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PloS One 2021Methanol is often considered as a non-competitive substrate for methanogenic archaea, but an increasing number of sulfate-reducing microorganisms (SRMs) have been...
Methanol is often considered as a non-competitive substrate for methanogenic archaea, but an increasing number of sulfate-reducing microorganisms (SRMs) have been reported to be capable of respiring with methanol as an electron donor. A better understanding of the fate of methanol in natural or artificial anaerobic systems thus requires knowledge of the methanol dissimilation by SRMs. In this study, we describe the growth kinetics and sulfur isotope effects of Desulfovibrio carbinolicus, a methanol-oxidizing sulfate-reducing deltaproteobacterium, together with its genome sequence and annotation. D. carbinolicus can grow with a series of alcohols from methanol to butanol. Compared to longer-chain alcohols, however, specific growth and respiration rates decrease by several fold with methanol as an electron donor. Larger sulfur isotope fractionation accompanies slowed growth kinetics, indicating low chemical potential at terminal reductive steps of respiration. In a medium containing both ethanol and methanol, D. carbinolicus does not consume methanol even after the cessation of growth on ethanol. Among the two known methanol dissimilatory systems, the genome of D. carbinolicus contains the genes coding for alcohol dehydrogenase but lacks enzymes analogous to methanol methyltransferase. We analyzed the genomes of 52 additional species of sulfate-reducing bacteria that have been tested for methanol oxidation. There is no apparent relationship between phylogeny and methanol metabolizing capacity, but most gram-negative methanol oxidizers grow poorly, and none carry homologs for methyltransferase (mtaB). Although the amount of available data is limited, it is notable that more than half of the known gram-positive methanol oxidizers have both enzymatic systems, showing enhanced growth relative to the SRMs containing only alcohol dehydrogenase genes. Thus, physiological, genomic, and sulfur isotopic results suggest that D. carbinolicus and close relatives have the ability to metabolize methanol but likely play a limited role in methanol degradation in most natural environments.
Topics: Cell Respiration; Desulfovibrio; Genome, Bacterial; Genomics; Methanol; Phylogeny; RNA, Ribosomal, 16S; Sulfur Isotopes
PubMed: 33444327
DOI: 10.1371/journal.pone.0245069 -
International Journal of Systematic and... May 2006A novel alkalitolerant, sulphate-reducing bacterium (strain RT2T) was isolated from alkaline district heating water. Strain RT2T was a motile vibrio (0.5-0.8 microm wide...
A novel alkalitolerant, sulphate-reducing bacterium (strain RT2T) was isolated from alkaline district heating water. Strain RT2T was a motile vibrio (0.5-0.8 microm wide and 1.4-1.9 microm long) and grew at pH 6.9-9.9 (optimum at pH 9.0-9.4) and at 16-47 degrees C (optimum at 43 degrees C). The genomic DNA G+C content was 64.7 mol%. A limited number of compounds were used as electron donors with sulphate as electron acceptor, including lactate, pyruvate, formate and hydrogen/acetate. Sulphite and thiosulphate also served as electron acceptors. Based on physiological and genotypic properties, the isolate was considered to represent a novel species of the genus Desulfovibrio, for which the name Desulfovibrio alkalitolerans sp. nov. is proposed. The type strain is RT2T (=DSM 16529T=JCM 12612T). The strain is the first alkali-tolerant member of the genus Desulfovibrio to be described.
Topics: Acetic Acid; Alkalies; Anti-Bacterial Agents; Base Composition; DNA, Bacterial; DNA, Ribosomal; Denmark; Desulfovibrio; Formates; Genes, rRNA; Hydrogen; Hydrogen-Ion Concentration; Lactic Acid; Molecular Sequence Data; Movement; Oxidation-Reduction; Phylogeny; Pyruvic Acid; RNA, Bacterial; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sulfates; Sulfites; Temperature; Water Microbiology
PubMed: 16627648
DOI: 10.1099/ijs.0.63909-0 -
Proceedings of the National Academy of... Jul 2010Intracellular magnetite crystal formation by magnetotactic bacteria has emerged as a powerful model for investigating the cellular and molecular mechanisms of...
