Degenerate PCR primers, UP-1 and UP-2r, for the amplification of DNA gyrase subunit B genes (gyrB) were designed by using consensus amino acid sequences gyrases from Escherichia coli, Pseudomonas putida, Bacillus subtilis. In addition to degenerate sequences, these primers have at 5' end which allow direct sequencing amplified products. With segments predicted size a variety gram-negative gram-positive genera. The nucleotide gyrB three P. putida strains determined directly fragments. base...

Phylogenetic analysis of the genus Pseudomonas was conducted by using combined gyrB and rpoD nucleotide sequences 31 validly described species (a total 125 strains). strains diverged into two major clusters designated intrageneric cluster I (IGC I) II II). IGC further split subclusters, 'P. aeruginosa complex', which included P. aeruginosa, alcaligenes, citronellolis, mendocina, oleovorans pseudoalcaligenes, stutzeri balearica stutzeri. three subclusters that were putida syringae complex'...

Bacterial strains were isolated from sponge and green algae which collected on the coast of Japan Palau. The phylogenetic relationships these isolates among marine species Cytophaga-Flavobacterium-Bacteroides complex analysed by using their gyrB nucleotide sequences translated peptide (GyrB) in addition to 16S rDNA sequences. These closely related previously characterized Flexibacter species, [Flexibacter] maritimus ovolyticus. are distantly flexilis, type genus Flexibacter, phylogenetically...

A moderately thermophilic chemoheterotrophic bacterium, strain Mat9-16(T), was isolated from microbial mats developed in hot spring water streams Yumata, Nagano, Japan. Cells of Mat9-16(T) were strictly anaerobic, Gram-stain-negative, non-sporulating, non-motile and short to long rods (2.0-15.5 mum length). Strain grew fermentatively with optimum growth at 45 degrees C, pH 7.0-7.5 1 % NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene revealed that affiliated an uncultivated...

The biodegradation of four different crude oil samples, namely, Arabian light, Dubai, Maya, and Shengli, by Acinetobacter sp. T4 a microbial consortium called SM8 was examined. exhibited higher activity than for the all samples. degree components differed according to oil, saturated fraction being more susceptible aromatic in extent found be order light > Dubai ≥ Maya = Shengli; samples with API gravity biodegradation. Saturated compounds smaller molecular weight were preferentially degraded...

ABSTRACT DNA was isolated from phenol-digesting activated sludge, and partial fragments of the 16S ribosomal (rDNA) gene encoding largest subunit multicomponent phenol hydroxylase (LmPH) were amplified by PCR. An analysis temperature gradient gel electrophoresis (TGGE) demonstrated that two major rDNA bands (bands R2 R3) LmPH P2 P3) appeared after sludge became acclimated to phenol. The nucleotide sequences these determined. In parallel, bacteria direct plating or enrichment either in batch...

ABSTRACT To identify the bacteria that play a major role in aerobic degradation of petroleum polynuclear aromatic hydrocarbons (PAHs) marine environment, were enriched from seawater by using 2-methylnaphthalene, phenanthrene, or anthracene as carbon and energy source. We found members genus Cycloclasticus became predominant enrichment cultures. The strains isolated this study could grow on crude oil degraded PAH components oil, including unsubstituted substituted naphthalenes,...

Summary We found that bacteria closely related to Alcanivorax became a dominant bacterial population in petroleum‐contaminated sea water when nitrogen and phosphorus nutrients were supplied adequate quantity. The predominance of was demonstrated under three experimental conditions: (i) batch cultures containing heavy oil; (ii) columns packed with oil‐coated gravel undergoing continuous flow; (iii) large‐scale tidal flux reactor mimics beach cycles fresh water. These results suggest are major...

Phylogenetic analysis of 20 Pseudomonas strains (Pseudomonas putida, fluorescens and chlororaphis) was conducted by using the nucleotide sequences genes for 16S rRNA, DNA gyrase B subunit (gyrB) RNA polymerase σ70factor (rpoD), which have been determined direct sequencing PCR-amplified fragments. On basis gyrB rpoD sequences, these were split into two major clusters: one including type strain P. putida all biovar A other strains, chlororaphis strain. In phylogenetic tree reconstructed from...

