evolution of the regulatory isozymes of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase present in the escherichia coli genealogy.the evolutionary history of isozymes for 3-deoxy-d-arabino-heptulosonate 7-phosphate (dahp) synthase has been constructed in a phylogenetic cluster of procaryotes (superfamily b) that includes escherichia coli. members of superfamily b that have been positioned on a phylogenetic tree by oligonucleotide cataloging possess one or more of four distinct isozymes of dahp synthase. dahp synthase-0 is insensitive to feedback inhibition, while dahp synthase-tyr, dahp synthase-trp, and dahp synthase-phe ...19862867085
the recent evolutionary origin of the phenylalanine-sensitive isozyme of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase in the enteric lineage of bacteria.evolutionary events that generated the three regulatory isozymes of 3-deoxy-d-arabino-heptulosonate 7-phosphate (dahp) synthase present in contemporary strains of escherichia coli have been proposed recently [ahmad et al. (1986) j bacteriol 165:146-154]. the phylogenetic subdivision of gram-negative prokaryotes studied (superfamily b) includes enteric bacteria, an oceanospirillum cluster, pseudomonad group i (e.g., pseudomonas aeruginosa), pseudomonad group v (e.g., xanthomonas), and the acineto ...19872888901
the phylogenetic origin of the bifunctional tyrosine-pathway protein in the enteric lineage of bacteria.because bifunctional enzymes are distinctive and highly conserved products of relatively infrequent gene-fusion events, they are particularly useful markers to identify clusters of organisms at different hierarchical levels of a phylogenetic tree. within the subdivision of gram-negative bacteria known as superfamily b, there are two distinctive types of tyrosine-pathway dehydrogenases: (1) a broad-specificity dehydrogenase (recently termed cyclohexadienyl dehydrogenase [cdh]) that can utilize ei ...19883386529
balneatrix alpica gen. nov., sp. nov., a bacterium associated with pneumonia and meningitis in a spa therapy 1987, an outbreak of pneumonia and meningitis caused by an unknown bacterium occurred in a spa therapy centre. nine isolates of this pathogen constituted a tight dna hybridization group. rrna-dna hybridization and 16s rrna sequencing showed that the studied bacteria represented a new branch in superfamily ii (= gamma subclass) of the proteobacteria, close to the genus oceanospirillum. the new bacterium was highly polymorphic and, in young cultures, had curved gram-negative cells, motile by po ...19938327781
genetic diversity of the biofilm covering montacuta ferruginosa (mollusca, bivalvia) as evaluated by denaturing gradient gel electrophoresis analysis and cloning of pcr-amplified gene fragments coding for 16s rrna.the shell of the bivalve montacuta ferruginosa, a symbiont living in the burrow of an echinoid, is covered with a rust-colored biofilm. this biofilm includes different morphotypes of bacteria that are encrusted with a mineral rich in ferric ion and phosphate. the aim of this research was to determine the genetic diversity and phylogenetic affiliation of the biofilm bacteria. also, the possible roles of the microorganisms in the processes of mineral deposition within the biofilm, as well as their ...19989726898
marinospirillum gen. nov., with descriptions of marinospirillum megaterium sp. nov., isolated from kusaya gravy, and transfer of oceanospirillum minutulum to marinospirillum minutulum comb. nov.two strains of helical, halophilic, gram-negative, heterotrophic bacteria were isolated from kusaya gravy which is a traditional japanese fermented brine. these strains were motile by means of a single polar or bipolar tuft flagellum. they had a large cell size, were helical, formed coccoid bodies, were microaerophilic and had quinone type q-8. the dna g + c content of the strains was 44-45 mol %. a detailed investigation of the phenotypic, chemotaxonomic and phylogenetic characteristics of the ...19989828435
polycyclic aromatic hydrocarbon degradation by a new marine bacterium, neptunomonas naphthovorans gen. nov., sp. nov.two strains of bacteria were isolated from creosote-contaminated puget sound sediment based on their ability to utilize naphthalene as a sole carbon and energy source. when incubated with a polycyclic aromatic hydrocarbon (pah) compound in artificial seawater, each strain also degraded 2-methylnaphthalene and 1-methylnaphthalene; in addition, one strain, nag-2n-113, degraded 2,6-dimethylnaphthalene and phenanthrene. acenaphthene was not degraded when it was used as a sole carbon source but was d ...19999872786
