among sulfate reducing ∂-Proteobacteria implicate these microbes in the production of abundant MGDG in anaerobic environments where the concentrations of phosphate are lower than 10 μM. Numerous predicted changes in the composition of the cell envelope and systems involved in transport, maintenance of cytoplasmic redox potential, central metabolism and regulatory pathways also suggest an impact of phosphate limitation on the susceptibility of sulfate reducing bacteria to other anthropogenic or environmental stresses.
Topics: Acclimatization; Adaptation, Physiological; Anaerobiosis; Desulfovibrio; Dose-Response Relationship, Drug; Mutation; Phosphates; Phosphorus
PubMed: 28030630
DOI: 10.1371/journal.pone.0168719 -
Scientific Reports Jun 2018Bacteria of the genus Desulfovibrio belong to the group of Sulphate Reducing Bacteria (SRB). SRB generate significant liabilities in the petroleum industry, mainly due...
Bacteria of the genus Desulfovibrio belong to the group of Sulphate Reducing Bacteria (SRB). SRB generate significant liabilities in the petroleum industry, mainly due to their ability to microbiologically induce corrosion, biofilm formation and HS production. Bacteriophages are an alternative control method for SRB, whose information for this group of bacteria however, is scarce. The present study developed a workflow for the identification of complete prophages in Desulfovibrio. Poly-lysogenesis was shown to be common in Desulfovibrio. In the 47 genomes analyzed 53 complete prophages were identified. These were classified within the order Caudovirales, with 69.82% belonging to the Myoviridade family. More than half the prophages identified have genes coding for lysozyme or holin. Four of the analyzed bacterial genomes present prophages with identity above 50% in the same strain, whose comparative analysis demonstrated the existence of colinearity between the sequences. Of the 17 closed bacterial genomes analyzed, 6 have the CRISPR-Cas system classified as inactive. The identification of bacterial poly-lysogeny, the proximity between the complete prophages and the possible inactivity of the CRISPR-Cas in closed bacterial genomes analyzed allowed the choice of poly-lysogenic strains with prophages belonging to the Myoviridae family for the isolation of prophages and testing of related strains for subsequent studies.
Topics: CRISPR-Cas Systems; Desulfovibrio; Genome, Bacterial; Phylogeny; Prophages
PubMed: 29915307
DOI: 10.1038/s41598-018-27423-z -
Microbial Genomics May 2021Endolithic microbial symbionts in the coral skeleton may play a pivotal role in maintaining coral health. However, compared to aerobic micro-organisms, research on the...
Endolithic microbial symbionts in the coral skeleton may play a pivotal role in maintaining coral health. However, compared to aerobic micro-organisms, research on the roles of endolithic anaerobic micro-organisms and microbe-microbe interactions in the coral skeleton are still in their infancy. In our previous study, we showed that a group of coral-associated (CAP), a genus of anaerobic green sulphur bacteria, was dominant in the skeleton of the coral . Though CAP is diverse, the 16S rRNA phylogeny presents it as a distinct clade separate from other free-living . In this study, we build on previous research and further characterize the genomic and metabolic traits of CAP by recovering two new high-quality CAP genomes - Prosthecochloris isoporae and Prosthecochloris sp. N1 - from the coral endolithic cultures. Genomic analysis revealed that these two CAP genomes have high genomic similarities compared with other and harbour several CAP-unique genes. Interestingly, different CAP species harbour various pigment synthesis and sulphur metabolism genes, indicating that individual CAPs can adapt to a diversity of coral microenvironments. A novel high-quality genome of sulfate-reducing bacterium (SRB)- Halodesulfovibrio lyudaonia - was also recovered from the same culture. The fact that CAP and various SRB co-exist in coral endolithic cultures and coral skeleton highlights the importance of SRB in the coral endolithic community. Based on functional genomic analysis of . P. sp. N1, . P. isoporae and . H. lyudaonia, we also propose a syntrophic relationship between the SRB and CAP in the coral skeleton.
Topics: Animals; Anthozoa; Bacteria; Chlorobi; DNA, Bacterial; Desulfovibrionaceae; Genome; Genomics; Metagenome; Phylogeny; RNA, Ribosomal, 16S; Sulfates
PubMed: 33952388
DOI: 10.1099/mgen.0.000574 -
Nature Communications Jul 2018Dietary lipids favor the growth of the pathobiont Bilophila wadsworthia, but the relevance of this expansion in metabolic syndrome pathogenesis is poorly understood....