Intracellular magnetite crystal formation by magnetotactic bacteria has emerged as a powerful model for investigating the cellular and molecular mechanisms of biomineralization, a process common to all branches of life. Although magnetotactic bacteria are phylogenetically diverse and their crystals morphologically diverse, studies to date have focused on a few, closely related species with similar crystal habits. Here, we investigate the process of magnetite biomineralization in Desulfovibrio magneticus sp. RS-1, the only reported species of cultured magnetotactic bacteria that is outside of the alpha-Proteobacteria and that forms bullet-shaped crystals. Using a variety of high-resolution imaging and analytical tools, we show that RS-1 cells form amorphous, noncrystalline granules containing iron and phosphorus before forming magnetite crystals. Using NanoSIMS (dynamic secondary ion mass spectroscopy), we show that the iron-phosphorus granules and the magnetite crystals are likely formed through separate cellular processes. Analysis of the cellular ultrastructure of RS-1 using cryo-ultramicrotomy, cryo-electron tomography, and tomography of ultrathin sections reveals that the magnetite crystals are not surrounded by membranes but that the iron-phosphorus granules are surrounded by membranous compartments. The varied cellular paths for the formation of these two minerals lead us to suggest that the iron-phosphorus granules constitute a distinct bacterial organelle.
Topics: Cryoelectron Microscopy; Crystallization; Cytoplasmic Granules; Desulfovibrio; Electron Microscope Tomography; Ferrosoferric Oxide; Iron; Magnetosomes; Microscopy, Electron, Transmission; Minerals; Periplasm; Phosphorus
PubMed: 20566879
DOI: 10.1073/pnas.1001290107 -
International Journal of Systematic and... Nov 2011A novel sulfate-reducing bacterium, designated C1TLV30(T), was isolated from wood falls at a depth of 1693 m in the Mediterranean Sea. Cells were motile vibrios (2-4 ×...
A novel sulfate-reducing bacterium, designated C1TLV30(T), was isolated from wood falls at a depth of 1693 m in the Mediterranean Sea. Cells were motile vibrios (2-4 × 0.5 µm). Strain C1TLV30(T) grew at temperatures between 15 and 45 °C (optimum 30 °C) and at pH 5.4-8.6 (optimum 7.3). It required NaCl for growth (optimum at 25 g NaCl l(-1)) and tolerated up to 80 g NaCl l(-1). Strain C1TLV30(T) used as energy sources: lactate, fumarate, formate, malate, pyruvate and ethanol. The end products from lactate oxidation were acetate, H(2)S and CO(2) in the presence of sulfate as terminal electron acceptor. Besides sulfate, thiosulfate and sulfite were also used as terminal electron acceptors, but not elemental sulfur, fumarate, nitrate or nitrite. Strain C1TLV30(T) possessed desulfoviridin and was piezophilic, growing optimally at 10 MPa (range 0-30 MPa). The membrane lipid composition of this strain was examined to reveal an increase in fatty acid chain lengths at high hydrostatic pressures. The G+C content of the genomic DNA was 49.6 % and the genome size was estimated at 3.5 ± 0.5 Mb. Phylogenetic analysis of the SSU rRNA gene sequence indicated that strain C1TLV30(T) was affiliated to the genus Desulfovibrio with Desulfovibrio profundus being its closest phylogenetic relative (similarity of 96.4 %). On the basis of SSU rRNA gene sequence comparisons and physiological characteristics, strain C1TLV30(T) ( = DSM 21447(T) = JCM 1548(T)) is proposed to be assigned to a novel species of the genus Desulfovibrio, Desulfovibrio piezophilus sp. nov.
