Desulfovibrio longus sp. nov., a sulfate-reducing bacterium isolated from an oil-producing well.

A novel type of sulfate-reducing bacteria with unusual morphology was isolated from an oil-producing well in the Paris Basin. The cells of this bacterium, strain SEBR 2582T (T = type strain), are long, thin, flexible rods, contain desulfoviridin, and are physiologically similar to members of the genus Desulfovibrio. On the basis of 16S rRNA sequence data, this strain should be included in the genus Desulfovibrio. However, strain SEBR 2582T differs from other members of this genus morphologically, physiologically, and phylogenetically. Thus, a new species, Desulfovibrio longus sp. nov., is proposed for this organism.     

Desulfovibrio longreachii sp. nov., a sulfate-reducing bacterium isolated from the Great Artesian Basin of Australia

Abstract A new mesophilic, thermotolerant sulfate-reducing bacterium, was isolated from the flowing bore waters of a deep aquifer, the Great Artesian Basin, Australia. The strain, designated isolate AB16910a, is a curved rod and resembled members of the genus Desulfovibrio . However, the isolate can be differentiated from other members of the Desulfovibrio species because of the high G+C content of 69±0.25% the 16S rRNA sequence data and other physiological characteristics. The name Desulfovibrio longreachii is proposed for the new isolate.     

Microbiological analysis of cryopegs from the Varandei Peninsula, Barents Sea

The paper deals with the microbiological characterization of water-saturated horizons in permafrost soils (cryopegs) found on the Varandei Peninsula (Barents Sea coast), 4-20 m deep. The total quantity of bacteria in the water of cryopegs was 3.5 x 10(8) cells/ml. The population of cultivated aerobic heterotrophic bacteria was 3-4 x 10(7) cells/ml and the number of anaerobic heterotrophic bacteria varied from 10(2) to 10(5) cells/ml depending on cultivation temperature and salinity. Sulfate-reducing bacteria and methanogenic archaea were found as hundreds and tens of cells per ml of water, respectively. A pure culture of a sulfate-reducing strain B15 was isolated from borehole 21 and characterized. Phylogenetic analysis has shown that the new bacterium is a member of the genus Desulfovibrio with Desulfovibrio mexicanus as its closest relative (96.5% similarity). However, the significant phenotypic differences suggest that strain B15 is a new species of sulfate-reducing bacteria.     

Characterization of Desulfomicrobium escambium sp. nov. and proposal to assign Desulfovibrio desulfuricans strain Norway 4 to the genus Desulfomicrobium

A sulfate-reducing bacterium, designated strain ESC1, was isolated and found to be a new species. Strain ESC1 is a strictly anaerobic, gram-negative, non-sporeforming, motile, short, round-ended rod often occurring in pairs. Of 31 fermentative substrates tested, only pyruvate was utilized. Sulfate enhanced growth with pyruvate and allowed growth with ethanol, lactate, formate and hydrogen. Both sulfate and thiosulfate were reduced. Lactate was incompletely oxidized to acetate and CO₂. The strain was desulfoviridin negative. The G+C content is 59.9%. These data suggested placement of strain ESC1 in the genus Desulfomicrobium. Comparative 16S rRNA analysis showed that strain ESC1 shares 98% rRNA sequence similarity with Desulfomicrobium baculatum and Desulfovibrio desulfuricans strain Norway 4. The latter two strains shared greater than 99% 16S rRNA sequence similarity. Strain ESC1 has been designated as the new species Desulfomicrobium escambium. We also recommend that D. desulfuricans strain Norway 4 be considered for reclassification as a Desulfomicrobium species.     