determination of total protein content of bacterial cells by sypro staining and flow assay has been developed for measuring protein biomass of marine planktonic bacteria by flow cytometry. the method was calibrated by using five species of bacteria (an arcobacter sp., a cytophaga sp., an oceanospirillum sp., a pseudoalteromonas sp., and a vibrio sp.) recently isolated from seawater samples and grown in culture at different temperatures. the intensity of sypro-protein fluorescence of these bacteria strongly correlated with their total protein content, measured by the bicinchon ...199910388732
artificial neural network based identification of environmental bacteria by gas-chromatographic and electrophoretic data.chemotaxonomic identification techniques are powerful tools for environmental micro-organisms, for which poor diagnostic schemes are available. whole cellular fatty acid methyl esters (fame) content is a stable bacterial profile, the analysis method is rapid, cheap, simple to perform and highly automated. whole-cell protein is an even more powerful tool because it yields information at or below the species level. the description of new species and genera and subsequent continuous rearrangement p ...200011084227
growth patterns of two marine isolates: adaptations to substrate patchiness?during bottle incubations of heterotrophic marine picoplankton, some bacterial groups are conspicuously favored. in an earlier investigation bacteria of the genus pseudoalteromonas rapidly multiplied in substrate-amended north sea water, whereas the densities of oceanospirillum changed little (h. eilers, j. pernthaler, and r. amann, appl. environ. microbiol. 66:4634-4640, 2000). we therefore studied the growth patterns of two isolates affiliating with pseudoalteromonas and oceanospirillum in bat ...200111526008
phylogenetic relationships of the helical-shaped bacteria in the alpha proteobacteria inferred from 16s rdna sequences.16s ribosomal rna gene sequences from seven strains of aquaspirillum peregrinum, aqu. itersonii, aqu. polymorphum, and oceanospirillum pusillum were compared with homologous sequences from other members of helical-shaped bacteria. the bootstrapped neighbor-joining tree, inferred from 887 aligned sites, placed the spirillum taxa assigned to aquaspirillum, oceanospirillum, azospirillum, magnetospirillum, rhodospirillum, and rhodocista of the proteobacteria in seven clusters of alpha proteobacteria ...199712501339
saccharospirillum impatiens gen. nov., sp. nov., a novel gamma-proteobacterium isolated from hypersaline ekho lake (east antarctica).five gram-negative, motile, aerobic to microaerophilic spirilla were isolated from various depths of the hypersaline, heliothermal and meromictic ekho lake (east antarctica). the strains are oxidase- and catalase-positive, metabolize a variety of sugars and carboxylic acids and have an absolute requirement for sodium ions. the predominant fatty acids of the organisms are c(16 : 1)omega7c, c(16 : 0) and c(18 : 1)omega7c, with c(10 : 1))3-oh, c(10 : 0) 3-oh, c(12 : 0) 3-oh, c(14 : 1)3-oh, c(14 : 0 ...200312807182
ghp, a new c-type green heme protein from halochromatium salexigens and other proteobacteria.we have isolated a minor soluble green-colored heme protein (ghp) from the purple sulfur bacterium, halochromatium salexigens, which contains a c-type heme. a similar protein has also been observed in the purple bacteria allochromatium vinosum and rhodopseudomonas cryptolactis. this protein has wavelength maxima at 355, 420, and 540 nm and remains unchanged upon addition of sodium dithionite or potassium ferricyanide, indicating either an unusually low or high redox potential, respectively. the ...200616817906
phylogenetic study of the genus oceanospirillum based on 16s rrna and gyrb genes: emended description of the genus oceanospirillum, description of pseudospirillum gen. nov., oceanobacter gen. nov. and terasakiella gen. nov. and transfer of oceanospirillum jannaschii and pseudomonas stanieri to marinobacterium as marinobacterium jannaschii comb. nov. and marinobacterium stanieri comb. no.the phylogenetic relationships of oceanospirillum strains were analysed by using the nucleotide sequences of 16s rrna and gyrb genes. results from sequence analysis demonstrated that the oceanospirillum core group consisted of four species, oceanospirillum linum, oceanospirillum maris, oceanospirillum beijerinckii and oceanospirillum multiglobuliferum, with enough distance to separate them as different species. however, four other oceanospirillum species occupied taxonomic positions separate fro ...200212054233
