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Katsuji Ueki - One of the best experts on this subject based on the ideXlab platform.

  • prevotella paludivivens sp nov a novel strictly anaerobic gram negative hemicellulose decomposing bacterium isolated from Plant Residue and rice roots in irrigated rice field soil
    International Journal of Systematic and Evolutionary Microbiology, 2007
    Co-Authors: Atsuko Ueki, Hiroshi Akasaka, Daisuke Suzuki, Atsuya Satoh, Katsuji Ueki
    Abstract:

    Two strictly anaerobic bacterial strains, KB7T and A42, were isolated from rice Plant Residue and living rice roots, respectively, from irrigated rice-field soil in Japan. These two strains were closely related to each other with 16S rRNA gene sequence similarity of 99.8 %. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. Growth was remarkably stimulated by the addition of haemin to the medium. The strains utilized various saccharides including xylan, xylose, pectin and carboxymethylcellulose and produced acetate and succinate with small amounts of formate and malate. The strains grew at 10–40 °C; optimum growth was observed at 30 °C and pH 5.7–6.7. Oxidase, catalase and nitrate-reducing activities were not detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C15 : 0 and iso-C17 : 0 3-OH. Menaquinones MK-11 and MK-11(H2) were the major respiratory quinones and the genomic DNA G+C content was 39.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. 16S rRNA gene sequence analysis showed that the most related species to both strains was Prevotella oulorum (92.8–92.9 % similarity). Prevotella veroralis and Prevotella melaninogenica were the next most closely related known species with sequence similarities of 91.9–92.4 %. Based on differences in the phylogenetic, ecological, physiological and chemotaxonomic characteristics between the two isolates and related species, it is proposed that strains KB7T and A42 represent a novel species, Prevotella paludivivens sp. nov. This is the first described Prevotella species derived from a natural habitat; all other Prevotella species are from mammalian sources. The type strain of Prevotella paludivivens is KB7T (=JCM 13650T=DSM 17968T).

  • prevotella paludivivens sp nov a novel strictly anaerobic gram negative hemicellulose decomposing bacterium isolated from Plant Residue and rice roots in irrigated rice field soil
    International Journal of Systematic and Evolutionary Microbiology, 2007
    Co-Authors: Atsuko Ueki, Hiroshi Akasaka, Daisuke Suzuki, Atsuya Satoh, Katsuji Ueki
    Abstract:

    Two strictly anaerobic bacterial strains, KB7(T) and A42, were isolated from rice Plant Residue and living rice roots, respectively, from irrigated rice-field soil in Japan. These two strains were closely related to each other with 16S rRNA gene sequence similarity of 99.8 %. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. Growth was remarkably stimulated by the addition of haemin to the medium. The strains utilized various saccharides including xylan, xylose, pectin and carboxymethylcellulose and produced acetate and succinate with small amounts of formate and malate. The strains grew at 10-40 degrees C; optimum growth was observed at 30 degrees C and pH 5.7-6.7. Oxidase, catalase and nitrate-reducing activities were not detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0), C(15 : 0) and iso-C(17 : 0) 3-OH. Menaquinones MK-11 and MK-11(H(2)) were the major respiratory quinones and the genomic DNA G+C content was 39.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. 16S rRNA gene sequence analysis showed that the most related species to both strains was Prevotella oulorum (92.8-92.9 % similarity). Prevotella veroralis and Prevotella melaninogenica were the next most closely related known species with sequence similarities of 91.9-92.4 %. Based on differences in the phylogenetic, ecological, physiological and chemotaxonomic characteristics between the two isolates and related species, it is proposed that strains KB7(T) and A42 represent a novel species, Prevotella paludivivens sp. nov. This is the first described Prevotella species derived from a natural habitat; all other Prevotella species are from mammalian sources. The type strain of Prevotella paludivivens is KB7(T) (=JCM 13650(T)=DSM 17968(T)).

  • paludibacter propionicigenes gen nov sp nov a novel strictly anaerobic gram negative propionate producing bacterium isolated from Plant Residue in irrigated rice field soil in japan
    International Journal of Systematic and Evolutionary Microbiology, 2006
    Co-Authors: Atsuko Ueki, Hiroshi Akasaka, Daisuke Suzuki, Katsuji Ueki
    Abstract:

    A strictly anaerobic, propionate-producing bacterial strain (WB4T) isolated from rice Plant Residue in anoxic rice-field soil in Japan was characterized phenotypically and phylogenetically. Cells were Gram-negative, non-motile, non-spore-forming, short rods. The strain utilized various sugars and produced propionate and acetate as major fermentation products with a small amount of succinate. The optimum growth temperature was 30 °C. Oxidase, catalase and nitrate-reducing activities were negative. The major cellular fatty acids were anteiso-C15 : 0, C15 : 0 and anteiso-C17 : 0 3-OH. Menaquinone MK-8(H4) was the major respiratory quinone. The genomic DNA G+C content was 39·3 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence placed the strain in the phylum ‘Bacteroidetes’. The closest relative to strain WB4T was an environmental clone from water contaminated with equine manure (sequence similarity of 99·7 %) and the strain formed a distinct cluster with other environmental clones mainly from freshwater sediments. The closest recognized species were members of the genus Dysgonomonas, with 16S rRNA gene sequence similarities of 90·9–89·8 %. Bacteroides merdae was the next closest recognized species (similarity of 88·7 % to the type strain). Given that the ecological, physiological and chemotaxonomic characteristics of strain WB4T were different from those of any related species, a new genus and species Paludibacter propionicigenes gen. nov., sp. nov., is proposed to accommodate it. The type strain is WB4T (=JCM 13257T=DSM 17365T).

  • propionicimonas paludicola gen nov sp nov a novel facultatively anaerobic gram positive propionate producing bacterium isolated from Plant Residue in irrigated rice field soil
    International Journal of Systematic and Evolutionary Microbiology, 2003
    Co-Authors: Hiroshi Akasaka, Atsuko Ueki, Satoshi Hanada, Yoichi Kamagata, Katsuji Ueki
    Abstract:

    Two propionate-producing strains (WdT and Wf) that were isolated anaerobically from Plant Residue of irrigated rice-field soil in Japan were characterized phenotypically and phylogenetically. The growth rate of strain WdT was very slow in basal medium, but both growth and propionate production were stimulated significantly by the addition of cyanocobalamin. Strain Wf grew well in basal medium and produced substantial amounts of fermentation products, including propionate. Other phenotypic and phylogenetic characteristics of the two isolates were almost identical. Both were facultatively anaerobic, but much better growth was observed under anaerobic conditions. Cells were Gram-positive, non-motile, non-spore-forming and pleomorphic rods with irregular V- or crescent-shaped cell arrangements. Fermentation products from glucose in the presence of excess cyanocobalamin were acetate, lactate, a small amount of succinate and CO2, in addition to propionate. Both oxidase and catalase activities were negative. The strains possessed meso-diaminopimelic acid in their peptidoglycan and their major cellular fatty acids were C13 : 0, anteiso-C15 : 0 and C15 : 0. The isolates had high genomic DNA G+C contents (68·7 and 67·4 mol%, respectively). Menaquinones MK-9(H4) and MK-10(H4) were the predominant respiratory quinones. Phylogenetic analysis based on 16S rDNA sequences placed both strains in the Actinobacteria, with Micropruina glycogenica as their closest relative (sequence similarity values of 95·8 and 95·7 %, respectively). Microlunatus phosphovorus and Friedmanniella antarctica were also related closely to the isolates. As their morphological, physiological and chemotaxonomic characteristics were distinctly different from those of any related species, Propionicimonas paludicola gen. nov., sp. nov. is proposed to accommodate these strains. The type strain of the novel species is WdT (=JCM 11933T=DSM 15597T).

  • phylogeny of numerically abundant culturable anaerobic bacteria associated with degradation of rice Plant Residue in japanese paddy field soil
    FEMS Microbiology Ecology, 2003
    Co-Authors: Hiroshi Akasaka, Tomoe Izawa, Katsuji Ueki, Atsuko Ueki
    Abstract:

    Culturable anaerobic bacterial populations on rice Plant Residue (straw and stubble with roots) in paddy field soil were found on the order of 109 CFU (colony-forming units) (g dry weight of Plant Residue)−1, and the percentages of spores were usually less than 1% of the total anaerobes. Anaerobic bacteria were isolated from each sample by picking up colonies on the roll tube agar used for the enumeration. The phylogenetic analysis of 47 isolates based on 16S rRNA gene sequences revealed that the composition of dominant culturable anaerobic bacteria on rice Plant Residue was rather simple. The most dominant group was closely related to the Cellulomonas species in the Actinobacteria phylum and accounted for more than 60% of the isolates for most of the samples. The second major group was also affiliated with the Actinobacteria phylum and tentatively named the ‘propionate-producing Actinobacteria group’ because the strains in the group commonly produced propionate. Strains in the third group, the ‘Prevotella-like group’, were Gram-negative, strictly anaerobic rods and placed in the Bacteroides phylum with 16S rRNA gene similarities of 86–92% to the closest relatives. Some other strains belonging to Betaproteobacteria and the clostridial group were also isolated. Most of the strains affiliated to the clostridial group were isolated from the heat-treated samples. Some phenotypic characteristics of representative strains of each group are also described.

