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Papers by Junta Sugiyama

Research paper thumbnail of Stenotrophomonas tumulicola sp. nov., a major contaminant of the stone chamber interior in the Takamatsuzuka Tumulus

International journal of systematic and evolutionary microbiology, Jan 11, 2015

During investigation of the biological contamination of the 1300-year-old mural paintings and pla... more During investigation of the biological contamination of the 1300-year-old mural paintings and plaster walls inside the stone chambers of the Takamatsuzuka and Kitora Tumuli (TT and KT) in Asuka-mura, Nara Prefecture, Japan, the identity of 17 bacterial isolates from blackish moldy spots and viscous gels (biofilms) collected from both tumuli (16 isolates from TT and one from KT) during our 2005-2007 microbiological survey was systematically elucidated. One cluster of the major bacterial isolates was assigned to the genus Stenotrophomonas (class Gammaproteobacteria) by phylogenetic analysis of the 16S rRNA gene sequences. These isolates were divided into two groups A and B. Group A comprised 15 TT isolates that took a phylogenetic position near S. chelatiphaga LPM-5T. Based on our analysis of the phenotypic (cultural, morphological, physiological, and chemotaxonomic) characters and genotypic/molecular ones (DNA base composition, DNA-DNA relatedness, and 16S rRNA and gyrB gene sequence...

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Research paper thumbnail of Candida tumulicola sp. nov. and Candida takamatsuzukensis sp. nov., novel yeast species assignable to the Candida membranifaciens clade, isolated from the stone …

… of Systematic and …, 2009

During a survey of the mycobiota in the stone chamber of the Takamatsu-zuka tumulus in the villag... more During a survey of the mycobiota in the stone chamber of the Takamatsu-zuka tumulus in the village of Asuka, Nara Prefecture, Japan, we isolated 19 yeast strains assigned to the genus Candida from various samples, taken mainly from mouldy spots where the colour of the ...

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Research paper thumbnail of Gluconacetobacter tumulicola sp. nov. and Gluconacetobacter asukensis sp. nov., isolated from the stone chamber interior of the Kitora Tumulus

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2012

Six Gram-negative, rod-shaped, non-spore-forming bacterial strains were isolated from small holes... more Six Gram-negative, rod-shaped, non-spore-forming bacterial strains were isolated from small holes on plaster walls of the stone chamber interior of the Kitora Tumulus in Asuka village, Nara Prefecture, Japan. These were investigated by means of a polyphasic approach. All the isolates were strictly aerobic and motile by peritrichous flagella. Phylogenetic trees generated based on 16S rRNA gene sequences identified two novel lineages (comprising five isolates and one isolate, respectively) within the genus Gluconacetobacter . The isolates were characterized by having Q-10 as the major ubiquinone system and C18 : 1ω7c (58.7–63.1 % of the total) as the predominant fatty acid. DNA–DNA hybridization experiments endorsed the species rank for the two lineages, for which the names Gluconacetobacter tumulicola sp. nov. (type strain K5929-2-1bT = JCM 17774T = NCIMB 14760T) and Gluconacetobacter asukensis sp. nov. (type strain K8617-1-1bT = JCM 17772T = NCIMB 14759T) are proposed.

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Research paper thumbnail of Polyphasic insights into the microbiomes of the Takamatsuzuka Tumulus and Kitora Tumulus

The Journal of General and Applied Microbiology

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Research paper thumbnail of Evolutionary relationships among basal fungi (Chytridiomycota and Zygomycota): Insights from molecular phylogenetics

The Journal of general and …, 2005

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Research paper thumbnail of Draft genome sequencing of the enigmatic yeast Saitoella complicata

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Research paper thumbnail of Draft genome sequencing of the enigmatic basidiomycete Mixia osmundae

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Research paper thumbnail of Detection of multiple insertions of group I introns in the nuclear small subunit ribosomal RNA gene from the ustilaginomycete Graphiola phoenicis parasitic on palm

The Journal of General and Applied Microbiology, 1998

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Research paper thumbnail of Phylogenetic positions of rust fungi parasitic on ferns: Evidence from 18S rDNA sequence analysis