Topics: Base Composition; Desulfovibrio; Fatty Acids; Geologic Sediments; Mediterranean Sea; Molecular Sequence Data; Oxidation-Reduction; Phylogeny; Seawater; Sodium Chloride; Sulfates
PubMed: 21169465
DOI: 10.1099/ijs.0.028670-0 -
International Journal of Systematic... Jul 1996Two moderately halophilic sulfate-reducing bacteria were isolated from an African oil pipeline and designated strains SEBR 3640 and SEBR 2840T (T = type strain). Both of...
Two moderately halophilic sulfate-reducing bacteria were isolated from an African oil pipeline and designated strains SEBR 3640 and SEBR 2840T (T = type strain). Both of these strains possess traits that define the genus Desulfovibrio. The cells of both isolates were motile curved rods that had a single polar flagellum and contained desulfoviridin, and both isolates utilized lactate, pyruvate, malate, fumarate, succinate, and ethanol in the presence of sulfate. Sulfite, thiosulfate, and elemental sulfur were also used as an electron acceptors in the presence of lactate. However, both strains tolerated higher concentrations of NaCl (up to 17%) than all other Desulfovibrio species except Desulfovibrio halophilus, which tolerated a similar level of NaCl. The results of a 16S rRNA gene sequence analysis also placed the designated type strain, strain SEBR 2840, in the genus Desulfovibrio but revealed that this organism was significantly different from D. halophilus and all other validly described Desulfovibrio species. On the basis of our results, we propose that strain SEBR 2840T is a member of a new species of the genus Desulfovibrio, Desulfovibrio gabonensis. The type strain of D. gabonensis is strain SEBR 2840 (= DSM 10636).
Topics: Base Sequence; DNA, Bacterial; Desulfovibrio; Fuel Oils; Lipids; Molecular Sequence Data; Oxidation-Reduction; Phylogeny; Pigments, Biological; RNA, Bacterial; RNA, Ribosomal, 16S; Sulfates
PubMed: 8782680
DOI: 10.1099/00207713-46-3-710 -
Journal of Bacteriology Oct 1966Campbell, L. Leon (University of Illinois, Urbana), Mary A. Kasprzycki, and John R. Postgate. Desulfovibrio africanus sp. n., a new dissimilatory sulfate-reducing...
Campbell, L. Leon (University of Illinois, Urbana), Mary A. Kasprzycki, and John R. Postgate. Desulfovibrio africanus sp. n., a new dissimilatory sulfate-reducing bacterium. J. Bacteriol. 92:1122-1127. 1966.-The strains Benghazi and Walvis Bay can be distinguished from 40 strains of Desulfovibrio and from D. gigas on the basis of morphological and immunological studies. Electron microscopy revealed polar lophotrichous flagellation similar to that of D. gigas but different from the characteristic single polar flagellum of the 40 strains of Desulfovibrio. Immunological evidence shows that the two strains are related to members of the genus Desulfovibrio but possess several common antigenic components not present in the other strains tested. The deoxyribonucleic acid of both strains has a buoyant density of 1.724 g/cc and a guanine plus cytosine content of 60.2%. Cell-free extracts of both organisms show absorption bands of cytochrome c(3) and desulfoviridin, characteristic for Desulfovibrio. The two organisms carry out the sulfate-linked lactate fermentation and neither will grow in the absence of sulfate. Both strains contain the enzymes of the dissimilatory pathway of sulfate reduction. Therefore, these studies have demonstrated that the Benghazi and Walvis Bay strains should be regarded as taxonomically distinct from other species of Desulfovibrio.
Topics: Cytochromes; Cytosine; DNA, Bacterial; Desulfovibrio; Fermentation; Flagella; Guanine; Lactates; Microscopy, Electron; Sulfates
PubMed: 5927208
DOI: 10.1128/jb.92.4.1122-1127.1966 -
International Journal of Systematic and... Mar 2018A novel slightly halophilic sulfate-reducing bacterium, designated strain P1BSR, was isolated from water of a saline lake in Tunisia. Strain P1BSR had motile (single...
