Junta Sugiyama - Profile on Academia.edu (original) (raw)

Papers by Junta Sugiyama

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...

… 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 ...

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.

The Journal of General and Applied Microbiology

2. A Brief History of the Major Phases, Microbial Disturbances, and Related Biodeterioration Prob... more 2. A Brief History of the Major Phases, Microbial Disturbances, and Related Biodeterioration Problems of the Paintings and Other Artifacts at Selected Ancient Tumuli and Caves The selected ancient tumuli (tombs) and caves are divided into four groups: TT, KT, other tumuli in Japan, and caves outside Japan. The profiles, microbial outbreaks, environmental conditions, and related deterioration problems encountered at these various tumuli and caves are briefly reviewed. 2-1. The Takamatsuzuka Tumulus The TT is located on the south slope of a small hill in Asuka-mura (Asuka village), Takaichi-gun (Takaichi county), Nara Prefecture, Japan. This tumulus was constructed by compacting layers of soil to form a two-tiered dome. The diameter of the lower dome is 23 m and that of the upper dome is 17.7 m (Ishizaki and Kigawa, 2011).

The Journal of general and …, 2005

Evolutionary relationships of the two basal fungal phyla Chytridiomycota and Zygomycota are revie... more Evolutionary relationships of the two basal fungal phyla Chytridiomycota and Zygomycota are reviewed in light of recent molecular phylogenetic investigation based on rDNA (nSSU, nLSU rDNA), entire mitochondrial genomes, and nuclear protein coding gene sequences (e.g., EF-1a a, RPB1). Accumulated molecular evidence strongly suggests that the two basal fungal phyla are not monophyletic. For example, the chytridiomycete order Blastocladiales appears to be closely related to the zygomycete order Entomophthorales. Within the Zygomycota, a monophyletic clade, consisting of the Dimargaritales, Harpellales, and Kickxellales, which is characterized by a shared unique septal ultrastructure, was identified. Moreover, evidence for the exclusion of zygomycete orders Amoebidiales and Eccrinales from the Fungi, and their placement at the Animal-Fungi boundary has been clearly documented. Microsporidia, a group of amitochondriate organisms currently under intensive study, is not supported as derived within the Fungi, but a fungal affinity cannot be ruled out. Taking these molecular phylogenetic studies into account, we proposed a hypothetical evolutionary framework of basal fungi.

The aim of this article is to describe the draft genome sequence of the anamorphic yeast Saitoell... more The aim of this article is to describe the draft genome sequence of the anamorphic yeast Saitoella complicata in the subphylum Taphrinomycotina and briefl y discuss the phylogenetic and evolutionary implications. The phylum Ascomycota consists of three subphyla Taphrinomycotina, Saccharomycotina, and Pezizomycotina (Hibbett et al., 2007). The subphylum Taphrinomycotina consists of the following four classes: Neolectomycetes, Pneumocystidomycetes, Schizosaccharomycetes, and Taphrinomycetes (Hibbett et al., 2007). Although the genus Saitoella belongs to the Taphrinomycotina, it does not belong to any class (Hibbett et al., 2007). The genus Saitoella consists of a single species, Saitoella complicata. We believe that this fungus is a key fungus to elucidate the phylogenetic relationships among the Taphrinomycotina. Saitoella was described as a new yeast genus with the type species S. complicata in 1987 (Goto et al., 1987). This anamorphic, saprobic yeast shares some characteristics with the yeast taxa of both phyla Ascomycota and Basidiomycota. For example, the negative diazonium blue B (DBB) reaction and negative extracellular DNase activity resemble characteristics of ascomycetous yeasts, whereas the positive urease activity, major ubiquinone system Q-10, and enteroblastic budding resemble those of basidiomycetous yeasts (Goto et al., 1987; Sugiyama et al., 1985). The 18S rDNA sequence comparison-based analysis showed that Saitoella and Taphrina form a monophyletic lineage that diverged prior to the separation of other ascomycetes (Nishida and Sugiyama, 1993). S. complicata Goto, Sugiy., Hamam. & Komag. NBRC 10748 (= JCM 7358, = IAM 12963; type strain) was used in this study. After the strain had been cultivated in YM broth (yeast extract, 3 g; malt extract, 3 g; peptone, 5 g; dextrose, 10 g; water, 1 L) at 25 C for 3 days, the cells were washed 3 times using TE buffer (pH 8.0). The genome DNA was extracted from 7 10 9 cells and purifi ed using a QIAamp DNA Micro Kit (QIAGEN). The genome sequencing was performed using the massively parallel DNA sequencer Roche GS FLX Titanium. The result of sequencing is summarized in Table 1. The assemblies of the reads were performed using the assembler software Newbler version 2.3 (454 sequencing, Roche). Assembly of the sequence data resulted in 7,981 contigs (12,981,880 bases). Those

The Journal of General and Applied Microbiology, 1998

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.