Dietary lipids favor the growth of the pathobiont Bilophila wadsworthia, but the relevance of this expansion in metabolic syndrome pathogenesis is poorly understood. Here, we showed that B. wadsworthia synergizes with high fat diet (HFD) to promote higher inflammation, intestinal barrier dysfunction and bile acid dysmetabolism, leading to higher glucose dysmetabolism and hepatic steatosis. Host-microbiota transcriptomics analysis reveal pathways, particularly butanoate metabolism, which may underlie the metabolic effects mediated by B. wadsworthia. Pharmacological suppression of B. wadsworthia-associated inflammation demonstrate the bacterium's intrinsic capacity to induce a negative impact on glycemic control and hepatic function. Administration of the probiotic Lactobacillus rhamnosus CNCM I-3690 limits B. wadsworthia-induced immune and metabolic impairment by limiting its expansion, reducing inflammation and reinforcing intestinal barrier. Our results suggest a new avenue for interventions against western diet-driven inflammatory and metabolic diseases.
Topics: Animals; Bilophila; Blood Glucose; Cytokines; Desulfovibrionaceae Infections; Diet, High-Fat; Dietary Fats; Fatty Liver; Gastrointestinal Microbiome; Lacticaseibacillus rhamnosus; Liver; Liver Function Tests; Male; Metabolic Networks and Pathways; Metabolic Syndrome; Mice; Mice, Inbred C57BL; Probiotics; Transcriptome
PubMed: 30022049
DOI: 10.1038/s41467-018-05249-7 -
BMC Genomics Apr 2012Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation,...
BACKGROUND
Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continuously fed biofilm reactor, and compared to both batch and reactor planktonic populations.
RESULTS
The functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenase as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from biofilm cells.
CONCLUSIONS
Even though both the planktonic and biofilm cells were oxidizing lactate and reducing sulfate, the biofilm cells were physiologically distinct compared to planktonic growth states due to altered abundances of genes/proteins involved in carbon/energy flow and extracellular structures. In addition, average expression values for multiple rRNA transcripts and respiratory activity measurements indicated that biofilm cells were metabolically more similar to exponential-phase cells although biofilm cells are structured differently. The characterization of physiological advantages and constraints of the biofilm growth state for sulfate-reducing bacteria will provide insight into bioremediation applications as well as microbially-induced metal corrosion.
Topics: Bacterial Proteins; Biofilms; Bioreactors; Carbohydrate Metabolism; Carbon; Cluster Analysis; Desulfovibrio vulgaris; Energy Metabolism; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Lactic Acid; Microscopy, Confocal; Models, Biological; Plankton; Principal Component Analysis; Proteomics; RNA, Messenger; Ribosomal Proteins; Sulfates
PubMed: 22507456
DOI: 10.1186/1471-2164-13-138 -
International Journal of Molecular... Jan 2022Copper (Cu) is an essential micronutrient required as a co-factor in the catalytic center of many enzymes. However, excess Cu can generate pleiotropic effects in the...
Copper (Cu) is an essential micronutrient required as a co-factor in the catalytic center of many enzymes. However, excess Cu can generate pleiotropic effects in the microbial cell. In addition, leaching of Cu from pipelines results in elevated Cu concentration in the environment, which is of public health concern. Sulfate-reducing bacteria (SRB) have been demonstrated to grow in toxic levels of Cu. However, reports on Cu toxicity towards SRB have primarily focused on the degree of toxicity and subsequent elimination. Here, Cu(II) stress-related effects on a model SRB, G20, is reported. Cu(II) stress effects were assessed as alterations in the transcriptome through RNA-Seq at varying Cu(II) concentrations (5 µM and 15 µM). In the pairwise comparison of control vs. 5 µM Cu(II), 61.43% of genes were downregulated, and 38.57% were upregulated. In control vs. 15 µM Cu(II), 49.51% of genes were downregulated, and 50.5% were upregulated. The results indicated that the expression of inorganic ion transporters and translation machinery was massively modulated. Moreover, changes in the expression of critical biological processes such as DNA transcription and signal transduction were observed at high Cu(II) concentrations. These results will help us better understand the Cu(II) stress-response mechanism and provide avenues for future research.