isolation from coastal sea water and characterization of bacterial strains involved in non-ionic surfactant degradation.a bacterial community degrading branched alkylphenol ethoxylate (ape) was selected from coastal sea water intermittently polluted by urban sewage. this community degraded more than 99% of a standard surfactant, triton x 100, but i.r. analysis of the remaining compound showed the accumulation of ape2 (alkylphenol with a two units length ethoxylated chain) which seemed very recalcitrant to further biodegradation. twenty-five strains were isolated from this community, essentially gram negative and ...19969144968
microbulbifer hydrolyticus gen. nov., sp. nov., and marinobacterium georgiense gen. nov., sp. nov., two marine bacteria from a lignin-rich pulp mill waste enrichment community.two numerically important bacteria in marine pulp mill effluent enrichment cultures were isolated. these organisms were gram-negative, rod-shaped, strictly aerobic bacteria. isolate ire-31t (t = type strain) produced hydrolytic enzymes for the breakdown of cellulose, xylan, chitin, gelatin, and tween 80. it also utilized a variety of monosaccharides, disaccharides, amino acids, and volatile fatty acids for growth. isolate kw-40t did not utilize natural polymers, but it could grow on a variety of ...19979103623
automated systems for identification of heterotrophic marine bacteria on the basis of their fatty acid composition.the fatty acid methyl ester composition of a total of 71 marine strains representing the genera alteromonas, deleya, oceanospirillum, and vibrio was determined by gas-liquid chromatographic analysis. over 70 different fatty acids were found. the predominant fatty acids were 16:0, 16:1 cis 9, summed-in-feature (sif) 4 (15:0 iso 2oh and/or 16:1 trans 9) and sif 7 (18:1 cis 11, 18:1 trans 9, and/or 18:1 trans 6) for all the strains considered, but minor quantitative variations could be used to dist ...199616535340
coral-associated bacterial assemblages: current knowledge and the potential for climate-driven impacts.the importance of associations between microorganisms and their invertebrate hosts is becoming increasingly apparent. an emerging field, driven by the necessity to understand the microbial relationships that both maximize coral health and cause coral disease, is the study of coral-bacteria interactions. in this article, we review our current understanding of the diversity, specificity, development, and functions of coral-associated bacteria. we also summarize what is known regarding the role of ...201021558231
amphritea atlantica gen. nov., sp. nov., a gammaproteobacterium from the logatchev hydrothermal vent field.a novel gram-negative, motile, aerobic rod-shaped bacterium was isolated from a bathymodiolus sp. specimen collected from the logatchev hydrothermal vent field at the mid-atlantic ridge. the novel strain, m41(t), was catalase- and oxidase-positive and metabolised various carbohydrates and amino acids. it grew well in marine broth with an optimal growth temperature of 31 degrees c to 34 degrees c (range 4-40 degrees c) and salinity requirement of 3% (range 0.3-9%). the ph range for growth was ph ...200818175678
phylogenetic composition of bacterioplankton assemblages from the arctic ocean.we analyzed the phylogenetic composition of bacterioplankton assemblages in 11 arctic ocean samples collected over three seasons (winter-spring 1995, summer 1996, and summer-fall 1997) by sequencing cloned fragments of 16s rrna genes. the sequencing effort was directed by denaturing gradient gel electrophoresis (dgge) screening of samples and the clone libraries. sequences of 88 clones fell into seven major lineages of the domain bacteria: alpha(36%)-, gamma(32%)-, delta(14%)-, and epsilon(1%)-p ...200211823184
identification of bacterial cells by chromosomal painting.chromosomal painting is a technique for the microscopic localization of genetic material. it has been applied at the subcellular level to identify regions of eukaryotic chromosomes. here we describe the development of bacterial chromosomal painting (bcp), a related technology for the identification of bacterial cells. purified genomic dnas from six bacterial strains were labeled by nick translation with the fluorochrome fluor-x, cy3, or cy5. the average size of the labeled fragments was ca. 50 t ...19979055426
