(1/183) Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments.

Three Gram-negative, rod-shaped, aerobic bacteria that were capable of degrading dimethylsulfoniopropionate (DMSP) were isolated from marine waters. These isolates (DSS-3(T), DSS-10 and ISM(T)) exhibited the ability to demethylate and cleave DMSP, as well as to degrade other sulfur compounds related to DMSP that are cycled in marine environments. Intracellular poly-beta-hydroxybutyrate inclusions, surface blebs and one polar, complex flagellum that rotated exclusively in the clockwise direction were observed for DSS-3(T). The outer membrane of ISM(T) was separated from the cytoplasm at the poles in a toga-like morphology. The primary fatty acid in both strains was C(18 : 1)omega7c. DNA G+C contents for the isolates were 68.0+/-0.1, 68.1+/-0.1 and 66.0+/-0.2 mol% for DSS-3(T), DSS-10 and ISM(T), respectively. 16S rRNA gene sequence analyses placed these organisms within the Roseobacter lineage of the alpha-PROTEOBACTERIA: Closely related species were Silicibacter lacuscaerulensis and Ruegeria atlantica (DSS-3(T) and DSS-10) and Roseovarius tolerans (ISM(T)). Neither DSS-3(T) nor ISM(T) exhibited 16S rRNA similarity >97 % or DNA-DNA hybridization values >45 % to their nearest described relatives. Genotypic and phenotypic analyses support the creation of two novel species: Silicibacter pomeroyi sp. nov. with strain DSS-3(T) (=ATCC 700808(T)=DSM 15171(T)) as the type strain, and Roseovarius nubinhibens sp. nov. with strain ISM(T) (=ATCC BAA-591(T)=DSM 15170(T)) as the type strain.  (+info)

(2/183) Oceanicaulis alexandrii gen. nov., sp. nov., a novel stalked bacterium isolated from a culture of the dinoflagellate Alexandrium tamarense (Lebour) Balech.

Five bacterial strains were isolated from a non-toxigenic strain of the marine dinoflagellate Alexandrium tamarense (Lebour) Balech CCMP 116 (NEPCC C116), during a survey of the diversity of bacteria associated with paralytic shellfish toxin-producing cultures of Alexandrium spp. (Dinophyta). All strains were strictly aerobic, Gram-negative, straight or curved rods. Cells were dimorphic, with stalks (or prosthecae) and non-motile or non-stalked and motile, by means of a single polar flagellum. The bacteria grew best at salt concentrations ranging from 2 to 10 % and growth occurred at 10 degrees C, but not at 50 degrees C. The G+C content of the chromosomal DNA of the strains was determined to be 61-62 mol%. Major cellular fatty acids of the bacteria presented a unique profile. 16S rRNA gene sequence analysis showed the five strains to be related to genera of budding bacteria of marine origin in the 'Alphaproteobacteria', namely, Hirschia, Maricaulis and Hyphomonas, although they exhibited substantial differences in morphology, substrate utilization and fatty acid profile to members of these genera. The five strains are proposed to comprise a new species of a new genus, Oceanicaulis alexandrii gen. nov., sp. nov., the type strain of which is C116-18(T) (=DSM 11625(T)=NCIMB 13905(T)).  (+info)

(3/183) Enzymes and genes of taurine and isethionate dissimilation in Paracoccus denitrificans.

Growth of the alpha-proteobacterium Paracoccus denitrificans NKNIS with taurine or isethionate as sole source of carbon involves sulfoacetaldehyde acetyltransferase (Xsc), which is presumably encoded by an xsc gene in subgroup 3, none of whose gene products has been characterized. The genome of the alpha-proteobacterium Rhodobacter sphaeroides 2.4.1 was interpreted to contain a nine-gene cluster encoding the inducible dissimilation of taurine, and this deduced pathway included a regulator, a tripartite ATP-independent transporter, taurine dehydrogenase (TDH; presumably TauXY) as well as Xsc (subgroup 3), a hypothetical protein and phosphate acetyltransferase (Pta). A similar cluster was found in P. denitrificans NKNIS, in contrast to an analogous cluster encoding an ATP-binding cassette transporter in Paracoccus pantotrophus. Inducible TDH, Xsc and Pta were found in extracts of taurine-grown cells of strain NKNIS. TDH oxidized taurine to sulfoacetaldehyde and ammonium ion with cytochrome c as electron acceptor. Whereas Xsc and Pta were soluble enzymes, TDH was located in the particulate fraction, where inducible proteins with the expected masses of TauXY (14 and 50 kDa, respectively) were detected by SDS-PAGE. Xsc and Pta were separated by anion-exchange chromatography. Xsc was effectively pure; the molecular mass of the subunit (64 kDa) and the N-terminal amino acid sequence confirmed the identification of the xsc gene. Inducible isethionate dehydrogenase (IDH), Xsc and Pta were assayed in extracts of isethionate-grown cells of strain NKNIS. IDH was located in the particulate fraction, oxidized isethionate to sulfoacetaldehyde with cytochrome c as electron acceptor and correlated with the expression of a 62 kDa protein. Strain NKNIS excreted sulfite and sulfate during growth with a sulfonate and no sulfite dehydrogenase was detected. There is considerable biochemical, genetic and regulatory complexity in the degradation of these simple molecules.  (+info)