A novel slightly halophilic sulfate-reducing bacterium, designated strain P1BSR, was isolated from water of a saline lake in Tunisia. Strain P1BSR had motile (single polar flagellum), Gram-negative, rod-shaped, non-spore-forming cells, occurring singly or in pairs. Strain P1BSR grew at temperatures between 15 and 45 °C (optimum 40 °C), and in a pH range between 6 and 8.5 (optimum pH 6.7). The strain required NaCl for growth (1 % w/v), and tolerated high NaCl concentration (up to 12 % w/v) with an optimum of 3 % (w/v). Sulfate, thiosulfate and sulfite served as terminal electron acceptors, but not elemental sulfur, fumarate, nitrate and nitrite. Strain P1BSR utilized lactate, pyruvate, formate, d-fructose and glycerol as carbon and energy sources. The main cellular fatty acid was C16 : 0 (50.8 %). The genomic DNA G+C content was 47.7 mol%. Phylogenetic analysis of 16S rRNA gene sequence similarity indicated that strain P1BSR was affiliated to the genus Desulfovibrio, with the type strains Desulfovibrio salexigens (96.51 %), Desulfovibrio zosterae (95.68 %), Desulfovibrio hydrothermalis (94.81 %) and Desulfovibrio ferrireducens (94.73 %) as its closest phylogenetic relatives. On the basis of genotypic, phenotypic and phylogenetic characteristics, it is proposed to assign strain P1BSR to a novel species of the genus Desulfovibrio, Desulfovibrio salinus sp. nov. The type strain is P1BSR (=DSM 101510=JCM 31065).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Desulfovibrio; Fatty Acids; Lakes; Oxidation-Reduction; Phylogeny; RNA, Ribosomal, 16S; Salinity; Sequence Analysis, DNA; Sulfates; Tunisia
PubMed: 29458461
DOI: 10.1099/ijsem.0.002567 -
FEMS Microbiology Letters Apr 2009Hopanoids are important lipid components of many bacterial groups and are therefore ubiquitous in soils, sediments, and rocks. Until recently, it was believed that the...
Hopanoids are important lipid components of many bacterial groups and are therefore ubiquitous in soils, sediments, and rocks. Until recently, it was believed that the synthesis of hopanoids is restricted to at least microaerophilic bacteria and consequently geological findings of hopanoids were used as an indication for oxygenated settings. Recent studies, however, demonstrated the biosynthesis of hopanoids under strictly anoxic conditions by a few bacterial groups, although their relevance is still unclear. We therefore extended our previous work studying hopanoid production among members of the genus Desulfovibrio, a group of sulphate-reducing bacteria (SRB) widely distributed in marine sediments, water-logged soils, and oil reservoirs. We found three species (Desulfovibrio halophilus, Desulfovibrio vulgaris Hildenborough, and Desulfovibrio africanus) to be devoid of hopanoids. In contrast, Desulfovibrio bastinii contains high amounts of nonextended hopanoids and bacteriohopanepolyols, with diploptene, 17beta(H),21beta(H)-bacteriohopane-32,33,34,35-tetrol, and 17beta(H),21beta(H)-35-aminobacteriohopane-32,33,34-triol being the major compounds. Because the moderately halophilic D. bastinii was isolated from a deep subsurface oil formation water, a contribution of hopanoids by SRB to the intrinsic oil hopanoid inventory is feasible, which would influence hopanoidal compositions often used for organic-geochemical characterization purposes. Nevertheless, our data indicate that hopanoid production might be common, but not obligate in the genus Desulfovibrio.
Topics: Anaerobiosis; Desulfovibrio; Lipid Metabolism; Lipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sulfur-Reducing Bacteria; Triterpenes; Water Microbiology
PubMed: 19222571
DOI: 10.1111/j.1574-6968.2009.01520.x -
Microbiology (Reading, England) Dec 2019Platinum and palladium are much sought-after metals of critical global importance in terms of abundance and availability. At the nano-scale these metals are of even...