Desulfovibrio brasiliensis sp. nov., a moderate halophilic sulfate-reducing bacterium from Lagoa Vermelha (Brazil) mediating dolomite formation

A novel halotolerant sulfate-reducing bacterium, Desulfovibrio brasiliensis strain LVform1, was isolated from sediments of a dolomite-forming hypersaline coastal lagoon, Lagoa Vermelha, in the state of Rio de Janeiro, Brazil. The cells are vibrio-shaped and 0.30 to 0.45 m by 1.0 to 3.5 m in size. These bacteria mediate the precipitation of dolomite [CaMg(CO₃)₂] in culture experiments. The strain was identified as a member of the genus Desulfovibrio in the -subclass of the Proteobacteria on the basis of its 16S rRNA gene sequence, its physiological and morphological properties. Strain LVform1 is obligate sodium-dependent and grows at NaCl concentrations of up to 15%. The 16S rRNA sequence revealed that this strain is closely related to Desulfovibrio halophilus (96.2% similarity) and to Desulfovibrio oxyclinae (96.8% similarity), which were both isolated from Solar Lake, a hypersaline coastal lake in the Sinai, Egypt. Strain LVform1 is barotolerant, growing under pressures of up to 370 bar (37 MPa). We propose strain LVform1 to be the type strain of a novel species of the genus Desulfovibrio, Desulfovibrio brasiliensis (type strain LVform1 = DSMZ No. 15816 and JCM No. 12178). The GenBank/EMBL accession number for the 16S rDNA sequence of strain LVform1 is AJ544687.     

Natural relationships among sulfate-reducing eubacteria

Phylogenetic relationships among 20 nonsporeforming and two endospore-forming species of sulfate-reducing eubacteria were inferred from comparative 16S rRNA sequencing. All genera of mesophilic sulfate-reducing eubacteria except the new genus Desulfomicrobium and the gliding Desulfonema species were included. The sporeforming species Desulfotomaculum ruminis and Desulfotomaculum orientis were found to be gram-positive organisms sharing 83% 16S rRNA sequence similarity, indicating that this genus is diverse. The gram-negative nonsporeforming species could be divided into seven natural groups: group 1, Desulfovibrio desulfuricans and other species of this genus that do not degrade fatty acids (this group also included "Desulfomonas" pigra); group 2, the fatty acid-degrading "Desulfovibrio" sapovorans; group 3, Desulfobulbus species; group 4, Desulfobacter species; group 5, Desulfobacterium species and "Desulfococcus" niacini; group 6, Desulfococcus multivorans and Desulfosarcina variabilis; and group 7, the fatty acid-oxidizing "Desulfovibrio" baarsii. (The quotation marks are used to indicate the need for taxonomic revision.) Groups 1 to 3 are incomplete oxidizers that form acetate as an end product; groups 4 to 7 are complete oxidizers. The data were consistent with and refined relationships previously inferred by oligonucleotide catalogs of 16S rRNA. Although the determined relationships are generally consistent with the existing classification based on physiology and other characteristics, the need for some taxonomic revision is indicated.     

Desulfovibrio Africans sp. n., a new dissimilatory sulfate-reducing bacterium

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.     

Sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 as a model for understanding bacterial mercury methylation

We propose the use of Desulfovibrio desulfuricans ND132 as a model species for understanding the mechanism of microbial Hg methylation. Strain ND132 is an anaerobic dissimilatory sulfate-reducing bacterium (DSRB), isolated from estuarine mid-Chesapeake Bay sediments. It was chosen for study because of its exceptionally high rates of Hg methylation in culture and its metabolic similarity to the lost strain D. desulfuricans LS, the only organism for which methylation pathways have been partially defined. Strain ND132 is an incomplete oxidizer of short-chain fatty acids. It is capable of respiratory growth using fumarate as an electron acceptor, supporting growth without sulfide production. We used enriched stable Hg isotopes to show that ND132 simultaneously produces and degrades methylmercury (MeHg) during growth but does not produce elemental Hg. MeHg produced by cells is mainly excreted, and no MeHg is produced in spent medium. Mass balances for Hg and MeHg during the growth of cultures, including the distribution between filterable and particulate phases, illustrate how medium chemistry and growth phase dramatically affect Hg solubility and availability for methylation. The available information on Hg methylation among strains in the genus Desulfovibrio is summarized, and we present methylation rates for several previously untested species. About 50% of Desulfovibrio strains tested to date have the ability to produce MeHg. Importantly, the ability to produce MeHg is constitutive and does not confer Hg resistance. A 16S rRNA-based alignment of the genus Desulfovibrio allows the very preliminary assessment that there may be some evolutionary basis for the ability to produce MeHg within this genus.     

