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GC-MS structural characterization of fatty acids from marine aerobic anoxygenic phototrophic bacteria.

The FA composition of 12 strains of marine aerobic anoxygenic phototrophic bacteria belonging to the genera Erythrobacter, Roseobacter, and Citromicrobium was investigated. GC-MS analyses of different types of derivatives were performed to determine the structures of the main FA present in these organisms. All the analyzed strains contained the relatively rare 11-methyloctadec-12-enoic acid, and three contained 12-methyl-octadec-11-enoic acid, which has apparently never been reported before. High amounts of the very unusual octadeca-5,11-dienoic acid were present in 9 of the 12 strains analyzed. A FA containing a furan ring was detected in three strains. Analytical data indicated that this FA was 10,13-epoxy-11-methyloctadeca-10,12-dienoic acid. A very interesting enzymatic peroxidation of the allylic carbon 10 of cis-vaccenic acid was observed in three strains. Deuterium labeling and GC-MS analyses enabled us to demonstrate that this enzymatic process involves the initial dioxygenase-mediated formation of 10-hydroperoxyoctadec-11(cis)-enoic acid, which is then isomerized to 10-hydroperoxyoctadec-11(trans)-enoic acid and converted to the corresponding hydroxyacids and oxoacids. Different biosynthetic pathways were proposed for these different compounds.

Bacteria, Aerobic↗

Phylogenetic and functional diversity of bacterioplankton during Alexandrium spp. blooms.

The phylogenetic and functional diversity of the bacterioplankton assemblage associated with blooms of toxic Alexandrium spp. was studied in three harbours of the NW Mediterranean. Denaturing gradient gel electrophoresis and DNA sequence analysis revealed the presence of a bacterium within the Roseobacter clade related to the presence of Alexandrium cells. Phylogenetic diversity was affected by the presence of Alexandrium spp., geographic situation and seasonality. In contrast, functional diversity, assessed with Biolog plates, was clearly affected by seasonality, but not by the presence of Alexandrium, indicating that the presence of the bacterium associated with the blooms was not enough to modify the metabolic pattern of the bacterioplankton assemblage.

Animals↗

Nitric oxide reductases of prokaryotes with emphasis on the respiratory, heme-copper oxidase type.

The investigation of respiratory N-oxide reduction as part of a biogeochemical process sustained by prokaryotes has roots over a century ago and has laid the groundwork for microbial nitric oxide (NO) biology and recognizing that NO is of bioenergetic importance as an electron acceptor in anaerobic environments. NO is an obligatory respiratory substrate of nitrate- and nitrite-denitrifying prokaryotes that release nitrous oxide or dinitrogen as products. We witness currently a broadening of the scope of NO functionality and an increase in awareness that other heme-based NO-metabolizing systems contribute to the overall capability of the prokaryotic cell to cope with NO both in anaerobic and aerobic environments, including the pathogen-host interface. NO reduction of newly recognized physiological importance is catalyzed by the pentaheme nitrite reductase, cytochrome c', flavohemoglobin and flavorubredoxin. Respiratory NO reductases are heme-nonheme Fe proteins that can be classified either in a short-chain group, which are complexes with cytochrome c, or a long-chain group, which have a fused quinol oxidase domain. Even though NORs are not proton pumps, both reductase groups are structural homologues of heme-copper oxidases. As a unique case, the short-chain NOR of Roseobacter denitrificans acts on oxygen, based on a heme b3-CuB center. In turn, certain heme-copper oxidases have significant turnover rates with NO. NOR mechanisms have been proposed from oxidase active site chemistry. Besides being a respiratory substrate, NO is also a signaling molecule that triggers gene expression of the principal components of NO respiration by members of the Crp-Fnr superfamily of transcription regulators.

Archaeal Proteins↗

Molecular microbial diversity of a soil sample and detection of ammonia oxidizers from Cape Evans, Mcmurdo Dry Valley, Antarctica.