Mycoscience, 1999

Molecular phylogenetic analyses of fern rusts were carried out based on 18S rDNA sequences. We se... more Molecular phylogenetic analyses of fern rusts were carried out based on 18S rDNA sequences. We sequenced the 18S rDNAs of fern rusts (Hyalopsora polypodii andUredinopsis intermedia) and non-fern rusts (Aecidium epimedii, Coleosporium asterum, Ochropsora kraunhiae, Puccinia suzutake andPhysopella ampelopsidis) and analyzed their phylogenetic relationships with other members of the Urediniomycetes. Our bootstrapped neighbor-joining tree obtained from these analyses showed that rust fungi were apparently monophyletic at high confidence level (100% bootstrap confidence). In this molecular phylogenetic tree, the two fern rusts did not occupy the basal position within the rust fungal lineage and did not form a monophyletic lineage. Two species of the Cronartiaceae (Peridermium harknessii, Cronartium ribicola) and one species of the Coleosporiaceae (Coleosporium asterum) grouped with the fern rusts. Therefore, our results suggested that the two fern rusts were not primitive. On the other hand,Mixia osmundae, which is parasitic on the primitive fernOsmunda, was phylogenetically far from the fern rusts.

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Research paper thumbnail of Rhodopseudomonas rutila Is a Later Subjective Synonym of Rhodopseudomonas palustris

Phenotypic, chemotaxonomic, and DNA-DNA hybridization studies of strains of Rhodopseudomonas ruti... more Phenotypic, chemotaxonomic, and DNA-DNA hybridization studies of strains of Rhodopseudomonas rutih Akiba et al. 1983 and Rhodopseudomonas palustris (Molisch 1907) van Niel 1944 demonstrated synonymy between the two species. We propose that they be classified into a single species, retaining the name R. palustris. Rhodopseudomonas rutila is a species of phototrophic purple nonsulfur bacteria which was validly published by Akiba

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Research paper thumbnail of A common group I intron between a plant parasitic fungus and its host

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Research paper thumbnail of Septal pore ultrastructure of Leucosporidium lari-marini, a basidiomycetous yeast, and its taxonomic implications

The Journal of General and Applied Microbiology, 1993

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Research paper thumbnail of Phylogenetic relationships of the helical-shaped bacteria in the alpha Proteobacteria inferred from 16S rDNA sequences

The Journal of general and applied microbiology, 1997

16S ribosomal RNA gene sequences from seven strains of Aquaspirillum peregrinum, Aqu. itersonii, ... more 16S ribosomal RNA gene sequences from seven strains of Aquaspirillum peregrinum, Aqu. itersonii, Aqu. polymorphum, and Oceanospirillum pusillum were compared with homologous sequences from other members of helical-shaped bacteria. The bootstrapped neighbor-joining tree, inferred from 887 aligned sites, placed the spirillum taxa assigned to Aquaspirillum, Oceanospirillum, Azospirillum, Magnetospirillum, Rhodospirillum, and Rhodocista of the Proteobacteria in seven clusters of alpha Proteobacteria separately from other shapes of bacteria. Aqu. peregrinum and Aqu. itersonii grouped together in 88% bootstrap support. They were more related to Rhodospirillum rubrum and Rsp. photometricum than Aqu. polymorphum. Aqu. polymorphum was close to Magnetospirillum gryphiswaldense, Mag. magnetotacticum, Rsp. fulvum, and Rsp. molischianum, and more close to Mag. gryphiswaldense. Oce. pusillum was not related to other spirillum taxa and was placed in a separate branch. Rhodocista was very closely r...

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Research paper thumbnail of Electrophoretic comparison of enzymes as a chemotaxonomic aid among Aspergillus taxa: (3) The identity of the xerophilic species A. penicillioides in subgenus Aspergillus section Restricti

The Journal of General and Applied Microbiology, 1996

ABSTRACT

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Research paper thumbnail of Fungal Diversity and Phylogeny with Emphasis on 18S Ribosomal DNA Sequence Divergence

Microbial Diversity in Time and Space, 1996

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Research paper thumbnail of Myc Res 2007 Higher-level Fungi

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Research paper thumbnail of Phylogenetic position of the marine subdivision of Agrobacterium species based on 16S rRNA sequence analysis

The Journal of General and Applied Microbiology, 1997

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Research paper thumbnail of Identity of the xerophilic species Aspergillus penicillioides: Integrated analysis of the genotypic and phenotypic characters