Biochemical and Immunological Study of Cell Envelope Proteins in Sulfate-Reducing Bacteria

The envelope proteins of 5 strains of the genus Desulfotomaculum and 12 strains of the genus Desulfovibrio were studied by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting. The Desulfovibrio strains exhibited a typical gram-negative cell envelope, whereas the cell envelope of Desulfotomaculum strains appeared to be gram-positive. A close relationship between strains of Desulfotomaculum nigrificans was observed. A comparison between different species of Desulfotomaculum revealed some degree of similarity between Desulfotomaculum nigrificans and Desulfotomaculum ruminis, whereas Desulfotomaculum orientis seemed unique. The strains of Desulfovibrio salexigens were quite different from the strains of the other species of Desulfovibrio. In two of the strains of Desulfovibrio desulfuricans, a species-specific antigen was observed. The strains of Desulfovibrio vulgaris, Desulfovibrio africanus, and Desulfovibrio gigas and one strain of Desulfovibrio desulfuricans exhibited a similar outer membrane protein profile and also showed very similar antigenic reactions.     

Corynebacterium aquatimens sp. nov., a lipophilic Corynebacterium isolated from blood cultures of a patient with bacteremia

An unknown lipophilic coryneform bacterium isolated from the blood cultures of a patient with bacteremia was characterized by phenotypic and molecular genetic methods. Chemical analysis revealed the presence of short chain mycolic acids consistent with the genus Corynebacterium. The DNA G+C content was 60.8mol%. Comparative 16S rRNA gene sequence analysis demonstrated that the isolate represents a new subline within the genus Corynebacterium. The closely phylogenetic relative of the unknown bacterium was found to be C. tuscaniense (97.8% sequence similarity). Partial rpoB gene sequence revealed that strain IMMIB L-2475(T) exhibited 13.5% sequence divergence with C. tuscaniense. The unknown bacterium was distinguished from C. tuscaniense by, DNA-DNA hybridization, cellular fatty acid profiles, MALDI-TOF analyses of cell extracts and biochemical tests. Based on the phylogenetic and phenotypic criteria, it is proposed that this bacterium be classified as new species, Corynebacterium aquatimens sp. nov., and is represented by strain IMMIB L-2475(T) (=DSM 45632(T)=CCUG 61574(T)).     

Psychrophilic Planococcus maitriensis sp.nov. from Antarctica

An orange pigmented bacterium, S1, was isolated from a cyanobacterial mat sample collected in the vicinity of Schirmacher Oasis, Maitri, the Indian station, in Antarctica. The bacterium is Gram-positive and possesses all the characteristics of the genus Planococcus. It is non-sporulating, motile and has A4alpha type peptidoglycan, MK-7 and MK-8 as the major menaquinones and anteiso-C(15:0) as the major fatty acid. Based on the phylogenetic characteristics, the bacterium S1 is identified as a close relative of Planococcus citreus with which it shares 98.12% similarity at the 16S rRNA gene level but exhibits a low similarity of 52% at the whole genome level. Apart from the above major differences, S1 also exhibits phenotypic differences with Planococcus citreus and other members of the genus Planococcus. Based on these differences, the bacterium S1 is identified as a new species of the genus Planococcus for which the name Planococcus maitriensis is proposed. The type strain of Planococcus maitriensis is S1(T) (= MTCC 4827; DSM 15305).     

一株牙鲆皮肤溃烂症病原菌的鉴定

从山东荣成养鱼场发病牙鲆分离到一株病原菌M3,革兰氏阴性,杆状,能运动,菌落半透明,用BIOLOG细菌鉴定系统不能鉴定。通过16S rDNA序列分析和同源性检索发现M3菌株与弧菌属的同源性较高,为94%～98%。系统发育学分析表明菌株M3与鳗弧菌关系最近,相似性为996%,其生化性状也和鳗弧菌的特征相似,故可把M3定为鳗弧菌(Vibrio anguillarum)。     

Desulfovibrio aerotolerans sp. nov., an oxygen tolerant sulphate-reducing bacterium isolated from activated sludge