Atsuko Ueki - One of the best experts on this subject based on the ideXlab platform.

  • prevotella paludivivens sp nov a novel strictly anaerobic gram negative hemicellulose decomposing bacterium isolated from Plant Residue and rice roots in irrigated rice field soil
    International Journal of Systematic and Evolutionary Microbiology, 2007
    Co-Authors: Atsuko Ueki, Hiroshi Akasaka, Daisuke Suzuki, Atsuya Satoh, Katsuji Ueki
    Abstract:

    Two strictly anaerobic bacterial strains, KB7T and A42, were isolated from rice Plant Residue and living rice roots, respectively, from irrigated rice-field soil in Japan. These two strains were closely related to each other with 16S rRNA gene sequence similarity of 99.8 %. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. Growth was remarkably stimulated by the addition of haemin to the medium. The strains utilized various saccharides including xylan, xylose, pectin and carboxymethylcellulose and produced acetate and succinate with small amounts of formate and malate. The strains grew at 10–40 °C; optimum growth was observed at 30 °C and pH 5.7–6.7. Oxidase, catalase and nitrate-reducing activities were not detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C15 : 0 and iso-C17 : 0 3-OH. Menaquinones MK-11 and MK-11(H2) were the major respiratory quinones and the genomic DNA G+C content was 39.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. 16S rRNA gene sequence analysis showed that the most related species to both strains was Prevotella oulorum (92.8–92.9 % similarity). Prevotella veroralis and Prevotella melaninogenica were the next most closely related known species with sequence similarities of 91.9–92.4 %. Based on differences in the phylogenetic, ecological, physiological and chemotaxonomic characteristics between the two isolates and related species, it is proposed that strains KB7T and A42 represent a novel species, Prevotella paludivivens sp. nov. This is the first described Prevotella species derived from a natural habitat; all other Prevotella species are from mammalian sources. The type strain of Prevotella paludivivens is KB7T (=JCM 13650T=DSM 17968T).

  • prevotella paludivivens sp nov a novel strictly anaerobic gram negative hemicellulose decomposing bacterium isolated from Plant Residue and rice roots in irrigated rice field soil
    International Journal of Systematic and Evolutionary Microbiology, 2007
    Co-Authors: Atsuko Ueki, Hiroshi Akasaka, Daisuke Suzuki, Atsuya Satoh, Katsuji Ueki
    Abstract:

    Two strictly anaerobic bacterial strains, KB7(T) and A42, were isolated from rice Plant Residue and living rice roots, respectively, from irrigated rice-field soil in Japan. These two strains were closely related to each other with 16S rRNA gene sequence similarity of 99.8 %. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. Growth was remarkably stimulated by the addition of haemin to the medium. The strains utilized various saccharides including xylan, xylose, pectin and carboxymethylcellulose and produced acetate and succinate with small amounts of formate and malate. The strains grew at 10-40 degrees C; optimum growth was observed at 30 degrees C and pH 5.7-6.7. Oxidase, catalase and nitrate-reducing activities were not detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0), C(15 : 0) and iso-C(17 : 0) 3-OH. Menaquinones MK-11 and MK-11(H(2)) were the major respiratory quinones and the genomic DNA G+C content was 39.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. 16S rRNA gene sequence analysis showed that the most related species to both strains was Prevotella oulorum (92.8-92.9 % similarity). Prevotella veroralis and Prevotella melaninogenica were the next most closely related known species with sequence similarities of 91.9-92.4 %. Based on differences in the phylogenetic, ecological, physiological and chemotaxonomic characteristics between the two isolates and related species, it is proposed that strains KB7(T) and A42 represent a novel species, Prevotella paludivivens sp. nov. This is the first described Prevotella species derived from a natural habitat; all other Prevotella species are from mammalian sources. The type strain of Prevotella paludivivens is KB7(T) (=JCM 13650(T)=DSM 17968(T)).

  • paludibacter propionicigenes gen nov sp nov a novel strictly anaerobic gram negative propionate producing bacterium isolated from Plant Residue in irrigated rice field soil in japan
    International Journal of Systematic and Evolutionary Microbiology, 2006
    Co-Authors: Atsuko Ueki, Hiroshi Akasaka, Daisuke Suzuki, Katsuji Ueki
    Abstract:

    A strictly anaerobic, propionate-producing bacterial strain (WB4T) isolated from rice Plant Residue in anoxic rice-field soil in Japan was characterized phenotypically and phylogenetically. Cells were Gram-negative, non-motile, non-spore-forming, short rods. The strain utilized various sugars and produced propionate and acetate as major fermentation products with a small amount of succinate. The optimum growth temperature was 30 °C. Oxidase, catalase and nitrate-reducing activities were negative. The major cellular fatty acids were anteiso-C15 : 0, C15 : 0 and anteiso-C17 : 0 3-OH. Menaquinone MK-8(H4) was the major respiratory quinone. The genomic DNA G+C content was 39·3 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence placed the strain in the phylum ‘Bacteroidetes’. The closest relative to strain WB4T was an environmental clone from water contaminated with equine manure (sequence similarity of 99·7 %) and the strain formed a distinct cluster with other environmental clones mainly from freshwater sediments. The closest recognized species were members of the genus Dysgonomonas, with 16S rRNA gene sequence similarities of 90·9–89·8 %. Bacteroides merdae was the next closest recognized species (similarity of 88·7 % to the type strain). Given that the ecological, physiological and chemotaxonomic characteristics of strain WB4T were different from those of any related species, a new genus and species Paludibacter propionicigenes gen. nov., sp. nov., is proposed to accommodate it. The type strain is WB4T (=JCM 13257T=DSM 17365T).

  • propionicimonas paludicola gen nov sp nov a novel facultatively anaerobic gram positive propionate producing bacterium isolated from Plant Residue in irrigated rice field soil
    International Journal of Systematic and Evolutionary Microbiology, 2003
    Co-Authors: Hiroshi Akasaka, Atsuko Ueki, Satoshi Hanada, Yoichi Kamagata, Katsuji Ueki
    Abstract:

    Two propionate-producing strains (WdT and Wf) that were isolated anaerobically from Plant Residue of irrigated rice-field soil in Japan were characterized phenotypically and phylogenetically. The growth rate of strain WdT was very slow in basal medium, but both growth and propionate production were stimulated significantly by the addition of cyanocobalamin. Strain Wf grew well in basal medium and produced substantial amounts of fermentation products, including propionate. Other phenotypic and phylogenetic characteristics of the two isolates were almost identical. Both were facultatively anaerobic, but much better growth was observed under anaerobic conditions. Cells were Gram-positive, non-motile, non-spore-forming and pleomorphic rods with irregular V- or crescent-shaped cell arrangements. Fermentation products from glucose in the presence of excess cyanocobalamin were acetate, lactate, a small amount of succinate and CO2, in addition to propionate. Both oxidase and catalase activities were negative. The strains possessed meso-diaminopimelic acid in their peptidoglycan and their major cellular fatty acids were C13 : 0, anteiso-C15 : 0 and C15 : 0. The isolates had high genomic DNA G+C contents (68·7 and 67·4 mol%, respectively). Menaquinones MK-9(H4) and MK-10(H4) were the predominant respiratory quinones. Phylogenetic analysis based on 16S rDNA sequences placed both strains in the Actinobacteria, with Micropruina glycogenica as their closest relative (sequence similarity values of 95·8 and 95·7 %, respectively). Microlunatus phosphovorus and Friedmanniella antarctica were also related closely to the isolates. As their morphological, physiological and chemotaxonomic characteristics were distinctly different from those of any related species, Propionicimonas paludicola gen. nov., sp. nov. is proposed to accommodate these strains. The type strain of the novel species is WdT (=JCM 11933T=DSM 15597T).

  • phylogeny of numerically abundant culturable anaerobic bacteria associated with degradation of rice Plant Residue in japanese paddy field soil
    FEMS Microbiology Ecology, 2003
    Co-Authors: Hiroshi Akasaka, Tomoe Izawa, Katsuji Ueki, Atsuko Ueki
    Abstract:

    Culturable anaerobic bacterial populations on rice Plant Residue (straw and stubble with roots) in paddy field soil were found on the order of 109 CFU (colony-forming units) (g dry weight of Plant Residue)−1, and the percentages of spores were usually less than 1% of the total anaerobes. Anaerobic bacteria were isolated from each sample by picking up colonies on the roll tube agar used for the enumeration. The phylogenetic analysis of 47 isolates based on 16S rRNA gene sequences revealed that the composition of dominant culturable anaerobic bacteria on rice Plant Residue was rather simple. The most dominant group was closely related to the Cellulomonas species in the Actinobacteria phylum and accounted for more than 60% of the isolates for most of the samples. The second major group was also affiliated with the Actinobacteria phylum and tentatively named the ‘propionate-producing Actinobacteria group’ because the strains in the group commonly produced propionate. Strains in the third group, the ‘Prevotella-like group’, were Gram-negative, strictly anaerobic rods and placed in the Bacteroides phylum with 16S rRNA gene similarities of 86–92% to the closest relatives. Some other strains belonging to Betaproteobacteria and the clostridial group were also isolated. Most of the strains affiliated to the clostridial group were isolated from the heat-treated samples. Some phenotypic characteristics of representative strains of each group are also described.