(4/183) Catellibacterium nectariphilum gen. nov., sp. nov., which requires a diffusible compound from a strain related to the genus Sphingomonas for vigorous growth.

A bacterial strain, designated AST4(T), was isolated from activated sludge. The bacterium did not show significant growth on nutrient broth, but growth was clearly stimulated by addition of supernatant from other bacterial cultures. Culture filtrate of a strain related to the genus Sphingomonas in particular increased the cell yield and growth rate of strain AST4(T). Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain AST4(T) is located within the 'Rhodobacter group' in the alpha-3 subclass of Proteobacteria, but is clearly distant from related genera in this group such as Paracoccus, Rhodobacter and Rhodovulum. Strain AST4(T) is a Gram-negative, non-motile, rod-shaped (0.6-0.8x1.3-2.0 micro m) and aerobic bacterium. It was not able to reduce nitrate to nitrite or N(2). No phototrophic growth was observed. Optimal growth occurred at 30 degrees C and pH 6.5-7.5. The dominant cellular fatty acid in the isolate was C(18 : 1)cis11. Ubiquinone-10 was the major respiratory quinone. The G+C content was 64.5 mol% (by HPLC). Based on the phylogenetic and phenotypic traits, the name Catellibacterium nectariphilum gen. nov., sp. nov. is proposed for this isolate; the type strain is AST4(T) (=NBRC 100046(T)=JCM 11959(T)=DSM 15620(T)).  (+info)

(5/183) Oceanicola granulosus gen. nov., sp. nov. and Oceanicola batsensis sp. nov., poly-beta-hydroxybutyrate-producing marine bacteria in the order 'Rhodobacterales'.

Three Gram-negative, chemoheterotrophic, non-motile, rod-shaped bacterial strains that accumulate poly-beta-hydroxybutyrate granules were isolated from the Bermuda Atlantic Time-series Study site by high-throughput culturing methods and characterized by polyphasic approaches. DNA-DNA hybridization, DNA G+C content and phylogenetic analyses based on 16S rRNA gene sequences divided the three isolates into two distinct genospecies that were clearly differentiated by fatty acid profiles, carbon source utilization patterns, antibiotic susceptibility and biochemical characteristics. The strains utilized a wide range of substrates, including pentoses, hexoses, oligosaccharides, sugar alcohols, organic acids and amino acids. DNA G+C contents were 71.5, 70.9 and 67.3 mol% for strains HTCC2516T, HTCC2523 and HTCC2597T, respectively. The most dominant fatty acid was 18 : 1omega7c in strains HTCC2516T and HTCC2523, and cyclo 19 : 0 in strain HTCC2597T. The type strains HTCC2516T and HTCC2597T were clearly differentiated by the presence or absence of 12 : 0, 12 : 1omega11c, 14 : 0, 15 : 0 and methyl 18 : 1. Phylogenetic analyses indicated that the strains formed a distinct monophyletic lineage within the Roseobacter clade in the order 'Rhodobacterales' of the Alphaproteobacteria, and which did not associate with any of the described genera. Genotypic and phenotypic differences of the isolates from the previously described genera support the description of Oceanicola granulosus gen. nov., sp. nov. with the type strain HTCC2516T (=ATCC BAA-861T=DSM 15982T=KCTC 12143T) and of Oceanicola batsensis sp. nov. with the type strain HTCC2597T (=ATCC BAA-863T=DSM 15984T=KCTC 12145T).  (+info)

(6/183) Oceanibulbus indolifex gen. nov., sp. nov., a North Sea alphaproteobacterium that produces bioactive metabolites.