The aim of our study was to estimate the uncultured eubacterial diversity of a soil sample collected below a dead seal, Cape Evans, McMurdo, Antarctica by an SSU rDNA gene library approach. Our study by sequencing of clones from SSU rDNA gene library approach revealed high diversity in the soil sample from Antarctica. More than 50% of clones showed homology to Cytophaga-Flavobacterium-Bacteroides group; sequences also belonged to alpha, beta, gamma proteobacteria, Thermus-Deinococcus and high GC gram-positive group; Phylogenetic analysis of the SSU rDNA clones showed the presence of species belonging to Cytophaga spp., Vitellibacter vladivostokensis, Aequorivita lipolytica, Aequorivita crocea, Flavobacterium spp., Flexibacter sp., Subsaxibacter broadyi, Bacteroidetes, Roseobacter sp., Sphingomonas baekryungensis, Nitrosospira sp., Nitrosomonas cryotolerans, Psychrobacter spp., Chromohalobacter sp., Psychrobacter okhotskensis, Psychrobacter fozii, Psychrobacter urativorans, Rubrobacter radiotolerans, Marinobacter sp., Rubrobacteridae, Desulfotomaculum aeronauticum and Deinococcus sp. The presence of ammonia oxidizing bacteria in Antarctica soil was confirmed by the presence of the amoA gene. Phylogenetic analysis revealed grouping of clones with their respective groups.

Ammonia↗

Phylogenetic diversity and activity of aerobic heterotrophic bacteria from a hypersaline oil-polluted microbial mat.

The diversity and function of aerobic heterotrophic bacteria (AHB) in cyanobacterial mats have been largely overlooked. We used culture-dependent and molecular techniques to explore the species diversity, degradative capacities and functional guilds of AHB in the photic layer (2mm) of an oil-polluted microbial mat from Saudi Arabia. Enrichment isolation was carried out at different salinities (5% and 12%) and temperatures (28 and 45 degrees C) and on various substrates (acetate, glycolate, Spirulina extract and crude oils). Counts of most probable number showed a numerical abundance of AHB in the range of 1.15-8.13x10(6) cellsg(-1) and suggested the presence of halotolerant and thermotolerant populations. Most of the 16S rRNA sequences of the obtained clones and isolates were phylogenetically affiliated to the groups Gammaproteobacteria, Bacteriodetes and Alphaproteobacteria. Groups like Deltaproteobacteria, Verrucomicrobia, Planctomycetes, Spirochaetes, Acidobacteria and Deinococcus-Thermus were only detected by cloning. The strains isolated on acetate and glycolate belonged to the genera Marinobacter, Halomonas, Roseobacter and Rhodobacter whereas the strains enriched on crude oil belonged to Marinobacter and Alcanivorax. Members of the Bacteriodetes group were only enriched on Spirulina extract indicating their specialization in the degradation of cyanobacterial dead cells. The substrate spectra of representative strains showed the ability of all AHB to metabolize cyanobacterial photosynthetic and fermentation products. However, the unique in situ conditions of the mat apparently favored the enrichment of versatile strains that grew on both the cyanobacterial exudates and the hydrocarbons. We conclude that AHB in cyanobacterial mats represent a diverse community that plays an important role in carbon-cycling within microbial mats.

Bacteria, Aerobic↗

Tateyamaria omphalii gen. nov., sp. nov., an alpha-Proteobacterium isolated from a top shell Omphalius pfeifferi pfeifferi.

A Gram-negative, strictly aerobic, coccoid to short rod-shaped marine bacterium strain MKT107(T) was isolated from the molluscan top shell Omphalius pfeifferi pfeifferi collected on the coast of Japan. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain MKT107(T) constitutes a new lineage in alpha-Proteobacteria related to the genera Nereida, Roseobacter, Staleya, Oceanibulbus and Sulfitobacter. Strain MKT107(T) was found to require salt for its growth and to be mesophilic. It contained 18:1omega7c and 16:0 as major cellular fatty acids and 3-OH 10:0 and 3-OH 12:0 as hydroxy fatty acids. The DNA base composition of the isolate was 61.6 mol% G+C. The major quinone was Q-10. Sufficient differences existed to distinguish this strain from currently recognized bacterial genera. Therefore, the isolate is classified as representing a new genus and species, Tateyamaria omphalii gen. nov., sp. nov. (type strain MKT107(T) =IAM 15108(T) =KCTC 12333(T); GenBank accession no. AB193438).

Alphaproteobacteria↗

Oxygen dependence of photosynthetic electron transport in a bacteriochlorophyll-containing rhizobium.