characterization of 16s rrna genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing, fermentative, and sulfide-oxidizing bacteria.oil field bacteria were characterized by cloning and sequencing of pcr-amplified 16s rrna genes. a variety of gram-negative, sulfate-reducing bacteria was detected (16 members of the family desulfovibrionaceae and 8 members of the family desulfobacteriaceae). in contrast, a much more limited number of anaerobic, fermentative, or acetogenic bacteria was found (one clostridium sp., one eubacterium sp., and one synergistes sp.). potential sulfide oxidizers and/or microaerophiles (thiomicrospira, ar ...19968633860
marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium.on the basis of phenotypical characteristics and analysis of 16s rrna sequence, a new species belonging to a new genus is described, and the name marinobacter hydrocarbonoclasticus is proposed. this organism, isolated from mediterranean seawater near a petroleum refinery, is a gram-negative, aerobic, rod-shaped bacterium. it grows at nacl concentrations of 0.08 to 3.5 m and uses various hydrocarbons as the sole source of carbon and energy. its dna has a guanine-plus-cytosine content of 52.7 mol% ...19921382536
phylogenetic analysis of bacterial communities associated with leaves of the seagrass halophila stipulacea by a culture-independent small-subunit rrna gene approach.the phylogenetic diversity of the bacterial community associated with leaves of the marine plant halophila stipulacea in the northern gulf of elat was examined by 16s rrna gene (rdna) sequence analyses of a clone library. for 59 clones corresponding to 51 ardra (amplified rdna restriction analysis) groups, the sequence of approximately 1 kb was determined, and the fraction of the corresponding ardra groups of the leaf library was calculated. the class proteobacteria was represented by 62.6% of t ...200010790514
endozoicomonas elysicola gen. nov., sp. nov., a gamma-proteobacterium isolated from the sea slug elysia ornata.a gram-negative, strictly aerobic, rod-formed bacterium, strain mkt110(t), was isolated from a mollusk, the sea slug elysia ornata collected in seawater off the coast of izu-miyake island, japan at a depth of 15m. comparative 16s rrna gene sequences analysis indicated that the isolate mkt110(t) constituted a novel lineage in gamma-proteobacteria related to the genera zooshikella, oceanospirillum, microbulbifer, marinobacter, saccharospirillum and pseudomonas. the strain mkt110(t) was closely rel ...200716904280
reinekea marinisedimentorum gen. nov., sp. nov., a novel gammaproteobacterium from marine coastal sediments.a gram-negative, oxidase- and catalase-positive, rod-shaped bacterium, designated strain kmm 3655(t), was isolated from a coastal marine sediment sample. the novel bacterium required sodium ions for growth and grew between 0.5 and 5 % nacl and at 4-37 degrees c, but not at 40 degrees c. it reduced nitrate, formed acids from glucose under aerobic and anaerobic conditions, utilized a limited spectrum of organic substrates and did not produce gelatinase, caseinase, amylase or chitinase. the major i ...200415143005
thalassospira lucentensis gen. nov., sp. nov., a new marine member of the alpha-proteobacteria.a novel bacterium from the mediterranean sea was isolated under oligotrophic conditions at in situ temperature after prolonged continuous culture. the isolates were initially characterized by partial 16s rrna gene sequencing. similarity searches of one of the isolates, qmt2t, indicated high sequence identity to the well-characterized rhodospirillum rubrum, [aquaspirillum] itersonii and [oceanospirillum] pusillum micro-organisms, which are representatives of the alpha-subclass of the proteobacter ...200212148640
olii, a unique restriction endonuclease that recognizes the discontinuous sequence 5'-cacnn ngtg-3'.a new type ii restriction endonuclease designated oli:i has been partially purified from the halophilic bacterium oceanospirillum linum 4-5d. oli:i recognizes the interrupted hexanucleotide palindrome 5'-cacnn nngtg-3' and cleaves it in the center generating blunt-ended dna fragments.200111239007
succession of pelagic marine bacteria during enrichment: a close look at cultivation-induced shifts.enrichment experiments with north sea bacterioplankton were performed to test if rapid incubation-induced changes in community structure explain the frequent isolation of members of a few particular bacterial lineages or if readily culturable bacteria are common in the plankton but in a state of dormancy. a metabolic inhibitor of cell division (nalidixic acid [na]) was added to substrate-amended (s+) and unamended (s-) grazer-free seawater samples, and shifts in community composition and per cel ...200011055904
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