Microbes and Environments
Online ISSN : 1347-4405
Print ISSN : 1342-6311
ISSN-L : 1342-6311
Volume 18 , Issue 3
Showing 1-8 articles out of 8 articles from the selected issue
Minireview
  • Akira Hiraishi
    Type: Others
    2003 Volume 18 Issue 3 Pages 105-125
    Published: 2003
    Released: October 08, 2003
    JOURNALS FREE ACCESS
    Dioxins are a group of chloroaromatic compounds known to be toxic and carcinogenic, and persistent environmental pollutants. How to remedy dioxin-polluted environments is one of the most challenging problems in environmental technology. From ecological and economical viewpoints, biological methods using particular microorganisms and microbial consortia capable of dioxin transformation and degradation have greater appeal than physicochemical methods in their application for environmental remediation. Large numbers of microorganisms capable of degrading dioxins and dioxin-like compounds have been isolated and characterized. Information about the biodiversity, ecophysiology and molecular biology of dioxin-degrading microorganisms has accumulated particularly during the past decade. There are three major modes of microbial degradation and transformation of dioxins; that is, oxidative degradation by aerobic bacteria containing aromatic hydrocarbon dioxygenases, reductive dechlorination by anaerobic microorganisms and fungal oxidation with cytochrome P-450, lignin peroxidases and laccases. This article overviews the current knowledge of microbial degradation and transformation of dioxins as well as the biodiversity of microorganisms involved. Strategies directed towards the bioremediation of dioxin-polluted environments are discussed.
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Regular Papers
  • Hiroyuki Ohta, Michie Yagi, Junko Suzuki, Nobuhide Fujitake, Makiko Wa ...
    Type: Regular Paper
    2003 Volume 18 Issue 3 Pages 126-132
    Published: 2003
    Released: October 08, 2003
    JOURNALS FREE ACCESS
    A small spherical black fungal sclerotium grain from podzolic soils, which was tentatively identified as the resting body of Cenococcum graniforme, was assumed as the source of green polynuclear quinone pigments in P type humic acid (K. Kumada and H.M. Hurst, Nature 214: 631-633, 1967). To examine the presence of bacteria inside sclerotium grains collected from an Andosol profile in Mt. Myoko, central Japan, the grains were repeatedly washed, ultrasonicated and then cultured on diluted nutrient broth. The sum of recovered bacteria as colony-forming units from the wash and ultrasonicate fractions was 1.46×106 (g fresh weight)-1: 88% of the count in the wash fractions (assumably resulting from grain surface and attached soil) and 12% in the ultrasonicate (inside grain). Thirty-one bacterial strains were isolated from the ultrasonicate fraction and their 16S rDNA partial sequences were determined. The predominant group was the Alphaproteobacteria (71%), chiefly the Sphingomonas group (52%). Representative isolates of the Sphingomonas group were examined for their ability to grow on naphthalenesulfonic acids as a model compound of polycyclic aromatic hydrocarbons (PAHs) and also on several phenolic acids. None of the isolates tested utilized the model PAH but many of them used p-hydroxy benzoic, vanillic, p-coumaric and ferulic acids for growth. Based on these results, the relationship between the predominance of Sphingomonas and the chemical character of the sclerotium grain was discussed.
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  • Constancio A. Asis, Jr., Katsuki Adachi, Akira Sugimoto, Kunihiro Ujih ...
    Type: Regular Paper
    2003 Volume 18 Issue 3 Pages 133-137
    Published: 2003
    Released: October 08, 2003
    JOURNALS FREE ACCESS
    We collected stem samples from sugarcane germplasm of wildtype (43 clones of Saccharum spontaneum and S. robustum), cultivated (34 clones of S. hybrid spp., S. sinense, and S. barberi), and related grass species (7 clones of Erianthus arundinaceus, Miscanthus floridulus, and Ripidium sp.) to survey the colonization and population of diazotrophic endophytes in apoplast solution. Using the acetylene reduction assay-most probable number (ARA-MPN) method, 11 clones of wildtype species, nine clones of cultivated species, and three clones of related grass species were colonized by diazotrophic endophytes. The population density of diazotrophic endophytes in all ARA-positive samples ranged from 102 to 108 cells mL-1 apoplast solution and differed among clones and species. The results indicate a differential colonization and population of diazotrophic endophytes in stem apoplast solution.
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  • Ryo Ohtomo, Masanori Saito
    Type: Regular Paper
    2003 Volume 18 Issue 3 Pages 138-144
    Published: 2003
    Released: October 08, 2003
    JOURNALS FREE ACCESS
    Klebsiella causes severe mastitis in dairy cattle and is a great concern for dairy farm management. The media previously used to detect Klebsiella, MacConkey-Inositol-Carbenicillin agar (MCIC) and Simons-Citrate agar supplemented with 1% inositol (SCAI), were not selective enough for samples from the dairy environment such as cow feces or cow bedding materials. We developed a new selective medium for Klebsiella. BIND (Brilliant green containing Inositol-Nitrate-Deoxycholate agar) medium contains myo-inositol and sodium nitrate as a sole carbon and nitrogen source, respectively, and is supplemented with brilliant green and deoxycholate. All Klebsiella strains isolated from the dairy environment grew well on the BIND plates. The growth of non-Klebsiella contaminants, which grew well on MCIC or SCAI, was effectively suppressed on BIND. All isolates that grew on BIND were identified as Klebsiella both by API testing and by 16S rDNA sequence alignment. We concluded that BIND was selective enough for the detection of Klebsiella species from dairy samples and therefore, helpful for monitoring Klebsiella populations in the dairy environment and for preventing the mastitis caused by Klebsiella.