Hiroshi Akasaka - One of the best experts on this subject based on the ideXlab platform.

  • prevotella paludivivens sp nov a novel strictly anaerobic gram negative hemicellulose decomposing bacterium isolated from Plant Residue and rice roots in irrigated rice field soil
    International Journal of Systematic and Evolutionary Microbiology, 2007
    Co-Authors: Atsuko Ueki, Hiroshi Akasaka, Daisuke Suzuki, Atsuya Satoh, Katsuji Ueki
    Abstract:

    Two strictly anaerobic bacterial strains, KB7T and A42, were isolated from rice Plant Residue and living rice roots, respectively, from irrigated rice-field soil in Japan. These two strains were closely related to each other with 16S rRNA gene sequence similarity of 99.8 %. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. Growth was remarkably stimulated by the addition of haemin to the medium. The strains utilized various saccharides including xylan, xylose, pectin and carboxymethylcellulose and produced acetate and succinate with small amounts of formate and malate. The strains grew at 10–40 °C; optimum growth was observed at 30 °C and pH 5.7–6.7. Oxidase, catalase and nitrate-reducing activities were not detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C15 : 0 and iso-C17 : 0 3-OH. Menaquinones MK-11 and MK-11(H2) were the major respiratory quinones and the genomic DNA G+C content was 39.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. 16S rRNA gene sequence analysis showed that the most related species to both strains was Prevotella oulorum (92.8–92.9 % similarity). Prevotella veroralis and Prevotella melaninogenica were the next most closely related known species with sequence similarities of 91.9–92.4 %. Based on differences in the phylogenetic, ecological, physiological and chemotaxonomic characteristics between the two isolates and related species, it is proposed that strains KB7T and A42 represent a novel species, Prevotella paludivivens sp. nov. This is the first described Prevotella species derived from a natural habitat; all other Prevotella species are from mammalian sources. The type strain of Prevotella paludivivens is KB7T (=JCM 13650T=DSM 17968T).

  • prevotella paludivivens sp nov a novel strictly anaerobic gram negative hemicellulose decomposing bacterium isolated from Plant Residue and rice roots in irrigated rice field soil
    International Journal of Systematic and Evolutionary Microbiology, 2007
    Co-Authors: Atsuko Ueki, Hiroshi Akasaka, Daisuke Suzuki, Atsuya Satoh, Katsuji Ueki
    Abstract:

    Two strictly anaerobic bacterial strains, KB7(T) and A42, were isolated from rice Plant Residue and living rice roots, respectively, from irrigated rice-field soil in Japan. These two strains were closely related to each other with 16S rRNA gene sequence similarity of 99.8 %. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. Growth was remarkably stimulated by the addition of haemin to the medium. The strains utilized various saccharides including xylan, xylose, pectin and carboxymethylcellulose and produced acetate and succinate with small amounts of formate and malate. The strains grew at 10-40 degrees C; optimum growth was observed at 30 degrees C and pH 5.7-6.7. Oxidase, catalase and nitrate-reducing activities were not detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0), C(15 : 0) and iso-C(17 : 0) 3-OH. Menaquinones MK-11 and MK-11(H(2)) were the major respiratory quinones and the genomic DNA G+C content was 39.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. 16S rRNA gene sequence analysis showed that the most related species to both strains was Prevotella oulorum (92.8-92.9 % similarity). Prevotella veroralis and Prevotella melaninogenica were the next most closely related known species with sequence similarities of 91.9-92.4 %. Based on differences in the phylogenetic, ecological, physiological and chemotaxonomic characteristics between the two isolates and related species, it is proposed that strains KB7(T) and A42 represent a novel species, Prevotella paludivivens sp. nov. This is the first described Prevotella species derived from a natural habitat; all other Prevotella species are from mammalian sources. The type strain of Prevotella paludivivens is KB7(T) (=JCM 13650(T)=DSM 17968(T)).

  • paludibacter propionicigenes gen nov sp nov a novel strictly anaerobic gram negative propionate producing bacterium isolated from Plant Residue in irrigated rice field soil in japan
    International Journal of Systematic and Evolutionary Microbiology, 2006
    Co-Authors: Atsuko Ueki, Hiroshi Akasaka, Daisuke Suzuki, Katsuji Ueki
    Abstract:

    A strictly anaerobic, propionate-producing bacterial strain (WB4T) isolated from rice Plant Residue in anoxic rice-field soil in Japan was characterized phenotypically and phylogenetically. Cells were Gram-negative, non-motile, non-spore-forming, short rods. The strain utilized various sugars and produced propionate and acetate as major fermentation products with a small amount of succinate. The optimum growth temperature was 30 °C. Oxidase, catalase and nitrate-reducing activities were negative. The major cellular fatty acids were anteiso-C15 : 0, C15 : 0 and anteiso-C17 : 0 3-OH. Menaquinone MK-8(H4) was the major respiratory quinone. The genomic DNA G+C content was 39·3 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence placed the strain in the phylum ‘Bacteroidetes’. The closest relative to strain WB4T was an environmental clone from water contaminated with equine manure (sequence similarity of 99·7 %) and the strain formed a distinct cluster with other environmental clones mainly from freshwater sediments. The closest recognized species were members of the genus Dysgonomonas, with 16S rRNA gene sequence similarities of 90·9–89·8 %. Bacteroides merdae was the next closest recognized species (similarity of 88·7 % to the type strain). Given that the ecological, physiological and chemotaxonomic characteristics of strain WB4T were different from those of any related species, a new genus and species Paludibacter propionicigenes gen. nov., sp. nov., is proposed to accommodate it. The type strain is WB4T (=JCM 13257T=DSM 17365T).

  • propionicimonas paludicola gen nov sp nov a novel facultatively anaerobic gram positive propionate producing bacterium isolated from Plant Residue in irrigated rice field soil
    International Journal of Systematic and Evolutionary Microbiology, 2003
    Co-Authors: Hiroshi Akasaka, Atsuko Ueki, Satoshi Hanada, Yoichi Kamagata, Katsuji Ueki
    Abstract:

    Two propionate-producing strains (WdT and Wf) that were isolated anaerobically from Plant Residue of irrigated rice-field soil in Japan were characterized phenotypically and phylogenetically. The growth rate of strain WdT was very slow in basal medium, but both growth and propionate production were stimulated significantly by the addition of cyanocobalamin. Strain Wf grew well in basal medium and produced substantial amounts of fermentation products, including propionate. Other phenotypic and phylogenetic characteristics of the two isolates were almost identical. Both were facultatively anaerobic, but much better growth was observed under anaerobic conditions. Cells were Gram-positive, non-motile, non-spore-forming and pleomorphic rods with irregular V- or crescent-shaped cell arrangements. Fermentation products from glucose in the presence of excess cyanocobalamin were acetate, lactate, a small amount of succinate and CO2, in addition to propionate. Both oxidase and catalase activities were negative. The strains possessed meso-diaminopimelic acid in their peptidoglycan and their major cellular fatty acids were C13 : 0, anteiso-C15 : 0 and C15 : 0. The isolates had high genomic DNA G+C contents (68·7 and 67·4 mol%, respectively). Menaquinones MK-9(H4) and MK-10(H4) were the predominant respiratory quinones. Phylogenetic analysis based on 16S rDNA sequences placed both strains in the Actinobacteria, with Micropruina glycogenica as their closest relative (sequence similarity values of 95·8 and 95·7 %, respectively). Microlunatus phosphovorus and Friedmanniella antarctica were also related closely to the isolates. As their morphological, physiological and chemotaxonomic characteristics were distinctly different from those of any related species, Propionicimonas paludicola gen. nov., sp. nov. is proposed to accommodate these strains. The type strain of the novel species is WdT (=JCM 11933T=DSM 15597T).

  • phylogeny of numerically abundant culturable anaerobic bacteria associated with degradation of rice Plant Residue in japanese paddy field soil
    FEMS Microbiology Ecology, 2003
    Co-Authors: Hiroshi Akasaka, Tomoe Izawa, Katsuji Ueki, Atsuko Ueki
    Abstract:

    Culturable anaerobic bacterial populations on rice Plant Residue (straw and stubble with roots) in paddy field soil were found on the order of 109 CFU (colony-forming units) (g dry weight of Plant Residue)−1, and the percentages of spores were usually less than 1% of the total anaerobes. Anaerobic bacteria were isolated from each sample by picking up colonies on the roll tube agar used for the enumeration. The phylogenetic analysis of 47 isolates based on 16S rRNA gene sequences revealed that the composition of dominant culturable anaerobic bacteria on rice Plant Residue was rather simple. The most dominant group was closely related to the Cellulomonas species in the Actinobacteria phylum and accounted for more than 60% of the isolates for most of the samples. The second major group was also affiliated with the Actinobacteria phylum and tentatively named the ‘propionate-producing Actinobacteria group’ because the strains in the group commonly produced propionate. Strains in the third group, the ‘Prevotella-like group’, were Gram-negative, strictly anaerobic rods and placed in the Bacteroides phylum with 16S rRNA gene similarities of 86–92% to the closest relatives. Some other strains belonging to Betaproteobacteria and the clostridial group were also isolated. Most of the strains affiliated to the clostridial group were isolated from the heat-treated samples. Some phenotypic characteristics of representative strains of each group are also described.