Bacteriochlorophyll-containing rhizobia, which form nitrogen-fixing nodules on the stems and roots of the legume Aeschynomene, grow photosynthetically only in the presence of oxygen or auxiliary electron acceptors. We show that, in whole cells of the Rhizobium strain BTAi 1, a single-turnover excitation flash photooxidized c-type cytochrome under aerobic but not anaerobic conditions. Light-induced fluorescence yield changes show that under anaerobic conditions, the primary acceptor quinone, Q(A), is predominantly in the reduced state and so unable to accept electrons. Thus, as is the case for the aerobic photosynthetic bacterium Roseobacter denitrificans, over-reduction of Q(A) likely prohibits photosynthesis under anaerobic conditions.

Aerobiosis↗

Analysis of community composition of biofilms in a submerged filter system for the removal of ammonia and phenol from industrial wastewater.

The bacterial diversity of a submerged filter, used for the removal of ammonia and phenol from an industrial wastewater with high salinity, was studied by a cultivation-independent approach based on PCR/TGGE (temperature-gradient gel electrophoresis). The wastewater treatment plant (laboratory scale) combined the nitrification and denitrification processes and consisted of two separated columns (one anoxic and one aerated) connected through a valve. The spatial diversity of bacterial communities in the plant biofilms was analysed by taking samples at four different heights in the system. TGGE profiles of PCR-amplified sequences of the 16 S rRNA gene (V3-hypervariable region) showed significant variations of the bacterial diversity, mainly depending on the concentration of O(2) along the system. Several bands separated by TGGE were reamplified and sequenced, in order to explore the composition of the microbial communities in the biofilms. Most of the sequenced bands (10 out of 13) were closely related to the 16 S rRNA gene of marine alpha-proteobacteria, mainly grouping in the periphery of the genus Roseobacter. Other sequences were related to those of gamma-proteobacteria, the nitrite oxidizer Nitrospira marina and anaerobic phenol-degrading bacteria of the Desulfobacteraceae.

Ammonia↗

Induction of larval settlement in the serpulid polychaete Hydroides elegans (Haswell): role of bacterial extracellular polymers.

Larval settlement in the marine polychaete Hydroides elegans is effectively mediated upon contact with the surface of marine bacterial films. Using the bacterium Roseobacter litoralis as a model strain, the effect of bacterial extracellular polymers (exopolymers) on larval settlement of H. elegans was investigated. Bioassays with exopolymer fractions dissociated from bacterial films evoked the initial stages of the larval settlement process, i.e. larvae slowed down, secreted a mucous thread and crawled over the surface. This response is typical of larvae that encounter an attractive bacterial film. In contrast, bioassays with exopolymers in association with UV-irradiated, metabolically inactive bacterial films evoked complete settlement. However, the percentage of responding larvae was negatively correlated with the magnitude of UV-dosage. Since UV energy crosslinks both intra- and extracellular proteinaceous components, it could not be distinguished whether the decrease in larval settlement was due to a modification of proteinaceous components of exopolymers or due the elimination of cellular activity. Nevertheless, the results ascribe bacterial exopolymers the role of an indicator of substratum suitability and provide evidence that the polysaccharide moiety of exopolymers does not complement this effect.

Animals↗

Sagittula stellata gen. nov., sp. nov., a lignin-transforming bacterium from a coastal environment.

A numerically important member of marine enrichment cultures prepared with lignin-rich, pulp mill effluent was isolated. This bacterium was gram negative and rod shaped, did not form spores, and was strictly aerobic. The surfaces of its cells were covered by blebs or vesicles and polysaccharide fibrils. Each cell also had a holdfast structure at one pole. The cells formed rosettes and aggregates. During growth in the presence of lignocellulose or cellulose particles, cells attached to the surfaces of the particles. The bacterium utilized a variety of monosaccharides, disaccharides, amino acids, and volatile fatty acids for growth. It hydrolyzed cellulose, and synthetic lignin preparations were partially solubilized and mineralized. As determined by 16S rRNA analysis, the isolate was a member of the alpha subclass of the phylum Proteobacteria and was related to the genus Roseobacter. A signature secondary structure of the 16S rRNA is proposed. The guanine-plus-cytosine content of the genomic DNA was 65.0 mol%. On the basis of the results of 16S rRNA sequence and phenotypic characterizations, the isolate was sufficiently different to consider it a member of a new genus. Thus, a novel genus and species, Sagittula stellata, are proposed; the type strain is E-37 (= ATCC 700073).