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

The self-splicing RNAs known as group I introns exist in many organisms, but their distribution i... more The self-splicing RNAs known as group I introns exist in many organisms, but their distribution is difficult to explain. We hypothesize that group I introns have been transferred between a parasite and its host. We describe here the discovery of a common group I intron sequence between a plant-parasitic fungus, Protomyces inouyei, and its host, Youngia japonica. It strongly supports our theory that the group I intron had been transferred from the host plant to the parasitic fungus in the course of evolution.

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

The Journal of General and Applied Microbiology, 1993

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...

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

Fungal Diversity and Phylogeny with Emphasis on 18S Ribosomal DNA Sequence Divergence

Microbial Diversity in Time and Space, 1996

D. S. Hibbett). a v a i l a b l e a t w w w . s c i e n c e d i r e c t . c o m j o u r n a l h o... more D. S. Hibbett). a v a i l a b l e a t w w w . s c i e n c e d i r e c t . c o m j o u r n a l h o m e p a g e : w w w . e l s e v i e r . c o m / l o c a t e / m y c r e s m y c o l o g i c a l r e s e a r c h 1 1 1 ( 2 0 0 7 ) 5 0 9 -5 4 7 Eumycota Lichens Molecular phylogenetics Mycota Nomenclature Systematics a b s t r a c t A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecanoromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae.

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

The Journal of General and Applied Microbiology, 1997

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.

Phycological Research, 1998

Twenty-eight axenio planktonic cyanobacterial strains (10 Microcystis, three Osciiiatoria, one Sp... more Twenty-eight axenio planktonic cyanobacterial strains (10 Microcystis, three Osciiiatoria, one Spiruiina, one Aphanizomenon, 13 Anabaena) were investigated for their fatty acid composition by measurement of nonpolar and hydroxy fatty acids. No 2-hydroxy fatty acids were detected in any strain, but 3-hydroxy fatty acids were detected in minor quantities in 24 strains. The highest portion of total fatty acids were non-polar fatty acids. Qualitative and quantitative analyses of 3-hydroxy fatty acids showed no taxonomic value in these strains, while the type of non-polar fatty acid composition was shown to be consistent within Microcystis and Anabaena strains, distinguishing them as type 4, characterized by the presence of 18:4, and type 2, characterized by 18;3 (a) of the Kenyon-Murata system. Two Osciiiatoria agardhii Gomont strains were also included in the type 2 group due to the presence of 18: 3 (a), but the difference in characteristics of 16:2 and 16:3 between 0. agardhii and Anabaena turther dmdeti type 2 into two subgroups: type 2A for Anabaena and type 2B for 0. agardhii. A simplified unweighted pair group method with arithmetic averages (UPGMA) dendrogram demonstrated that the classification of 28 strains {Microcystis spp., Anabaena spp,, Aphanizomenon fios-aquae (Lemmermann) Ralfs f. graciie (Lemmermann) Elenkin, 0. agardhii and Spiruiinasubsaisa Oersted ex Gomont based on numerical analysis of nonpolar fatty acids corresponded to morphological species criteria, suggesting that non-polar fatty acid composition is a valuable chemical marker in the taxonomy of planktonic cyanobacteria. However, the fatty acid composition in Csciiiatoria raciborskii is similar to that of Microcystis and very different from that of 0. agardhii, suggesting its special position in Osciiiatoria and the chemical diversity in the genus Osciiiatoria.

Antonie van …, 2000

The ubiquinone (coenzyme Q) systems were determined for 176 teleomorphic isolates, 14 anamorphic ... more The ubiquinone (coenzyme Q) systems were determined for 176 teleomorphic isolates, 14 anamorphic isolates, and three samples of fruit-bodies of Dendrosphaera eberhardtii, which belonged to Eurotiales, Onygenales, and related taxa. In Eurotiales, Ascosphaera had Q-9, whereas Bettsia had Q-10. All isolates of Monascaceae had the Q-10 system, whereas those of four genera of Pseudeurotiaceae had the Q-10(H 2 ) system. The Q-10(H 2 ) system was found in genera of Trichocomaceae, except for Aspergillus, Penicillium, Paecilomyces, and their related taxa. However, Thermoascus had the Q-9 system. In Onygenales, members of Arthrodermataceae had Q-9, and those of Gymnoascaceae had Q-10(H 2 ). Isolates of Myxotrichaceae were characterized by Q-10(H 2 ) with few exceptions, which had Q-10. The quinones of Onygenaceae belonged to complex systems, i.e., Q-9, 0-10 and 0-10(H 2 ), and a combination of two systems. Families Onygenaceae and Trichocomaceae are likely a phylogenetic heterogeneity. Ubiquinone analysis provides a very useful criterion of great promise for classifying eurotialean taxa and also for identifying their isolates.