A new mesophilic sulphate-reducing bacterium, designated strain DvO5(T) (T=type strain), was isolated from the outermost sulphate reduction-positive most-probable-number tube (10(-6) dilution) of an activated sludge sample, which had been oxygenated at 100% air saturation for 120 h. The motile, Gram-negative, curved 1 by 2-5 microm and non-spore-forming cells of strain DvO5(T) existed singly or in chains. Strain DvO5(T) grew optimally at 29 degrees C, pH 6.9 and 0.05% (w/v) NaCl in a medium containing lactate, sulphate and yeast extract. Sulphite, thiosulphate and elemental sulphur also served as electron acceptors whereas nitrate, nitrite or ferric iron were not reduced. Lactate, pyruvate, H(2) (with acetate as carbon source), ethanol and glycerol efficiently supported growth as electron donors. Pyruvate and malate were fermented. Strain DvO5(T) reduced oxygen by oxidising endogenous polyglucose at rates ranging from 0.4 to 6.0 nmol O(2)/mg protein min depending on the oxygen concentration, the highest rates being observed at atmospheric oxygen saturation. The G+C content of the DNA was 57.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain DvO5(T) was a member of the genus Desulfovibrio with D. magneticus (98.2% 16S rRNA gene sequence similarity) and D. burkinensis (97.5% 16S rRNA gene sequence similarity) being its closest relatives among validly described species. A similar phylogenetic affiliation was obtained by sequence analyses of the genes encoding the alpha and the beta subunit of dissimilatory sulphite reductase (dsrAB) as well as the alpha subunit of adenosine-5'-phosphosulphate reductase (apsA) of strain DvO5(T). On the basis of genotypic and phenotypic characteristics, strain DvO5(T) (DSM 16695(T), JCM 12613(T)) is proposed as the type strain of a new species, Desulfovibrio aerotolerans sp. nov.     

Isolation and characterization of Methylophaga sulfidovorans sp. nov.: an obligately methylotrophic, aerobic, dimethylsulfide oxidizing bacterium from a microbial mat

Abstract: Sediment from a microbial mat from the South-West coast of the Netherlands consumed dimethylsulfide (DMS) under oxic and anoxic conditions. From this sediment, a Gram-negative, oval DMS oxidizing bacterium, strain RB-1, was isolated. Its substrate range is typical of an obligately methylotrophic organism. Enzyme analysis revealed the presence of the ribulose monophosphate pathway for carbon assimilation, and the ability to use the linear dissimilatory pathway via formate to carbon dioxide, as well as the cyclic pathway via the ribulose monophosphate route for carbon dissimilation. 16S rRNA sequence analysis showed high similarity with species belonging to the genus Methylophaga . Because of the specific dimethylsulfide and hydrogen sulfide oxidizing capacity, the new isolate was named Methylophaga sulfidovorans .     

Identification of a bacterium that specifically catalyzes the reductive dechlorination of polychlorinated biphenyls with doubly flanked chlorines

A microorganism whose growth is linked to the dechlorination of polychlorinated biphenyls (PCBs) with doubly flanked chlorines was identified. Identification was made by reductive analysis of community 16S ribosomal DNA (rDNA) sequences from a culture enriched in the presence of 2,3,4,5-tetrachlorobiphenyl (2,3,4,5-CB), which was dechlorinated at the para position. Denaturing gradient gel electrophoresis (DGGE) analysis of total 16S rDNA extracted from the culture led to identification of three operational taxonomic units (OTUs 1, 2, and 3). OTU 1 was always detected when 2,3,4,5-CB or other congeners with doubly flanked chlorines were present and dechlorinated. Only OTUs 2 and 3 were detected in the absence of PCBs and when other PCBs (i.e., PCBs lacking doubly flanked chlorines) were not dechlorinated. Partial sequences of OTUs 2 and 3 exhibited 98.2% similarity to the sequence of "Desulfovibrio caledoniensis" (accession no. DCU53465). A sulfate-reducing vibrio isolated from the culture generated OTUs 2 and 3. This organism could not dechlorinate 2,3,4,5-CB. From these results we concluded that OTU 1 represents the dechlorinating bacterium growing in a coculture with a Desulfovibrio sp. The 16S rDNA sequence of OTU 1 is most similar to the 16S rDNA sequence of bacterium o-17 (89% similarity), an ortho-PCB-dechlorinating bacterium. The PCB dechlorinator, designated bacterium DF-1, reductively dechlorinates congeners with doubly flanked chlorines when it is supplied with formate or H(2)-CO(2) (80:20).     