Platinum and palladium are much sought-after metals of critical global importance in terms of abundance and availability. At the nano-scale these metals are of even higher value due to their catalytic abilities for industrial applications. is able to capture ionic forms of both of these metals, reduce them and synthesize elemental nanoparticles. Despite this ability, very little is known about the biological pathways involved in the formation of these nanoparticles. Proteomic analysis of in response to platinum and palladium has highlighted those proteins involved in both the reductive pathways and the wider stress-response system. A core set of 13 proteins was found in both treatments and consisted of proteins involved in metal transport and reduction. There were also seven proteins that were specific to either platinum or palladium. Overexpression of one of these platinum-specific genes, a NiFe hydrogenase small subunit (Dde_2137), resulted in the formation of larger nanoparticles. This study improves our understanding of the pathways involved in the metal resistance mechanism of and is informative regarding how we can tailor the bacterium for nanoparticle production, enhancing its application as a bioremediation tool and as a way to capture contaminant metals from the environment.
Topics: Bacterial Proteins; Biodegradation, Environmental; Desulfovibrio; Hydrogenase; Metal Nanoparticles; Models, Biological; Palladium; Particle Size; Platinum; Proteomics
PubMed: 31361216
DOI: 10.1099/mic.0.000840 -
International Journal of Systematic and... Sep 2007Two novel sulfate-reducing bacterial strains, designated E-2(T) and IMP-2, were isolated from geographically distinct locations. Strain E-2(T) was recovered from marine...
Two novel sulfate-reducing bacterial strains, designated E-2(T) and IMP-2, were isolated from geographically distinct locations. Strain E-2(T) was recovered from marine sediments near Sfax (Tunisia), whereas strain IMP-2 originated from oilfield production fluids in the Gulf of Mexico. Cells were Gram-negative, non-sporulated, motile, vibrio-shaped or sigmoid. They were strictly anaerobic, mesophilic and moderately halophilic. Sulfate, sulfite, thiosulfate and elemental sulfur served as electron acceptors, but not nitrate or nitrite. H(2) (with acetate as carbon source), formate, fumarate, lactate, malate, pyruvate, succinate and fructose were used as electron donors in the presence of sulfate as terminal electron acceptor. Lactate was oxidized incompletely to acetate. Fumarate and pyruvate were fermented. Desulfoviridin and c-type cytochromes were present. 16S rRNA gene sequence analysis of the two strains showed that they were phylogenetically similar (99.0 % similarity) and belonged to the genus Desulfovibrio, with Desulfovibrio indonesiensis and Desulfovibrio gabonensis as their closest phylogenetic relatives. The G+C content of the DNA was respectively 60.4 and 62.7 mol% for strains E-2(T) and IMP-2. DNA-DNA hybridization experiments revealed that the novel strains had a high genomic relatedness, suggesting that they belong to the same species. We therefore propose that the two isolates be affiliated to a novel species of the genus Desulfovibrio, Desulfovibrio marinus sp. nov. The type strain is strain E-2(T) (=DSM 18311(T) =JCM 14040(T)).
Topics: Anaerobiosis; Bacterial Typing Techniques; Base Composition; Cytochromes c; DNA, Bacterial; DNA, Ribosomal; Desulfovibrio; Fermentation; Genes, rRNA; Geologic Sediments; Hydrogensulfite Reductase; Locomotion; Mexico; Molecular Sequence Data; Nucleic Acid Hybridization; Oxidation-Reduction; Phylogeny; RNA, Bacterial; RNA, Ribosomal, 16S; Sequence Homology, Nucleic Acid; Sulfates; Temperature; Tunisia; Water Microbiology
PubMed: 17766893
DOI: 10.1099/ijs.0.64790-0