Daisuke Suzuki - One of the best experts on this subject based on the ideXlab platform.

  • prevotella paludivivens sp nov a novel strictly anaerobic gram negative hemicellulose decomposing bacterium isolated from Plant Residue and rice roots in irrigated rice field soil
    International Journal of Systematic and Evolutionary Microbiology, 2007
    Co-Authors: Atsuko Ueki, Hiroshi Akasaka, Daisuke Suzuki, Atsuya Satoh, Katsuji Ueki
    Abstract:

    Two strictly anaerobic bacterial strains, KB7(T) and A42, were isolated from rice Plant Residue and living rice roots, respectively, from irrigated rice-field soil in Japan. These two strains were closely related to each other with 16S rRNA gene sequence similarity of 99.8 %. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. Growth was remarkably stimulated by the addition of haemin to the medium. The strains utilized various saccharides including xylan, xylose, pectin and carboxymethylcellulose and produced acetate and succinate with small amounts of formate and malate. The strains grew at 10-40 degrees C; optimum growth was observed at 30 degrees C and pH 5.7-6.7. Oxidase, catalase and nitrate-reducing activities were not detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0), C(15 : 0) and iso-C(17 : 0) 3-OH. Menaquinones MK-11 and MK-11(H(2)) were the major respiratory quinones and the genomic DNA G+C content was 39.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. 16S rRNA gene sequence analysis showed that the most related species to both strains was Prevotella oulorum (92.8-92.9 % similarity). Prevotella veroralis and Prevotella melaninogenica were the next most closely related known species with sequence similarities of 91.9-92.4 %. Based on differences in the phylogenetic, ecological, physiological and chemotaxonomic characteristics between the two isolates and related species, it is proposed that strains KB7(T) and A42 represent a novel species, Prevotella paludivivens sp. nov. This is the first described Prevotella species derived from a natural habitat; all other Prevotella species are from mammalian sources. The type strain of Prevotella paludivivens is KB7(T) (=JCM 13650(T)=DSM 17968(T)).

  • prevotella paludivivens sp nov a novel strictly anaerobic gram negative hemicellulose decomposing bacterium isolated from Plant Residue and rice roots in irrigated rice field soil
    International Journal of Systematic and Evolutionary Microbiology, 2007
    Co-Authors: Atsuko Ueki, Hiroshi Akasaka, Daisuke Suzuki, Atsuya Satoh, Katsuji Ueki
    Abstract:

    Two strictly anaerobic bacterial strains, KB7T and A42, were isolated from rice Plant Residue and living rice roots, respectively, from irrigated rice-field soil in Japan. These two strains were closely related to each other with 16S rRNA gene sequence similarity of 99.8 %. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. Growth was remarkably stimulated by the addition of haemin to the medium. The strains utilized various saccharides including xylan, xylose, pectin and carboxymethylcellulose and produced acetate and succinate with small amounts of formate and malate. The strains grew at 10–40 °C; optimum growth was observed at 30 °C and pH 5.7–6.7. Oxidase, catalase and nitrate-reducing activities were not detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C15 : 0 and iso-C17 : 0 3-OH. Menaquinones MK-11 and MK-11(H2) were the major respiratory quinones and the genomic DNA G+C content was 39.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. 16S rRNA gene sequence analysis showed that the most related species to both strains was Prevotella oulorum (92.8–92.9 % similarity). Prevotella veroralis and Prevotella melaninogenica were the next most closely related known species with sequence similarities of 91.9–92.4 %. Based on differences in the phylogenetic, ecological, physiological and chemotaxonomic characteristics between the two isolates and related species, it is proposed that strains KB7T and A42 represent a novel species, Prevotella paludivivens sp. nov. This is the first described Prevotella species derived from a natural habitat; all other Prevotella species are from mammalian sources. The type strain of Prevotella paludivivens is KB7T (=JCM 13650T=DSM 17968T).

  • paludibacter propionicigenes gen nov sp nov a novel strictly anaerobic gram negative propionate producing bacterium isolated from Plant Residue in irrigated rice field soil in japan
    International Journal of Systematic and Evolutionary Microbiology, 2006
    Co-Authors: Atsuko Ueki, Hiroshi Akasaka, Daisuke Suzuki, Katsuji Ueki
    Abstract:

    A strictly anaerobic, propionate-producing bacterial strain (WB4T) isolated from rice Plant Residue in anoxic rice-field soil in Japan was characterized phenotypically and phylogenetically. Cells were Gram-negative, non-motile, non-spore-forming, short rods. The strain utilized various sugars and produced propionate and acetate as major fermentation products with a small amount of succinate. The optimum growth temperature was 30 °C. Oxidase, catalase and nitrate-reducing activities were negative. The major cellular fatty acids were anteiso-C15 : 0, C15 : 0 and anteiso-C17 : 0 3-OH. Menaquinone MK-8(H4) was the major respiratory quinone. The genomic DNA G+C content was 39·3 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence placed the strain in the phylum ‘Bacteroidetes’. The closest relative to strain WB4T was an environmental clone from water contaminated with equine manure (sequence similarity of 99·7 %) and the strain formed a distinct cluster with other environmental clones mainly from freshwater sediments. The closest recognized species were members of the genus Dysgonomonas, with 16S rRNA gene sequence similarities of 90·9–89·8 %. Bacteroides merdae was the next closest recognized species (similarity of 88·7 % to the type strain). Given that the ecological, physiological and chemotaxonomic characteristics of strain WB4T were different from those of any related species, a new genus and species Paludibacter propionicigenes gen. nov., sp. nov., is proposed to accommodate it. The type strain is WB4T (=JCM 13257T=DSM 17365T).

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  • prevotella paludivivens sp nov a novel strictly anaerobic gram negative hemicellulose decomposing bacterium isolated from Plant Residue and rice roots in irrigated rice field soil
    International Journal of Systematic and Evolutionary Microbiology, 2007
    Co-Authors: Atsuko Ueki, Hiroshi Akasaka, Daisuke Suzuki, Atsuya Satoh, Katsuji Ueki
    Abstract:

    Two strictly anaerobic bacterial strains, KB7T and A42, were isolated from rice Plant Residue and living rice roots, respectively, from irrigated rice-field soil in Japan. These two strains were closely related to each other with 16S rRNA gene sequence similarity of 99.8 %. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. Growth was remarkably stimulated by the addition of haemin to the medium. The strains utilized various saccharides including xylan, xylose, pectin and carboxymethylcellulose and produced acetate and succinate with small amounts of formate and malate. The strains grew at 10–40 °C; optimum growth was observed at 30 °C and pH 5.7–6.7. Oxidase, catalase and nitrate-reducing activities were not detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C15 : 0 and iso-C17 : 0 3-OH. Menaquinones MK-11 and MK-11(H2) were the major respiratory quinones and the genomic DNA G+C content was 39.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. 16S rRNA gene sequence analysis showed that the most related species to both strains was Prevotella oulorum (92.8–92.9 % similarity). Prevotella veroralis and Prevotella melaninogenica were the next most closely related known species with sequence similarities of 91.9–92.4 %. Based on differences in the phylogenetic, ecological, physiological and chemotaxonomic characteristics between the two isolates and related species, it is proposed that strains KB7T and A42 represent a novel species, Prevotella paludivivens sp. nov. This is the first described Prevotella species derived from a natural habitat; all other Prevotella species are from mammalian sources. The type strain of Prevotella paludivivens is KB7T (=JCM 13650T=DSM 17968T).

  • prevotella paludivivens sp nov a novel strictly anaerobic gram negative hemicellulose decomposing bacterium isolated from Plant Residue and rice roots in irrigated rice field soil
    International Journal of Systematic and Evolutionary Microbiology, 2007
    Co-Authors: Atsuko Ueki, Hiroshi Akasaka, Daisuke Suzuki, Atsuya Satoh, Katsuji Ueki
    Abstract:

    Two strictly anaerobic bacterial strains, KB7(T) and A42, were isolated from rice Plant Residue and living rice roots, respectively, from irrigated rice-field soil in Japan. These two strains were closely related to each other with 16S rRNA gene sequence similarity of 99.8 %. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. Growth was remarkably stimulated by the addition of haemin to the medium. The strains utilized various saccharides including xylan, xylose, pectin and carboxymethylcellulose and produced acetate and succinate with small amounts of formate and malate. The strains grew at 10-40 degrees C; optimum growth was observed at 30 degrees C and pH 5.7-6.7. Oxidase, catalase and nitrate-reducing activities were not detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0), C(15 : 0) and iso-C(17 : 0) 3-OH. Menaquinones MK-11 and MK-11(H(2)) were the major respiratory quinones and the genomic DNA G+C content was 39.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. 16S rRNA gene sequence analysis showed that the most related species to both strains was Prevotella oulorum (92.8-92.9 % similarity). Prevotella veroralis and Prevotella melaninogenica were the next most closely related known species with sequence similarities of 91.9-92.4 %. Based on differences in the phylogenetic, ecological, physiological and chemotaxonomic characteristics between the two isolates and related species, it is proposed that strains KB7(T) and A42 represent a novel species, Prevotella paludivivens sp. nov. This is the first described Prevotella species derived from a natural habitat; all other Prevotella species are from mammalian sources. The type strain of Prevotella paludivivens is KB7(T) (=JCM 13650(T)=DSM 17968(T)).