Bacterial Adhesion↗

Antarctobacter heliothermus gen. nov., sp. nov., a budding bacterium from hypersaline and heliothermal Ekho Lake.

Four Gram-negative, aerobic, pointed and budding bacteria were isolated from various depths of the hypersaline, heliothermal and meromictic Ekho Lake (Vestfold Hills, East Antarctica). The cells contained storage granules and formed rosettes. Daughter cells may be motile. Growth required sodium ions. Nitrate was reduced to nitrite, and dissimilatory reduction of nitrite was possible. DNase and gelatinase were produced. Glutamate was metabolized with and without an additional source of combined nitrogen. The most abundant fatty acid was C18:1; other fatty acids present in lower concentrations were C12:1 3-OH, C16:1, C16:0, C18:0 and C19:0 cyc. The main polar lipids were phosphatidylglycerol and phosphatidylcholine. The DNA base composition was 62.3-62.8 mol% G + C. 16S rDNA sequence comparisons showed the isolates to be phylogenetically related to the genera Sagittula and Roseobacter. Morphological, physiological and genotypic differences to these and distinct characteristics supported the description of a new genus and a new species, Antarctobacter heliothermus gen. nov., sp. nov. The type strain is EL-219T (= DSM 11445T).

Antarctic Regions↗

Roseovarius tolerans gen. nov., sp. nov., a budding bacterium with variable bacteriochlorophyll a production from hypersaline Ekho Lake.

Eight Gram-negative, aerobic, pointed and budding bacteria were isolated from various depths of the hypersaline, heliothermal and meromictic Ekho Lake (Vestfold Hills, East Antarctica). The cells contained storage granules and daughter cells could be motile. Bacteriochlorophyll a was sometimes produced, but production was repressed by constant dim light. The strains tolerated a wide range of temperature, pH, concentrations of artificial seawater and NaCl, but had an absolute requirement for sodium ions. Glutamate was metabolized with and without an additional source of combined nitrogen. The dominant fatty acid was C18:1; other characteristic fatty acids were C18:2, C12:0 2-OH, C12:1 3-OH, C16:1, C16:0 and C18:0. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The DNA G+C base composition was 62-64 mol%. 16S rRNA gene sequence comparisons showed that the isolates were phylogenetically close to the genera Antarctobacter, 'Marinosulfonomonas', Octadecabacter, Sagittula, Sulfitobacter and Roseobacter. Morphological, physiological and genotypic differences to these previously described and distinct genera support the description of a new genus and a new species, Roseovarius tolerans gen. nov., sp. nov. The type strain is EL-172T (= DSM 11457T).

Bacteriochlorophylls↗

Staleya guttiformis gen. nov., sp. nov. and Sulfitobacter brevis sp. nov., alpha-3-Proteobacteria from hypersaline, heliothermal and meromictic antarctic Ekho Lake.

Two Gram-negative, aerobic, pointed and budding bacteria were isolated from various depths of hypersaline, heliothermal and meromictic Ekho Lake (Vestfold Hills, East Antarctica). 16S rRNA gene sequence comparisons show the isolates to be phylogenetically close to the genera Sulfitobacter and Roseobacter. Cells can be motile and contain storage granules. Sulfite addition does not stimulate growth. Isolate EL-38T can produce bacteriochlorophyll a and has a weak requirement for sodium ions; polar lipids include phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified amino lipid, but not diphosphatidylgycerol. The dominant fatty acid is 18:1omega7c; other characteristic fatty acids are 3-OH 10:0, 3-OH 14:1, 16:0, 18:0, 18:2 and 19:1. The DNA base composition is 55.0-56.3 mol% G+C. Isolate EL-162T has an absolute requirement for sodium ions. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified amino lipid are present in the polar lipids. Dominant fatty acids of this isolate are 18:1omega7c and 18:1omega9c as well as 18:2 which is present as two isomers. Other characteristic fatty acids are 3-OH 10:0, 3-OH 14:1, 16:0 and 18:0. The G+C content is 57.9-58.1 mol%. Morphological, physiological and genotypic differences from related, thus far known genera support the description of Staleya guttiformis gen. nov. and sp. nov. with EL-38T (= DSM 11458T) as the type strain and of Sulfitobacter brevis sp. nov. with the type strain EL-162T (= DSM 11443T).