Abstract Dioxygenases that catalyze the cleavage of aromatic ring are classified into two groups according to their mode fission. Substrates ring-cleavage dioxygenases usually contain hydroxyl on adjacent carbons, and intradiol enzymes cleave between these groups. Extradiol in contrast one hydroxylated carbon its nonhydroxylated carbon. In this study, we determined complete nucleotide sequence nahC, structural gene for 1,2-dihydroxynaphthalene dioxygenase encoded NAH7 plasmid Pseudomonas...

Variation in the adhesive protein gene sequences of Mytilus edulis, M. galloprovincialis, and trossulus collected Delaware, Kamaishi (Japan), Alaska, respectively, was analyzed by polymerase chain reaction (PCR) using two sets oligonucleotide primers. The first set, Me 13 14, designed to amplify repetitive region. length amplified fragments highly variable, even among samples same species. Another 15 16, a part nonrepetitive uniform each species differed interspecifically; 180, 168, 126 bp...

Microorganisms in the environment can often adapt to use xenobiotic chemicals as novel growth and energy substrates. Specialized enzyme systems metabolic pathways for degradation of man-made compounds such chlorobiphenyls chlorobenzenes have been found microorganisms isolated from geographically separated areas world. The genetic characterization an increasing number aerobic (substituted) aromatic different bacteria has made it possible compare similarities organization sequence which exist...

The nucleotide sequences of the Acinetobacter calcoaceticus benABC genes encoding a multicomponent oxygenase for conversion benzoate to nonaromatic cis-diol were determined. enzyme, 1,2-dioxygenase, is composed hydroxylase component, encoded by benAB, and an electron transfer benC. Comparison deduced amino acid BenABC with related sequences, including those toluate, toluene, benzene, naphthalene 1,2-dioxygenases, indicated that similarly sized subunits components derived from common...

ABSTRACT The conventional methods for identifying mycobacterial species are based on their phenotypic characterization. Since some problematic slow growers, taxonomy takes several weeks or months to identify. ribosomal DNA (rDNA) sequence-based identification strategy has been adopted solve this problem. More recently, the gyrB sequences have shown be useful phylogenetic markers of species. We determined 43 slowly growing strains belonging 15 in genus Mycobacterium . frequencies base...

Three strains, FYK2301M01(T), FYK2301M18 and FYK2301M52, all being Gram-negative, spherical, motile facultatively anaerobic, were isolated from a marine alga (Porphyra sp.) collected on Mikura Island, Japan. Colonies of the strains circular pink-pigmented Marine Agar 2216 (Difco) at 25 degrees C. Cells reproduced by binary fission. The G+C content DNA was 73 mol%. major isoprenoid quinone MK-6. Phylogenetic analysis based 16S rRNA gene sequences indicated that are members WPS-1 group...

Microbiologically influenced corrosion of steel in anaerobic environments has been attributed to hydrogenotrophic microorganisms. A sludge sample collected from the bottom plate a crude-oil storage tank was used inoculate medium containing iron (Fe(0)) granules, which then incubated anaerobically at 37 degrees C under an N(2)-CO(2) atmosphere enrich for microorganisms capable using as sole source electrons. methanogen, designated strain KA1, isolated enrichment culture. An analysis its 16S...

Earlier studies have shown that the major porin species in Pseudomonas aeruginosa outer membrane is protein F (OprF), which produces channels wider than those produced by Escherichia coli porins. In contrast, Yoshihara and Nakae ((1989) J. Biol. Chem. 264, 6297-6301) reported has no pore-forming activity as measured flux of L-arabinose, P. membrane, being proteins C, D, E, are much narrower E. channels. this study, we followed purification scheme closely possible, found had a specific for...

The RpoN protein was originally identified in Escherichia coli as a sigma (sigma) factor essential for the expression of nitrogen regulons. In present study we cloned Pseudomonas putida rpoN gene and its product with an apparent molecular weight 78,000. A mutant constructed by vitro insertion mutagenesis kanamycin cassette. P. then isolated replacement intact chromosomal through homologous recombination. Examination phenotypes thus obtained allowed identification series metabolic functions...