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  • Moriya Ohkuma, Hajime Shimizu, Taksawan Thongaram, Saori Kosono, Kazuh ...
    Type: Regular Paper
    2003 Volume 18 Issue 3 Pages 145-151
    Published: 2003
    Released: October 08, 2003
    JOURNALS FREE ACCESS
    Gut portions of soil-feeding termites belonging to the subfamily Termitinae generally show extensive alkalinity. An alkaliphilic and xylanolytic bacterium, strain SM-XY60, was isolated from the gut of such a soil-feeding termite Sinocapritermes mushae. This bacterium was a strictly aerobic endospore-forming rod, capable of growth at pH 6.5 to 10.5, and showing optimal growth at pH 9. The strain grew well on an alkaline medium containing K2CO 3, but not Na2CO3. 16S rDNA analysis and physiological characterization revealed this strain to be a member of the genus Paenibacillus but distinct from any known species. The xylanase produced by the alkaline growing cells showed substantial activity and stability at high pH, implying an adaptation of the enzyme to the gut alkaline environment. The isolation of this alkaliphile suggests that the insect gut is of ecological significance for alkaliphiles.
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  • Taksawan Thongaram, Saori Kosono, Moriya Ohkuma, Yuichi Hongoh, Makio ...
    Type: Regular Paper
    2003 Volume 18 Issue 3 Pages 152-159
    Published: 2003
    Released: October 08, 2003
    JOURNALS FREE ACCESS
    We screened alkaliphilic bacteria from the first proctodaeal region (P1) of the hindgut, which is known to show high alkalinity and K+ richness, of several species of higher termites. Phylogenetic analyses based on the 16S rDNA sequence revealed that most isolates were affiliated with known alkaliphilic bacilli, frequently isolated from soil. Though many physiological characteristics of the isolated strains were similar to those of soil alkaliphilic bacilli, some strains showed a distinctive NaCl sensitivity. Many strains grew better in an alkaline medium containing K2CO3 than one containing Na2CO3. One strain, closely related to the xylanolytic and alkaliphilic Paenibacillus sp. SM-XY60 from the soil-feeding termite Sinocapritermes mushae, was also isolated. Culture-independent analysis showed that bacteria closely related to our isolated alkaliphiles widely inhabit the termite gut. Our results also suggested that some alkaliphilic bacilli in soil share ecological niches in the termite gut.
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  • Mitsuru Eguchi, Erina Fujiwara-Nagata, Nobukazu Miyamoto
    Type: Regular Paper
    2003 Volume 18 Issue 3 Pages 160-166
    Published: 2003
    Released: October 08, 2003
    JOURNALS FREE ACCESS
    Vibriosis caused by Vibrio anguillarum serotype J-O-1 seriously affects the freshwater fish ayu (Plecoglossus altivelis) in Lake Biwa, Japan. Survival patterns of V. anguillarum were investigated in aged lake water (ALW) supplemented with or without 0.75% NaCl. It was found that 0.1-1.0% of V. anguillarum cells maintained the ability to form colonies even after 6 weeks in 0.75% NaCl-ALW. Under the same starved conditions, MPN counts with liquid medium were 100 times higher than CFU counts. When exposed to sterilized aged lake water without NaCl, V. anguillarum entered a non-culturable state within half a day. As the mineralization activity of non-culturable cells was still 0.1-5.4% of that in the culturable phase, this physiological state can be described as "viable but non-culturable". However, all attempts to return to a culturable state including re-infection were un-successful. The non-culturable cells in ALW lost all pathogenicity in fish. Since a longer exposure to ALW resulted in less mineralization activity, the non-culturable state of V. anguillarum cells in freshwater seems to reflect a phase of decay leading to cell death. However, certain environmental factors such as coldness and microaerobiosis seem to help the pathogen to survive longer in freshwater without a loss of culturability.
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  • Hui Zhang, Hongwei Luo, Yoichi Kamagata
    Type: Regular Paper
    2003 Volume 18 Issue 3 Pages 167-173
    Published: 2003
    Released: October 08, 2003
    JOURNALS FREE ACCESS
    Burkholderia kururiensis KP23 was isolated as a trichloroethylene (TCE)-degrading bacterium. Its degrading activity was induced by phenol, suggesting that the degradation is catalyzed by a phenol hydroxylase (PH). To elucidate the involvement of the PH in the degradation of TCE, the gene cluster for the enzyme was cloned and sequenced. The structural genes (phkABCDEFG) and cognate regulatory gene (phkR) were identified in a divergent transcriptional organization. The products are homologous to those of dmpRKLMNOPQ of Pseudomonas putida CF600, sharing 30-62% identity of amino acid sequence, indicating that the PH is a multi-component enzyme. Disruption of phkD encoding a large oxygenase subunit of the enzyme completely abolished the utilization of phenol as well as degradation of TCE by strain KP23. In addition, a disruptant of phkR was not able to grow on phenol and showed no activity to degrade TCE, indicating that PhkR is an activator and controls the expression of phkABCDEFG.
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