Alphaproteobacteria↗

Taxonomic characterization of Ketogulonigenium vulgare gen. nov., sp. nov. and Ketogulonigenium robustum sp. nov., which oxidize L-sorbose to 2-keto-L-gulonic acid.

Four bacterial strains that oxidize L-sorbose to 2-keto-L-gulonic acid, a key intermediate in the synthesis of vitamin C, were isolated from soils of geographically distinct locations. All were Gram-negative, facultatively anaerobic, chemoheterotrophic rods. Comparative analysis revealed nearly identical 16S rDNA sequences amongst them (99.7-100% identical) and identified them as members of the alpha-subclass of the Proteobacteria. Phylogenetic analysis identified the closest taxonomically defined genus as Roseobacter (92.1-92.8% identical). On the basis of phylogenetic, phenotypic and genotypic analyses, a new genus is proposed, Ketogulonigenium gen. nov. Based upon these analyses, we also propose the reclassification of strain DSM 4025TP, originally identified as Gluconobacter oxydans, to the genus Ketogulonigenium. Two species are proposed: the type species Ketogulonigenium vulgare gen. nov., sp. nov., consisting of strains 62A-12APP, 266-13BPP and the type strain K. vulgare DSM 4025TP, and Ketogulonigenium robustum gen. nov., sp. nov., consisting of the type strain K. robustum X6LTP (= NRRL B-21627 = KCTC 0858BP). The species affiliation of the fifth strain (291-19PP) remains unresolved.

Base Sequence↗

Leisingera methylohalidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide.

A marine methylotroph, designated strain MB2T, was isolated for its ability to grow on methyl bromide as a sole carbon and energy source. Methyl chloride and methyl iodide also supported growth, as did methionine and glycine betaine. A limited amount of growth was observed with dimethyl sulfide. Growth was also noted with unidentified components of the complex media marine broth 2216, yeast extract and Casamino acids. No growth was observed on methylated amines, methanol, formate, acetate, glucose or a variety of other substrates. Growth on methyl bromide and methyl iodide resulted in their oxidation to CO2 with stoichiometric release of bromide and iodide, respectively. Strain MB2T exhibited growth optima at NaCl and Mg2+ concentrations similar to that of seawater. Phylogenetic analysis of the 16S rDNA sequence placed this strain in the alpha-Proteobacteria in proximity to the genera Ruegeria and Roseobacter. It is proposed that strain MB2T (= ATCC BAA-92T = DSM 14336T) be designated Leisingera methylohalidivorans gen. nov., sp. nov..

Alphaproteobacteria↗

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.

Base Composition↗

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).

Acids↗

Jannaschia cystaugens sp. nov., an Alexandrium (Dinophyceae) cyst formation-promoting bacterium from Hiroshima Bay, Japan.

Heterotrophic bacteria isolated from water samples taken from Hiroshima Bay, Japan, and referred to as Alexandrium (Dinophyceae) cyst formation-promoting bacteria, were assigned to the Roseobacter-Sulfitobacter-Silicibacter group within the alpha-Proteobacteria on the basis of nearly complete 16S rRNA gene sequences. Phylogenetic analyses showed that two strains, CFPB-A9T and CFPB-A5, are closely related to each other and that their closest relative was Jannaschia helgolandensis (95.9 % sequence similarity). These strains were Gram-negative, motile, obligately aerobic rods that required sodium ions and 2-7 % sea salts for growth and did not produce bacteriochlorophyll a. Their optimal growth temperature was 25-30 degrees C. The strains had Q-10 as the dominant respiratory quinone. Primary cellular fatty acid in both strains was 18 : 1omega7c. The DNA G + C contents of strains CFPB-A9T and CFPB-A5 were 59.1 and 59.2 mol%, respectively. Based on physiological, biological, chemotaxonomic and phylogenetic data, the strains are considered to represent a novel species, Jannaschia cystaugens sp. nov., with type strain CFPB-A9T (= LMG 22015T = NBRC 100362T).

Bacteriochlorophyll A↗