Toru Shigematsu

Burkholderia kururiensis sp. nov., a trichloroethylene (TCE)-degrading bacterium isolated from an aquifer polluted with TCE.

A trichloroethylene (TCE)-degrading bacterium was isolated from an aquifer sample collected at a TCE-polluted site in Japan by enriching with phenol as sole carbon source. The isolate, designated strain KP23T, was a Gram-negative, oval-shaped micro-organism. A phylogenetic study based on 16S rRNA gene sequences indicated that strain KP23T should be placed in the genus Burkholderia. Cellular fatty acids of the strain were mainly composed of C16:0, cyclopropanic acid C17:0 and cyclopropanic acid C19:0. Strain KP23T also contained notable amounts of C13:1 and C17:1. The G + C content of total DNA was 64.8 mol%. Strain KP23T oxidized various sugars and sugar alcohols as sole carbon source such as galactose, glucose, mannose, maltose, glycerol, inositol and mannitol. Comparisons of its phenotypic and genotypic characteristics with other known species belonging to the genus Burkholderia suggested that strain KP23T represents a new species in the genus. The name Burkholderia kururiensis is proposed for this species, with strain KP23T as the type strain (= JCM 10599T).

Influence of Ni2+ and Co2+ on methanogenic activity and the amounts of coenzymes involved in methanogenesis

The requirement of Ni2+ and Co2+ addition on methanogenic activity and the coenzymes involved in methanogenesis were investigated in anaerobic continuous cultivation with synthetic wastewater using acetate as the sole carbon source. Addition of Ni2+ and Co2+ to the synthetic wastewater drastically increased the maximum dilution rate of the cultivation. The concentrations of coenzymes F430 and corrinoids in the biomass increased to 0.62 micromol-Ni/g-VSS and 0.67 micromol-Co/g-VSS, respectively with the increase of the dilution rate. Methanogenic activity of the culture broth also increased with an increase of dilution rate. However, without addition of Ni2+ and Co2+, F430 and corrinoids were not detected in the biomass and methanogenic activity was only a trace level at a dilution rate of 0.025 d(-1). When the amounts of Ni2+ and Co2+ added at a dilution rate of 0.6 d(-1) were lowered in steps, the concentrations of F430 and corrinoids in the biomass and methanogenic activity decreased with decreasing amounts of Ni2+ and Co2+ added. These results suggest that Ni2+ and Co2+ were required for the methane-producing reactions via increases of coenzymes F430 and corrinoids.

Effect of Dilution Rate on Structure of a Mesophilic Acetate-Degrading Methanogenic Community during Continuous Cultivation

The community structures of two mesophilic acetate-degrading methanogenic consortia enriched at dilution rates of 0.025 and 0.6 d(-1) were analyzed by fluorescence in situ hybridization (FISH) and phylogenetic analyses based on 16S rDNA clonal sequences and quantitative real-time polymerase chain reaction (PCR). FISH experiments with archaeal and bacterial domain-specific probes showed that archaeal cells were predominant and only a small number of bacterial cells were detected at both dilution rates. In the domain Archaea, the number of cells closely related to Methanosarcina barkeri was shown to be greater at the high dilution rate using FISH with species-specific probes. Taxonomic analyses based on rDNA clonal sequences obtained at the low and high dilution rates showed that 43% of 100 clones and 72% of 92 clones, respectively, were affiliated with the domain Archaea and the remainders at each dilution rate were affiliated with the domain Bacteria. Within the domain Archaea, all rDNA clones at both dilution rates were affiliated with the genera Methanosaeta or Methanosarcina of the aceticlastic methanogens. Within the domain Bacteria, the rDNA clones obtained at the low dilution rate were affiliated with four phyla, Firmicutes (36%), Bacteroidetes (9%), Chloroflexi (6%) and candidate division OP12 (5%). The rDNA clones obtained at the high dilution rate were affiliated with four phyla, Firmicutes (16%), Bacteroidetes (8%), Proteobacteria (1%) and candidate division OP12 (3%). Real-time quantitative PCR experiments showed that the number of rDNA sequences affiliated with the genus Methanosarcina was greater at the high dilution rate. In addition, a significant number of rDNA sequences affiliated with the genus Methanoculleus were detected only at the low dilution rate. Detection of a hydrogenotrophic methanogen at the low dilution rate suggests that the syntrophic acetate oxidation by hydrogenotrophic methanogens and acetate-oxidizing bacteria could occur at the low dilution rate.