Topics: Bacterial Proteins; Biological Phenomena; Copper; Desulfovibrio; Stress, Physiological; Sulfates; Transcriptome
PubMed: 35163324
DOI: 10.3390/ijms23031396 -
Biological & Pharmaceutical Bulletin 2018Acarbose and voglibose are the most widely used diabetes drugs as glycosidase inhibitors. In this study, the use of these two inhibitors significantly increased the... (Comparative Study)
Comparative Study
Acarbose and voglibose are the most widely used diabetes drugs as glycosidase inhibitors. In this study, the use of these two inhibitors significantly increased the content of starch in large intestine, and altered the concentration of short-chain fatty acids (SCFAs) by affecting the intestinal microbiota. However, there are some differences in the intestinal microbiome of the two groups of mice, mainly in bacteria such as Bacteroidaceae bacteroides and Desulfovibrionaceae desulfovibrio. The productions of acetate and propionate in caecum in voglibose group were significantly higher than those in acarbose group and two kinds of glycosidase inhibitors were close in the production of butyrate in caecum. The Tax4Fun analysis based on Kyoto Encyclopedia of Genes and Genomes (KEGG) data indicated that different productions of acetate and propionate between acarbose group and voglibose group may be related to 2-oxoisovalerate dehydrogenase and pyruvate oxidase. In addition, in-vitro experiments suggested that voglibose had less effect on epithelial cells than acarbose after direct stimulation. According to the recent researches of SCFAs produced by intestinal microbiota, our comparative study shown higher concentration of these beneficial fatty acids in the lumen of voglibose-treated mice, which implied a lower level of inflammation.
Topics: Acarbose; Animals; Bacteroidaceae; Caco-2 Cells; Desulfovibrionaceae; Epithelial Cells; Fatty Acids, Volatile; Gastrointestinal Microbiome; Glycoside Hydrolase Inhibitors; Humans; Inositol; Intestinal Mucosa; Intestines; Male; Mice; Mice, Inbred ICR; Starch
PubMed: 29962399
DOI: 10.1248/bpb.b17-00978 -
Proceedings of the National Academy of... Aug 2013Sulfate-reducing bacteria (SRB) colonize the guts of ∼50% of humans. We used genome-wide transposon mutagenesis and insertion-site sequencing, RNA-Seq, plus mass... (Comparative Study)
Comparative Study
Sulfate-reducing bacteria (SRB) colonize the guts of ∼50% of humans. We used genome-wide transposon mutagenesis and insertion-site sequencing, RNA-Seq, plus mass spectrometry to characterize genetic and environmental factors that impact the niche of Desulfovibrio piger, the most common SRB in a surveyed cohort of healthy US adults. Gnotobiotic mice were colonized with an assemblage of sequenced human gut bacterial species with or without D. piger and fed diets with different levels and types of carbohydrates and sulfur sources. Diet was a major determinant of functions expressed by this artificial nine-member community and of the genes that impact D. piger fitness; the latter includes high- and low-affinity systems for using ammonia, a limiting resource for D. piger in mice consuming a polysaccharide-rich diet. Although genes involved in hydrogen consumption and sulfate reduction are necessary for its colonization, varying dietary-free sulfate levels did not significantly alter levels of D. piger, which can obtain sulfate from the host in part via cross-feeding mediated by Bacteroides-encoded sulfatases. Chondroitin sulfate, a common dietary supplement, increased D. piger and H2S levels without compromising gut barrier integrity. A chondroitin sulfate-supplemented diet together with D. piger impacted the assemblage's substrate utilization preferences, allowing consumption of more reduced carbon sources and increasing the abundance of the H2-producing Actinobacterium, Collinsella aerofaciens. Our findings provide genetic and metabolic details of how this H2-consuming SRB shapes the responses of a microbiota to diet ingredients and a framework for examining how individuals lacking D. piger differ from those who harbor it.
Topics: Animals; Bromodeoxyuridine; Chondroitin Sulfates; DNA Primers; DNA Transposable Elements; Desulfovibrio; Diet; Dietary Supplements; Feces; Gas Chromatography-Mass Spectrometry; Gastrointestinal Tract; Genetic Vectors; Humans; Hydrogen Sulfide; Mass Spectrometry; Mice; Mutagenesis; Sequence Analysis, DNA; Species Specificity
PubMed: 23898195
DOI: 10.1073/pnas.1312524110