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S Harayama

Publications and source records attributed to S Harayama.

At least 19 recordsLinked to original sources
PubMed2001

Time-of-flight mass spectrometric analysis of high-molecular-weight alkanes in crude oil by silver nitrate chemical ionization after laser desorption.

Time-of-flight mass spectrometry was used for the first time to analyze the hydrocarbons in crude oil. Alkanes in the saturated fraction of a crude oil sample were chemically ionized by the laser desorption of silver nitrate, and the silver-attached C24-C60 alkanes were resolved with mass accuracy below 7 ppm. This technique was used to evaluate the biodegradation of aliphatic hydrocarbons and cycloalkanes by oil-degrading microorganisms resident in seawater. It is shown that the aliphatic hydrocarbons were degraded in the range of 60-80%, while the mono-, di-, tri-, tetra-, and pentacycloalkanes were degraded in the range of 40-55, 20-30, 10-16, 5-9, and <5%, respectively. Its high sensitivity and speed of application could result in an analysis by laser desorption silver chemical ionization time-of-flight mass spectrometry being the method of choice for determining high-molecular-weight hydrocarbons in various petroleum products.

Biodegradation, Environmental↗
PubMed2001

Analysis of long-side-chain alkylaromatics in crude oil for evaluation of their fate in the environment.

It has long been believed that the n-hexane fraction of crude oil only contains saturates. However, we found that one-third of its content was aromatics with long alkyl side chains and that these aromatics could be separated from the saturates by preparative thin-layer chromatography. The separated alkylaromatic fraction was characterized by UV-visible, NMR and mass spectrometries. A gas chromatographic-mass spectrometric analysis showed the presence of a homologous series of long-side-chain n-alkylaromatics, namely mono-, di-, and tri-n-alkylbenzenes in the C7-C27 range (the subscript to C indicates the total number of carbon atoms in the alkyl side chain) and di- and tri-n-alkylbenzothiophenes in the C3-C22 range. The biodegradation of these crude oil components by a natural bacterial population in seawater and their photooxidation by artificial sunlight were investigated. The n-alkylbenzenes were found to be quite susceptible to biodegradation but resistant to photooxidation, whereas the n-alkylbenzothiophenes were almost completely photooxidized and substantially biodegraded.

Bacteria↗
PubMed2001

ICB database: the gyrB database for identification and classification of bacteria.

The Identification and Classification of Bacteria (ICB) database (http:/www.mbio.co.jp/icb) contains currently available information about the DNA gyrase subunit B (gyrB) gene in bacteria. The database is designed to provide the scientific community with a reference point for using gyrB as an evolutionary and taxonomic marker. Nucleic and amino acid sequence data are currently available for over 850 strains, along with alignments at several different taxonomic levels and an exhaustive review of primer selection and background information.

Bacteria↗
PubMed2001

The predatory soil flagellate Heteromita globosa stimulates toluene biodegradation by a Pseudomonas sp.

A model food chain was established to investigate the influence of grazing by flagellates on bacteria degrading toluene in batch culture. The rate of toluene consumed by a Pseudomonas sp. strain PS+ (max. 0.37 fmol cell(-1) h(-1)) was significantly higher in the presence of the bacterivorous flagellate Heteromita globosa (max. 1.38 fmol cell(-1) h(-1)). A maximum increase of up to 7.5 times was observed in the rate of toluene consumed by these bacteria during exponential growth of this flagellate. Carbon conversion efficiency (CCE) of bacteria to flagellate biomass was estimated to be 33.4% based on measured biovolumes and published values for carbon contents. However, the CCE for toluene-derived carbon was lower (max. 4.9%) when calculations were based on incorporation of [ring-U-(14)C]toluene into biomass of flagellates grazing on labelled bacteria. The findings suggest a potential role for flagellates in bioremediation processes.

Animals↗
PubMed2001

Diversity in kinetics of trichloroethylene-degrading activities exhibited by phenol-degrading bacteria.