Isolation and characterization of a unicellular manganese-oxidizing bacterium from a freshwater lake in northwestern Russia

A unicellular manganese-oxidizing bacterium (strain L7), isolated from Lake Ladoga, is identified as "Siderocapsa" sp. according to its morphology. However, this bacterium belongs to the phylogenetic cluster of Pseudomonas putida. The physiological characteristics (utilization of sugars, polyatomic alcohols, organic acids, and phenolic substrates as carbon and energy sources) also indicate the similarity of strain L7 to representatives of the genus Pseudomonas. The growing culture oxidizes Mn(II); the rate of oxidation depends on the type of added organic substrate. Carbonate requirement for this process indicates mixotrophic metabolism. The relatedness of the isolated bacterium to the representatives of the genus Pseudonomas and their phenotypic similarity provide a basis for considering strain L7 not as "Siderocapsa" sp., but as a new species, Pseudomonas siderocapsa sp. nov., of the P. putida cluster.     

Desulfovibrio mexicanus sp. nov., a Sulfate-reducing Bacterium Isolated from an Upflow Anaerobic Sludge Blanket (UASB) Reactor Treating Cheese Wastewaters

A mesophilic sulfate-reducing bacterium, designated strain Lup1^T(T=type strain) was isolated from a Mexican UASB digester treating cheese factory wastewater. The non-motile, Gram-negative, curved and non-spore-forming cells (1.7–2.5×0.5 μm) existed singly or in chains. Optimum growth occurred at 37°C and pH 7.2 in a medium containing lactate and thiosulfate. Strain Lup1^Tused pyruvate, formate, Casamino acids, serine, cysteine, H₂and ethanol as electron donors in the presence of thiosulfate as an electron acceptor and fermented pyruvate, Casamino acids, cysteine, and serine. Sulfate, elemental sulfur, and sulfite also served as electron acceptors but not nitrate or fumarate. Thiosulfate was disproportionated to sulfate and sulfide. The G+C content of the DNA was 66 mol%. Phylogenetic analysis based on 16S rDNA revealed that strain Strain Lup1^Twas a member of the genus Desulfovibrio withDesulfovibrio aminophilus being the closest relative (similarity value of 91%). As strain Lup1^Tis physiologically and phylogenetically different from other Desulfovibrio species, it is designated Desulfovibrio mexicanus sp. nov. (=DSM 13116).     

Diversity and origin of Desulfovibrio species: phylogenetic definition of a family

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.     

Biochemical and spectroscopic characterization of an aldehyde oxidoreductase isolated from Desulfovibrio aminophilus

Aldehyde oxidoreductase (AOR) activity has been found in a number of sulfate-reducing bacteria. The enzyme that is responsible for the conversion of aldehydes to carboxylic acids is a mononuclear molybdenum enzyme belonging to the xanthine oxidase family. We report here the purification and characterization of AOR isolated from the sulfate-reducing bacterium Desulfovibrio (D.) aminophilus DSM 12254, an aminolytic strain performing thiosulfate dismutation. The enzyme is a homodimer (ca. 200 kDa), containing a molybdenum centre and two [2Fe-2S] clusters per monomer. UV/Visible and electron paramagnetic resonance (EPR) spectra of D. aminophilus AOR recorded in as-prepared and reduced states are similar to those obtained in AORs from Desulfovibrio gigas, Desulfovibrio desulfuricans and Desulfovibrio alaskensis. Despite AOR from D. aminophilus is closely related to other AORs, it presents lower activity towards aldehydes and no activity towards N-heterocyclic compounds, which suggests another possible role for this enzyme in vivo. A comparison of the molecular and EPR properties of AORs from different Desulfovibrio species is also included.