The Journal of General and Applied Microbiology, 1999

We examined the identity of Aspergillus penicillioides, the typical xerophilic and strictly anamo... more We examined the identity of Aspergillus penicillioides, the typical xerophilic and strictly anamorphic species, using an integrated analysis of the genotypic and phenotypic characters. Our experimental methods on two genotypic characters, i.e., DNA base composition using the HPLC method and DNA relatedness using the nitrocellulose filter hybridization technique between A. flavus, A. oryzae, and their close relations revealed a good agreement with the values by buoyant density (for DNA base composition) and spectrophotometric determination (for DNA relatedness) reported by Kurtzman et al. in 1986. On the basis of these comparisons, we examined DNA base composition and DNA relatedness of six selected strains of A. penicillioides, including IFO 8155 (originally described as A. vitricola), one strain of A. restrictus, and the respective strains from Eurotium amstelodami, E. repens, and E. rubrum. As a result, five strains within A. penicillioides, including the neotype strain NRRL 4548, had G+C contents of 46 to 49 mol%, whereas IFO 8155 had 50 mol%. A. restrictus had 52 mol%, and three Eurotium species ranged from 46 to 49 mol%. The DNA relatedness between A. penicillioides (five strains), except for IFO 8155, exhibited values greater than 70%, but the DNA complementarity between four strains and IFO 8155 in A. penicillioides revealed values of less than 40%. DNA relatedness values between three species of Eurotium were 65 to 72%. We determined 18S, 5.8S, and ITS rDNA sequences as other genotypic characters from A. penicillioides (six strains), A. restrictus, and related teleomorphic species of Eurotium. In three phylogenetic trees inferred from these sequences, five strains of A. penicillioides, including the neotype strain, were closely related to each other, whereas IFO 8155 was distantly related and grouped with other xerophilic species. Our results have suggested that A. penicillioides typified by NRRL 4548 and A. penicillioides IFO 8155 (ex holotype of A. vitricola) are not conspecific. The enzyme patterns as a genotypic character and general morphology and conidial ornamentation types as phenotypic characters supported this conclusion. Therefore the name A. vitricola Ohtsuki, typified by the holotype strain IFO 8155, should be revived. Evolutionary affinities among Aspergillus species and related teleomorphs, including the xerophilic taxa, are discussed.

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Research paper thumbnail of Chemotaxonomy of planktonic cyanobacteria based on non-polar and 3-hydroxy fatty acid composition

Phycological Research, 1998

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Research paper thumbnail of Ubiquinone systems in fungi. V. Distribution and taxonomic implications of ubiquinones in Eurotiales, Onygenales and the related plectomycete genera, except for …

Antonie van …, 2000

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Research paper thumbnail of Stenotrophomonas tumulicola sp. nov., a major contaminant of the stone chamber interior in the Takamatsuzuka Tumulus

International journal of systematic and evolutionary microbiology, Jan 11, 2015

During investigation of the biological contamination of the 1300-year-old mural paintings and pla... more During investigation of the biological contamination of the 1300-year-old mural paintings and plaster walls inside the stone chambers of the Takamatsuzuka and Kitora Tumuli (TT and KT) in Asuka-mura, Nara Prefecture, Japan, the identity of 17 bacterial isolates from blackish moldy spots and viscous gels (biofilms) collected from both tumuli (16 isolates from TT and one from KT) during our 2005-2007 microbiological survey was systematically elucidated. One cluster of the major bacterial isolates was assigned to the genus Stenotrophomonas (class Gammaproteobacteria) by phylogenetic analysis of the 16S rRNA gene sequences. These isolates were divided into two groups A and B. Group A comprised 15 TT isolates that took a phylogenetic position near S. chelatiphaga LPM-5T. Based on our analysis of the phenotypic (cultural, morphological, physiological, and chemotaxonomic) characters and genotypic/molecular ones (DNA base composition, DNA-DNA relatedness, and 16S rRNA and gyrB gene sequence...

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Research paper thumbnail of Candida tumulicola sp. nov. and Candida takamatsuzukensis sp. nov., novel yeast species assignable to the Candida membranifaciens clade, isolated from the stone …

… of Systematic and …, 2009

During a survey of the mycobiota in the stone chamber of the Takamatsu-zuka tumulus in the villag... more During a survey of the mycobiota in the stone chamber of the Takamatsu-zuka tumulus in the village of Asuka, Nara Prefecture, Japan, we isolated 19 yeast strains assigned to the genus Candida from various samples, taken mainly from mouldy spots where the colour of the ...