Whole-cell kinetics of phenol- and trichloroethylene (TCE)-degrading activities expressed by 13 phenol-degrading bacteria were analyzed. The Ks (apparent affinity constant in Haldane's equation) values for TCE were unexpectedly diverse, ranging from 11 microM to over 800 microM. The Vmax/Ks values for phenol were three orders of magnitude higher than the values for TCE in all bacteria analyzed, suggesting that these bacteria preferentially degrade phenol rather than TCE. A positive correlation between Ks for phenol and Ks for TCE was found, i.e., bacteria exhibiting high Ks values for phenol showed high Ks values for TCE, and vice versa. A comparison of the Ks values allowed grouping of these bacteria into three types, i.e., low-, moderate- and high-Ks types. Pseudo-first-order degradation-rate constants for TCE at 3.8 microM were found to be adequate to rapidly discriminate among the three types of bacteria. When bacteria were grown on phenol at the initial concentration of 2 mM, Comamonas testosteroni strain R5, a representative of low-Ks bacteria, completely degraded TCE at 3.8 microM, while strain P-8, a representative of high-Ks bacteria, did not. A mixed culture of these two bacteria poorly degraded TCE under the same conditions, where P-8 outgrew R5. These results suggest that low-Ks bacteria should be selectively grown for effective bioremediation of TCE-contaminated groundwater.

Betaproteobacteria↗
PubMed2001

Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting.

Denaturing gradient gel electrophoresis of PCR-amplified 16S ribosomal DNA (rDNA) fragments has frequently been applied to the fingerprinting of natural bacterial populations (PCR/DGGE). In this study, sequences of bacterial universal primers frequently used in PCR/DGGE were compared with 16S rDNA sequences that represent recently proposed divisions in the domain Bacteria. We found mismatches in 16S rDNA sequences from some groups of bacteria. Inosine residues were then introduced into the bacterial universal primers to reduce amplification biases caused by these mismatches. Using the improved primers, phylotypes affiliated with Verrucomicrobia and candidate division OP11, were detected in DGGE fingerprints of groundwater populations, which have not been detected by PCR/DGGE with conventional universal primers.

Bacteria↗
PubMed2001

Bacterial populations occuring in a trichloroethylene-contaminated aquifer during methane injection.

Soil core samples were obtained from a trichloroethylene (TCE)-contaminated aquifer before and after the start of methane biostimulation. DNA was extracted directly from the soil samples, and denaturing gradient gel electrophoresis (DGGE) was used to analyse bacterial 16S ribosomal DNA fragments that were PCR amplified from these DNA samples. This analysis consistently detected two phylotypes in the methane-injected samples. These phylotypes were closely related to Methylobacter and Methylomonas, both belonging to type I methanotrophs. A competitive DGGE analysis using Methylosinus trichosporium OB3b cells as an internal quantitative standard showed that these populations accounted for 10(8)-10(9) cells g(-1) soil. These results showed that type I methanotrophs formed a significant proportion of the bacterial community during methane biostimulation. The implications of this finding for TCE bioremediation were discussed.

Biodegradation, Environmental↗
PubMed2001

Molecular detection of marine bacterial populations on beaches contaminated by the Nakhodka tanker oil-spill accident.

In January 1997, the tanker Nakhodka sank in the Japan Sea, and more than 5000 tons of heavy oil leaked. The released oil contaminated more than 500 km of the coastline, and some still remained even by June 1999. To investigate the long-term influence of the Nakhodka oil spill on marine bacterial populations, sea water and residual oil were sampled from the oil-contaminated zones 10, 18, 22 and 29 months after the accident, and the bacterial populations in these samples were analysed by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA fragments. The dominant DGGE bands were sequenced, and the sequences were compared with those in DNA sequence libraries. Most of the bacteria in the sea water samples were classified as the Cytophaga-Flavobacterium-Bacteroides phylum, alpha-Proteobacteria or cyanobacteria. The bacteria detected in the oil paste samples were different from those detected in the sea water samples; they were types related to hydrocarbon degraders, exemplified by strains closely related to Sphingomonas subarctica and Alcanivorax borkumensis. The sizes of the major bacterial populations in the oil paste samples ranged from 3.4 x 10(5) to 1.6 x 10(6) bacteria per gram of oil paste, these low numbers explaining the slow rate of natural attenuation.

Accidents↗
PubMed2001

Biodegradation of n-alkylcycloalkanes and n-alkylbenzenes via new pathways in Alcanivorax sp. strain MBIC 4326.