Roseateles depolymerans gen. nov., sp. nov., a new bacteriochlorophyll a-containing obligate aerobe belonging to the beta-subclass of the Proteobacteria.

Strains 61AT (T = type strain) and 61B2, the first bacteriochlorophyll (BChl) a-containing obligate aerobes to be classified in the beta-subclass of the Proteobacteria, were isolated from river water. The strains were originally isolated as degraders of poly(hexamethylene carbonate) (PHC). The organisms can utilize PHC and some other biodegradable plastics. The strains grow only under aerobic conditions. Good production of BChl a and caroterioid pigments is achieved on PHC agar plates and an equivalent production is observed under oligotrophic conditions on agar medium. Spectrometric results suggest that BChl a is present in light-harvesting complex I and the photochemical reaction centre. The main carotenoids are spirilloxanthin and its precursors. Analysis of the 16S rRNA gene sequence indicated that the phylogenetic positions of the two strains are similar to each other and that their closest relatives are the genera Rubrivivax, ideonella and Leptothrix with similarities of 96.3, 96.2 and 96.1%, respectively. The cells are motile, straight rods and contain poly-beta-hydroxybutyrate granules. Ubiquinone-8 is the predominant quinone. Vitamins are not required for growth. The G + C content of genomic DNA is 66.2-66.3 mol%. Genetic and phenotypic features suggest that the strains represent a new genus in the beta-subclass which is evenly distant from known genera. Consequently, the name Roseateles depolymerans gen. nov., sp. nov. is proposed for the strains; the type strain of Roseateles depolymerans is strain 61AT (= DSM 11813T).

Microbial community of a mesophilic propionate-degrading methanogenic consortium in chemostat cultivation analyzed based on 16S rRNA and acetate kinase genes

AbstractnWe constructed a mesophilic anaerobic chemostat that was continuously nfed with synthetic wastewater containing propionate as the sole source nof carbon and energy. Steady-state conditions were achieved below the ncritical dilution rate of 0.3xa0dnn−1nn with almost complete substrate degradation. The propionate-degrading nmethanogenic communities in the chemostat at dilution rates of 0.01, n0.08, and 0.3xa0dnn−1nn were analyzed using molecular biological techniques. Fluorescence in nsitu hybridization with archaeal and bacterial domain-specific probes nshowed that archaeal cells predominated throughout the three dilution nrates. Archaeal-16S rRNA gene clone library analysis and quantitative nreal-time polymerase chain reaction studies showed that hydrogenotrophicn methanogen rRNA genes closely related to nnMethanoculleusnn was detected at a dilution rate of 0.01xa0dnn−1nn, whereas rRNA genes closely related to the nnMethanoculleusnn and nnMethanospirillumnn genera were detected at dilution rates of 0.08 and 0.3xa0dnn−1nn. The aceticlastic methanogen, nnMethanosaetann, was detected throughout the three dilution rates. Bacterial-rRNA gene nclone library analysis and denaturing gradient gel electrophoresis ndemonstrated that rRNA genes affiliated with the genus nnSyntrophobacternn predominated at the low dilution rate, whereas rRNA genes affiliated nwith the phylum nnFirmicutesnn predominated at the higher dilution rates. A significant number of rRNAn genes affiliated with the genus nnPelotomaculumnn were detected at dilution rate of 0.3xa0dnn−1nn. The diversity of genes encoding acetate kinase agreed closely with then results of the rRNA gene analysis. The dilution rates significantly naltered the archaeal and bacterial communities in the propionate-fed nchemostat.n