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Research paper thumbnail of Gluconacetobacter tumulicola sp. nov. and Gluconacetobacter asukensis sp. nov., isolated from the stone chamber interior of the Kitora Tumulus

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2012

Six Gram-negative, rod-shaped, non-spore-forming bacterial strains were isolated from small holes... more Six Gram-negative, rod-shaped, non-spore-forming bacterial strains were isolated from small holes on plaster walls of the stone chamber interior of the Kitora Tumulus in Asuka village, Nara Prefecture, Japan. These were investigated by means of a polyphasic approach. All the isolates were strictly aerobic and motile by peritrichous flagella. Phylogenetic trees generated based on 16S rRNA gene sequences identified two novel lineages (comprising five isolates and one isolate, respectively) within the genus Gluconacetobacter . The isolates were characterized by having Q-10 as the major ubiquinone system and C18 : 1ω7c (58.7–63.1 % of the total) as the predominant fatty acid. DNA–DNA hybridization experiments endorsed the species rank for the two lineages, for which the names Gluconacetobacter tumulicola sp. nov. (type strain K5929-2-1bT = JCM 17774T = NCIMB 14760T) and Gluconacetobacter asukensis sp. nov. (type strain K8617-1-1bT = JCM 17772T = NCIMB 14759T) are proposed.

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Research paper thumbnail of Polyphasic insights into the microbiomes of the Takamatsuzuka Tumulus and Kitora Tumulus

The Journal of General and Applied Microbiology

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Research paper thumbnail of Evolutionary relationships among basal fungi (Chytridiomycota and Zygomycota): Insights from molecular phylogenetics

The Journal of general and …, 2005

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Research paper thumbnail of Draft genome sequencing of the enigmatic yeast Saitoella complicata

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Research paper thumbnail of Draft genome sequencing of the enigmatic basidiomycete Mixia osmundae

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Research paper thumbnail of Detection of multiple insertions of group I introns in the nuclear small subunit ribosomal RNA gene from the ustilaginomycete Graphiola phoenicis parasitic on palm

The Journal of General and Applied Microbiology, 1998

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Research paper thumbnail of Phylogenetic positions of rust fungi parasitic on ferns: Evidence from 18S rDNA sequence analysis

Mycoscience, 1999

Molecular phylogenetic analyses of fern rusts were carried out based on 18S rDNA sequences. We se... more Molecular phylogenetic analyses of fern rusts were carried out based on 18S rDNA sequences. We sequenced the 18S rDNAs of fern rusts (Hyalopsora polypodii andUredinopsis intermedia) and non-fern rusts (Aecidium epimedii, Coleosporium asterum, Ochropsora kraunhiae, Puccinia suzutake andPhysopella ampelopsidis) and analyzed their phylogenetic relationships with other members of the Urediniomycetes. Our bootstrapped neighbor-joining tree obtained from these analyses showed that rust fungi were apparently monophyletic at high confidence level (100% bootstrap confidence). In this molecular phylogenetic tree, the two fern rusts did not occupy the basal position within the rust fungal lineage and did not form a monophyletic lineage. Two species of the Cronartiaceae (Peridermium harknessii, Cronartium ribicola) and one species of the Coleosporiaceae (Coleosporium asterum) grouped with the fern rusts. Therefore, our results suggested that the two fern rusts were not primitive. On the other hand,Mixia osmundae, which is parasitic on the primitive fernOsmunda, was phylogenetically far from the fern rusts.

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Research paper thumbnail of Rhodopseudomonas rutila Is a Later Subjective Synonym of Rhodopseudomonas palustris

Phenotypic, chemotaxonomic, and DNA-DNA hybridization studies of strains of Rhodopseudomonas ruti... more Phenotypic, chemotaxonomic, and DNA-DNA hybridization studies of strains of Rhodopseudomonas rutih Akiba et al. 1983 and Rhodopseudomonas palustris (Molisch 1907) van Niel 1944 demonstrated synonymy between the two species. We propose that they be classified into a single species, retaining the name R. palustris. Rhodopseudomonas rutila is a species of phototrophic purple nonsulfur bacteria which was validly published by Akiba

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Research paper thumbnail of A common group I intron between a plant parasitic fungus and its host

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Septal pore ultrastructure of Leucosporidium lari-marini, a basidiomycetous yeast, and its taxonomic implications

The Journal of General and Applied Microbiology, 1993

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Research paper thumbnail of Phylogenetic relationships of the helical-shaped bacteria in the alpha Proteobacteria inferred from 16S rDNA sequences