The degradation of long-chain n-alkylbenzenes and n-alkylcyclohexanes by Alcanivorax sp. strain MBIC 4326 was investigated. The alkyl side chain of these compounds was mainly processed by beta-oxidation. In the degradation of n-alkylcyclohexanes, cyclohexanecarboxylic acid was formed as an intermediate. This compound was further transformed to benzoic acid via 1-cyclohexene-1-carboxylic acid.

Benzene Derivatives↗
PubMed2001

PhcS represses gratuitous expression of phenol-metabolizing enzymes in Comamonas testosteroni R5.

We identified an open reading frame, designated phcS, downstream of the transcriptional activator gene (phcR) for the expression of multicomponent phenol hydroxylase (mPH) in Comamonas testosteroni R5. The deduced product of phcS was homologous to AphS of C. testosteroni TA441, which belongs to the GntR family of transcriptional regulators. The transformation of Pseudomonas aeruginosa PAO1c (phenol negative, catechol positive) with pROR502 containing phcR and the mPH genes conferred the ability to grow on phenol, while transformation with pROR504 containing phcS, phcR, and mPH genes did not confer this ability. The disruption of phcS in strain R5 had no effect on its phenol-oxygenating activity in a chemostat culture with phenol. The phenol-oxygenating activity was not expressed in strain R5 grown in a chemostat with acetate. In contrast, the phenol-oxygenating activity in the strain with a knockout phcS gene when grown in a chemostat with acetate as the limiting growth factor was 66% of that obtained in phenol-grown cells of the strain with a knockout in the phcS gene. The disruption of phcS and/or phcR and the complementation in trans of these defects confirm that PhcS is a trans-acting repressor and that the unfavorable expression of mPH in the phcS knockout cells grown on acetate requires PhcR. These results show that the PhcS protein repressed the gratuitous expression of phenol-metabolizing enzymes in the absence of the genuine substrate and that strain R5 acted by an unknown mechanism in which the PhcS-mediated repression was overcome in the presence of the pathway substrate.

Acetates↗
PubMed2001

Enhanced mineralization of benzo[a]pyrene in the presence of nonaqueous phase liquids.

Bacterial mineralization of [7-14C]benzo[a]pyrene (BaP) to 14CO2 was enhanced by the presence of nonaqueous phase liquids (NAPLs). Mineralization of BaP was affected differently by different NAPLs, and the mode of enhancement of mineralization by a NAPL most likely occurred by a combination of cometabolic and physical effects. Mineralization was enhanced to the greatest extent when BaP was dissolved in a high-boiling distillation product of diesel fuel.

Alkanes↗
PubMed2000

Barnacle cement proteins. Importance of disulfide bonds in their insolubility.

Barnacles produce a cement that is a proteinaceous underwater adhesive for their secure attachment to the substratum. The biochemical properties of the cement have not previously been elucidated, because the insolubility of the cement proteins hampers their purification and characterization. We developed a non-hydrolytic method to render soluble most of the cement components, thereby allowing the proteins to be analyzed. Megabalanus rosa cement could be almost completely rendered soluble by its reduction with 0.5 m dithiothreitol at 60 degrees C in a 7 m guanidine hydrochloride solution, the high concentration of dithiothreitol being indispensable to achieve this. The effectiveness of this reduction treatment was confirmed by the detachment of the barnacle from the substratum. Three proteins comprising up to 94% of the whole cement were identified as the major cement components. The cDNA clone of one of these major proteins was isolated, and the site-specific expression of the gene in the basal portion of the adult barnacle, where the cement glands are located, was demonstrated. A sequence analysis revealed this cement component to be a novel protein of 993 amino acid residues, including a signal peptide. This is the first report of the major component of the barnacle cement protein complex.

Amino Acid Sequence↗
PubMed2000

An effective family shuffling method using single-stranded DNA.

Family shuffling, which is one of the most powerful techniques for in vitro protein evolution, always involves the problem of reassembling the gene fragments into parental gene sequences, because such a process prevents the formation of chimeric sequences. In order to improve the efficiency of hybrid formation in family shuffling, single-stranded DNAs (ssDNAs) were used as templates. The ssDNAs of two catechol 2,3-dioxygenase genes, nahH and xylE, were prepared, the xylE strand being complementary to the nahH strand. When these ssDNAs were digested by DNase I and reassembled, chimeric genes were obtained at a rate of 14%, which was much higher than the rate of less than 1% obtained by shuffling with double-stranded DNAs. Chimeric catechol 2,3-dioxygenases that were more thermally stable than the parental enzymes, XylE and NahH, were obtained by this ssDNA-based DNA shuffling.