In vitro evaluation of physiological activity of vinegar produced from barley-, sweet potato-, and rice-shochu post-distillation slurry

Vinegar was produced from barley-, sweet potato-, and rice-shochu post-distillation slurry using jar fermentor within 19 hrs. All the vinegars showed radical-scavenging activity, angiotensin I converting enzyme (ACE) inhibition and advanced glycation endproducts (AGE) inhibition in vitro. The radical-scavenging activity of the vinegar produced from sweet potato-shochu post-distillation slurry was higher than that of other two kinds of vinegar on the organic matter basis. The ACE inhibitory activities of all the vinegars were higher than that of each post-distillation slurry. The main components that showed ACE inhibitory activity would be peptides, and their content increased during acetic acid fermentation. Regarding AGE inhibition, only rice-shochu post-distillation slurry did not show such activity, but the other two post-distillation slurries and all the vinegars showed clear inhibitory activity. The activity appeared to depend on the concentration of amino groups except for sweet potato-shochu post-distillation slurry and the vinegar produced from it.

Purification and gene cloning of the oxygenase component of the terephthalate 1,2-dioxygenase system from Delftia tsuruhatensis strain T7.

The terephthalate 1,2-dioxygenase system (TERDOS) was found in cell extracts of Delftia tsuruhatensis strain T7 (=IFO16741) grown in terephthalate-salt medium. The cell extract was separated by anion exchange chromatography to yield two fractions (R and Z) that were necessary for oxygenation of terephthalate with NADH and Fe(2+). The oxygenase component of TERDOS (TerZ) was purified from fraction Z by gel filtration chromatography to near homogeneity. An alpha(3)beta(3) subunit structure was deduced from the molecular masses of 235, 46 and 17 kDa of the native complex and the alpha- and beta-subunits, respectively. The N-terminal amino acid sequences of the two subunits of TerZ allowed polymerase chain reaction primers to be deduced and the DNA sequence of the alpha-subunit was determined. The amino acid sequence of the alpha-subunit (TerZalpha) showed significant similarities to the large subunits of multicomponent ring-hydroxylating oxygenases. Two motifs in the deduced amino acid sequence, a Rieske [2Fe-2S] center and a mononuclear Fe(II) binding site, were observed. Phylogenetic analyses indicated that TerZalpha and the large oxygenase component subunits ortho-halobenzoate 1,2-dioxygenase and salicylate-5-hydroxylase form a cluster that is distant from the rest of the large oxygenase subunits of multicomponent ring-hydroxylating oxygenases.

Immunostimulation-mediated antitumor activity by preconditioning with rice-shochu distillation residue against implanted tumor in mice

We investigated the ability of rice-shochu postdistillation residue (RSDR) to stimulate the activity of macrophages. RSDR significantly stimulated mouse macrophage activity and induced significant IL-12 production in vitro. In syngeneic C38 solid tumor model in mice, a diet containing 1.0% RSDR caused a significant suppression of tumor growth and prolonged the life span of the tumor-bearing mice. Further, using this model, mice fed for 21 days with RSDR showed significantly increased levels of serum IL-12 and IFN-γ compared with controls. Moreover, the splenic NK cell activity of mice fed with RSDR was significantly elevated compared with that of mice on a normal diet and thereby suppressed C38 tumor growth. We also investigated the tumor growth suppressing effect of RSDR using a tumor model of B16-F10 melanoma cells. Dietary preconditioning with RSDR significantly suppressed B16-F10 tumor growth. Moreover, RSDR significantly increased the production of IL-12 either before or after B16-F10 tumor implantation. These results suggest that dietary RSDR suppresses tumor growth by stimulating the immune system of the host.