A water sample from the North Sea was used to isolate the abundant heterotrophic bacteria that are able to grow on complex marine media. Isolation was by serial dilution and spread plating. Phylogenetic analysis of nearly complete 16S rRNA gene sequences revealed that one of the strains, HEL-45T, had 97.4% sequence similarity to Sulfitobacter mediterraneus and 96.5 % sequence similarity to Staleya guttiformis. Strain HEL-45T is a Gram-negative, non-motile rod and obligate aerobe and requires sodium and 1-7% sea salts for growth. It contains storage granules and does not produce bacteriochlorophyll. Optimal growth temperatures are 25-30 degrees C. The DNA base composition (G+C content) is 60.1 mol%. Strain HEL-45T has Q10 as the dominant respiratory quinone. The major polar lipids are phosphatidyl glycerol, diphosphatidyl glycerol, phosphatidyl choline, phosphatidyl ethanolamine and an aminolipid. The fatty acids comprise 18 : 1omega7c, 18 : 0, 16 : 1omega7c, 16 : 0, 3-OH 10 : 0, 3-OH 12 : 1 (or 3-oxo 12 : 0) and traces of an 18 : 2 fatty acid. Among the hydroxylated fatty acids only 3-OH 12 : 1 (or 3-oxo 12 : 0) appears to be amide linked, whereas 3-OH 10 : 0 appears to be ester linked. The minor fatty acid components (between 1 and 7%) allow three subgroups to be distinguished in the Sulfitobacter/Staleya clade, placing HEL-45T into a separate lineage characterized by the presence of 3-OH 12 : 1 (or 3-oxo 12 : 0) and both ester- and amide-linked 16 : 1omega7c phospholipids. HEL-45T produces indole and derivatives thereof, several cyclic dipeptides and thryptanthrin. Phylogenetic analysis of 16S rRNA gene sequences and chemotaxonomic data support the description of a new genus and species, to include Oceanibulbus indolifex gen. nov., sp. nov., with the type strain HEL-45T (=DSM 14862T=NCIMB 13983T).  (+info)

(7/183) Loktanella salsilacus gen. nov., sp. nov., Loktanella fryxellensis sp. nov. and Loktanella vestfoldensis sp. nov., new members of the Rhodobacter group, isolated from microbial mats in Antarctic lakes.

A taxonomic study was performed on 26 strains isolated from microbial mats in Antarctic lakes of the Vestfold Hills and the McMurdo Dry Valleys. Phylogenetic analysis based on 16S rRNA gene sequences placed these strains within the Rhodobacter group of the alpha-subclass of the Proteobacteria. Sequence similarity values for the strains with their nearest phylogenetic neighbours (Jannaschia, Octadecabacter and Ketogulonicigenium) ranged between 94.0 and 95.8%. DNA-DNA hybridizations and comparison of repetitive extragenic palindromic DNA-PCR (rep-PCR) fingerprinting patterns revealed that these strains are members of three distinct species. The isolates are Gram-negative, chemoheterotrophic, non-motile rods and their DNA G+C contents range from 59.4 to 66.4 mol%. Whole-cell fatty acid profiles are similar and the primary fatty acid in all the strains is 18 : 1 omega7c (74.1-87.7% of total). Genotypic results together with phenotypic characteristics allowed the differentiation of these species from related recognized species of the alpha-Proteobacteria and the strains are assigned to a new genus, Loktanella gen. nov., with three novel species: Loktanella salsilacus sp. nov. (type species), consisting of ten strains with LMG 21507T (=CIP 108322T) as type strain; Loktanella fryxellensis sp. nov., consisting of 12 strains with LMG 22007T (=CIP 108323T) as type strain; and Loktanella vestfoldensis sp. nov., consisting of four strains with LMG 22003T (=CIP 108321TT) as type strain.  (+info)

(8/183) Chemotaxis of Silicibacter sp. strain TM1040 toward dinoflagellate products.

The alpha-proteobacteria phylogenetically related to the Roseobacter clade are predominantly responsible for the degradation of organosulfur compounds, including the algal osmolyte dimethylsulfoniopropionate (DMSP). Silicibacter sp. strain TM1040, isolated from a DMSP-producing Pfiesteria piscicida dinoflagellate culture, degrades DMSP, producing 3-methylmercaptopropionate. TM1040 possesses three lophotrichous flagella and is highly motile, leading to a hypothesis that TM1040 interacts with P. piscicida through a chemotactic response to compounds produced by its dinoflagellate host. A combination of a rapid chemotaxis screening assay and a quantitative capillary assay were used to measure chemotaxis of TM1040. These bacteria are highly attracted to dinoflagellate homogenates; however, the response decreases when homogenates are preheated to 80 degrees C. To help identify the essential attractant molecules within the homogenates, a series of pure compounds were tested for their ability to serve as attractants. The results show that TM1040 is strongly attracted to amino acids and DMSP metabolites, while being only mildly responsive to sugars and the tricarboxylic acid cycle intermediates. Adding pure DMSP, methionine, or valine to the chemotaxis buffer resulted in a decreased response to the homogenates, indicating that exogenous addition of these chemicals blocks chemotaxis and suggesting that DMSP and amino acids are essential attractant molecules in the dinoflagellate homogenates. The implication of Silicibacter sp. strain TM1040 chemotaxis in establishing and maintaining its interaction with P. piscicida is discussed.  (+info)