Catechol 2,3-Dioxygenase↗
PubMed2000

Reclamation of an activated-sludge microbial consortium by selective biostimulation.

Our previous study showed that an activated-sludge process broke down at the phenol-loading rate of 1.5 g l(-1) day(-1), when non-flocculating bacteria (called R6T and R10) overgrew the sludge, resulting in a sludge washout. In this study, we attempted to circumvent this breakdown problem by reclaiming the consortium structure. Activated sludge was fed phenol, and the phenol-loading rate was increased stepwise from 0.5 g l(-1) day(-1) to 1.0 g l(-1) day(-1) and then to 1.5 g l(-1) day(-1). Either galactose or glucose (at 0.5 g l(-1) day(-1)) was also supplied to the activated sludge from the phenol-loading rate of 1.0 g l(-1) day(-1). Pure culture experiments have suggested galactose to be a preferential substrate for a floc-forming bacterium (R6F) that predominantly degrades phenol under low phenol-loading conditions. Supplying galactose allowed sustainment of the R6F population and suppression of the overgrowth of R6T and R10 at the phenol-loading rate of 1.5 g l(-1) day(-1). This measure allowed the activated-sludge process to treat phenol at a phenol-loading rate up to 1.5 g l(-1) day(-1), although it broke down at 2.0 g l(-1) day(-1). In contrast, supplying glucose reduced the R6F population and allowed the activated-sludge process to break down at the phenol-loading rate of 1.0 g l(-1) day(-1). This study demonstrated that reclamation of the activated-sludge consortium by selective biostimulation of the floc-forming population improved the phenol-treating ability of the process.

Bacteria↗
PubMed2000

Conservative Structure of the Plaque Matrix Protein of Mussels in the Genus Mytilus.

The complementary DNA encoding the byssal plaque matrix protein (fp-2) of the mussel Mytilus coruscus was isolated. The predicted amino acid sequence (474 amino acids) consists of four parts: the signal peptide, the amino-terminal nonrepetitive domain, the central repetitive domain containing 11 repeats of an epidermal growth factor-like motif, and the carboxy-terminal nonrepetitive domain. The amino acid sequence is 82.7%, similar to that of fp-2 of Mytilus galloprovincialis, and the basic structure including number and motif of repeats is highly conservative. Amino acid substitutions are less frequent in "consensus positions" of the central repetitive domain (13.1%), and most of them are changes from irregular amino acids to regular ones. Thus, the structure of fp-2 was found to be conservative between species. It was presumed that the basic structure of fp-2 is unchangeable to maintain the flexible and durable matrix structure and that variation is not required because fp-2 is protected by other surface proteins.

Journal Article↗
PubMed2000

Intrageneric relationships among Micromonospora species deduced from gyrB-based phylogeny and DNA relatedness.

The phylogenetic structure of genus Micromonospora within actinomycetes was examined by analysing the gyrB sequences of 15 validly described species and four subspecies. All but one of the Micromonospora strains formed a tight cluster, as had previously been demonstrated by a 16S rDNA-based phylogenetic analysis. However, the intrageneric relationships deduced from the gyrB-based phylogeny were different from those based on their 16S rDNA sequences. To examine which phylogeny would be more relevant for classifying genus Micromonospora, DNA-DNA hybridization experiments were performed. The gyrB-based classification agrees with the results of the DNA-DNA hybridization studies, indicating that this classification method is useful for analysing the phylogenetic relationships of high G+C Gram-positive bacteria at the level of the genomic species. Genus Micromonospora was reclassified into the following 14 species: Micromonospora echinospora, Micromonospora pallida, Micromonospora nigra, Micromonospora purpureochromogenes, Micromonospora aurantiaca, Micromonospora carbonacea, Micromonospora chalcea, Micromonospora chersina, Micromonospora coerulea, Micromonospora gallica, Micromonospora halophytica, Micromonospora inositola, Micromonospora olivasterospora and Micromonospora rosaria.

DNA Gyrase↗