The Journal of general and applied microbiology, 1997

16S ribosomal RNA gene sequences from seven strains of Aquaspirillum peregrinum, Aqu. itersonii, ... more 16S ribosomal RNA gene sequences from seven strains of Aquaspirillum peregrinum, Aqu. itersonii, Aqu. polymorphum, and Oceanospirillum pusillum were compared with homologous sequences from other members of helical-shaped bacteria. The bootstrapped neighbor-joining tree, inferred from 887 aligned sites, placed the spirillum taxa assigned to Aquaspirillum, Oceanospirillum, Azospirillum, Magnetospirillum, Rhodospirillum, and Rhodocista of the Proteobacteria in seven clusters of alpha Proteobacteria separately from other shapes of bacteria. Aqu. peregrinum and Aqu. itersonii grouped together in 88% bootstrap support. They were more related to Rhodospirillum rubrum and Rsp. photometricum than Aqu. polymorphum. Aqu. polymorphum was close to Magnetospirillum gryphiswaldense, Mag. magnetotacticum, Rsp. fulvum, and Rsp. molischianum, and more close to Mag. gryphiswaldense. Oce. pusillum was not related to other spirillum taxa and was placed in a separate branch. Rhodocista was very closely r...

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Research paper thumbnail of Electrophoretic comparison of enzymes as a chemotaxonomic aid among Aspergillus taxa: (3) The identity of the xerophilic species A. penicillioides in subgenus Aspergillus section Restricti

The Journal of General and Applied Microbiology, 1996

ABSTRACT

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Research paper thumbnail of Fungal Diversity and Phylogeny with Emphasis on 18S Ribosomal DNA Sequence Divergence

Microbial Diversity in Time and Space, 1996

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Research paper thumbnail of Myc Res 2007 Higher-level Fungi

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Research paper thumbnail of Phylogenetic position of the marine subdivision of Agrobacterium species based on 16S rRNA sequence analysis

The Journal of General and Applied Microbiology, 1997

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Research paper thumbnail of Identity of the xerophilic species Aspergillus penicillioides: Integrated analysis of the genotypic and phenotypic characters

The Journal of General and Applied Microbiology, 1999

We examined the identity of Aspergillus penicillioides, the typical xerophilic and strictly anamo... more We examined the identity of Aspergillus penicillioides, the typical xerophilic and strictly anamorphic species, using an integrated analysis of the genotypic and phenotypic characters. Our experimental methods on two genotypic characters, i.e., DNA base composition using the HPLC method and DNA relatedness using the nitrocellulose filter hybridization technique between A. flavus, A. oryzae, and their close relations revealed a good agreement with the values by buoyant density (for DNA base composition) and spectrophotometric determination (for DNA relatedness) reported by Kurtzman et al. in 1986. On the basis of these comparisons, we examined DNA base composition and DNA relatedness of six selected strains of A. penicillioides, including IFO 8155 (originally described as A. vitricola), one strain of A. restrictus, and the respective strains from Eurotium amstelodami, E. repens, and E. rubrum. As a result, five strains within A. penicillioides, including the neotype strain NRRL 4548, had G+C contents of 46 to 49 mol%, whereas IFO 8155 had 50 mol%. A. restrictus had 52 mol%, and three Eurotium species ranged from 46 to 49 mol%. The DNA relatedness between A. penicillioides (five strains), except for IFO 8155, exhibited values greater than 70%, but the DNA complementarity between four strains and IFO 8155 in A. penicillioides revealed values of less than 40%. DNA relatedness values between three species of Eurotium were 65 to 72%. We determined 18S, 5.8S, and ITS rDNA sequences as other genotypic characters from A. penicillioides (six strains), A. restrictus, and related teleomorphic species of Eurotium. In three phylogenetic trees inferred from these sequences, five strains of A. penicillioides, including the neotype strain, were closely related to each other, whereas IFO 8155 was distantly related and grouped with other xerophilic species. Our results have suggested that A. penicillioides typified by NRRL 4548 and A. penicillioides IFO 8155 (ex holotype of A. vitricola) are not conspecific. The enzyme patterns as a genotypic character and general morphology and conidial ornamentation types as phenotypic characters supported this conclusion. Therefore the name A. vitricola Ohtsuki, typified by the holotype strain IFO 8155, should be revived. Evolutionary affinities among Aspergillus species and related teleomorphs, including the xerophilic taxa, are discussed.

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Research paper thumbnail of Chemotaxonomy of planktonic cyanobacteria based on non-polar and 3-hydroxy fatty acid composition

Phycological Research, 1998

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Research paper thumbnail of Ubiquinone systems in fungi. V. Distribution and taxonomic implications of ubiquinones in Eurotiales, Onygenales and the related plectomycete genera, except for …

Antonie van …, 2000

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