Gluconacetobacter tumulisoli sp. nov., Gluconacetobacter takamatsuzukensis sp. nov. and Gluconacetobacter aggeris sp. nov., isolated from Takamatsuzuka Tumulus samples before and during the dismantling work in 2007

Nishijima, Miyuki; Tazato, Nozomi; Harita, Yutaka; Tomita, Junko; Kigawa, Rika; Sano, Chie; Sugiyama, Junta

doi:10.1099/ijs.0.051292-0

Cited by 28 publications

(20 citation statements)

References 15 publications

(45 reference statements)

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“…After the introduction of novel nitrogen-fixing acetic acid bacteria associated with coffee plants of the two species, G. johannae and G. azotocaptans, G. azotocaptans strain DS1 was reported to show additional plant growth promoting mechanisms such as producing IAA (indole-3-acetic acid, heteroauxin), solubilizing phosphate, and providing biological control against several fungal pathogens and to promote the growth of some corn varieties [14][15][16]. Though still not be surveyed for nitrogen fixing ability, the five recently introduced Gluconacetobacter species including G. tumulicola, G. asukensis, G. tumulisoli, G. takamatsuzukensis, and G. aggeris showed the growth on nitrogen-free LGI medium [17,18].…”

Section: Introductionmentioning

confidence: 99%

The Traits of the Plant Growth Promoting Acetic Acid Bacterium, Nguyenibacter Vanlangensis

Bui

et al. 2019

JST

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Two Nguyenibacter vanlangensis strains TN01LGIT and VTH-AC01 isolated by an enrichment approach using nitrogen free LGI medium from Asian rice isolation sources are expected as an additional PGPB within the Acetobacteraceae family. In this study, nitrogen fixing capability of the two N. vanlangensis strains was confirmed through nitrogenase activity’s detection by acetylene reduction analysis...

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Section: Introductionmentioning

confidence: 99%

The Traits of the Plant Growth Promoting Acetic Acid Bacterium, Nguyenibacter Vanlangensis

Bui

et al. 2019

JST

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“…Based on the sequence data, molecular phylogenetic analyses were made using the standard method. Representative studies that used our methods include Kiyuna et al (2008Kiyuna et al ( , 2011Kiyuna et al ( , 2012Kiyuna et al ( , 2015Kiyuna et al ( , 2017 and An et al (2009) for the major/noteworthy fungal colonizers, Nagatsuka et al (2009Nagatsuka et al ( , 2016Nagatsuka et al ( , 2017 for yeast and yeast-like colonizers, and Tazato et al (2012Tazato et al ( , 2015, Nishijima et al (2013Nishijima et al ( , 2017aNishijima et al ( , 2017b, and Handa et al (2016Handa et al ( , 2017, for the major/noteworthy bacterial colonizers. These original papers have revealed the identities of the TT and KT microbial isolates in question, proposing one novel genus, seventeen novel species, and six novel combinations in total, as listed in Supplementary Materials of this review.…”

Section: -3 Culture-dependent Methods: Isolation Cultivation and mentioning

confidence: 99%

“…These actions contribute to the progress of science. The majority of our 730 TT and KT microbial isolates (molds, yeasts, and bacteria) (Anonymous, 2016; cf., <http://www.riken.jp/en/pr/ topics/2016/20160719_1>) in addition to our previous depositions closely related to 16 original papers Handa et al, 2016Handa et al, , 2017Kiyuna et al, 2008Kiyuna et al, , 2011Kiyuna et al, , 2012Kiyuna et al, , 2015Kiyuna et al, , 2017Nagatsuka et al, 2009Nagatsuka et al, , 2016Nagatsuka et al, , 2017Nishijima et al, 2013Nishijima et al, , 2017aNishijima et al, , 2017bTazato et al, 2012Tazato et al, , 2015; also see Supplementary Materials) are available to researchers in microbiology, conservation science, and related fields around the world through the Japan Collection of Microorganisms (JCM), operated by the RIKEN BioResource Center in Tsukuba, Japan.…”

Section: Conclusion Lessons and Future Perspectivesmentioning

confidence: 99%

“…Initially, these acetic-acid-producing bacteria were not isolated from the TT samples by the cultivation method we used but were identified using a molecular phylogenetic approach using denaturing gradient gel electrophoresis (DGGE). This result suggested that the acetic-acid-producing bacteria might have been present in the samples collected during the dismantling or in the TT burial mound soil (see Subsection 8-2 of this review; Nishijima et al, 2013). Therefore, we have used the enrichment culture method on samples from which the DGGE results suggested the existence of acetic-acid-producing bacteria.…”

Section: -8 Gluconacetobactermentioning

confidence: 99%

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Polyphasic insights into the microbiomes of the Takamatsuzuka Tumulus and Kitora Tumulus

Sugiyama¹,

Kiyuna²,

Nishijima³

et al. 2017

J. Gen. Appl. Microbiol.

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Microbial outbreaks and related biodeterioration problems have affected the 1300-year-old multicolor (polychrome) mural paintings of the special historic sites Takamatsuzuka Tumulus (TT) and Kitora Tumulus (KT). Those of TT are designated as a national treasure. The microbiomes of these tumuli, both located in Asuka village, Nara, Japan, are critically reviewed as the central subject of this report. Using culture-dependent methods (conventional isolation and cultivation), we conducted polyphasic studies of the these microbial communities and identified the major microbial colonizers (Fusarium spp., Trichoderma spp., Penicillium spp., dark Acremonium spp., novel Candida yeast spp., Bacillus spp., Ochrobactrum spp., Stenotrophomonas tumulicola, and a few actinobacterial genera) and noteworthy microbial members (Kendrickiella phycomyces, Cephalotrichum verrucisporum (∫ ∫ ∫ ∫ ∫Doratomyces verrucisporus), Sagenomella striatispora, Sagenomella griseoviridis, two novel Cladophialophora spp., Burgoa anomala, one novel species Prototheca tumulicola, five novel Gluconacetobacter spp., three novel Bordetella spp., and one novel genus and species Krasilnikoviella muralis) involved in the biodeterioration of mural paintings, plaster walls, and stone chamber interiors. In addition, we generated microbial community data from TT and KT samples using cultureindependent methods (molecular biological methods, including PCR-DGGE, clone libraries, and pyrosequence analysis). These data are comprehensively presented, in contrast to those derived from culture-dependent methods. Furthermore, the microbial communities detected using both methods are analytically compared, and, as a result, the complementary roles of these methods and approaches are highlighted. In related contexts, knowledge of similar biodeterioration problems affecting other prehistoric cave paintings, mainly at Lascaux in France and Altamira in Spain, are referred to and commented upon. Based on substrate preferences (or ecological grouping) and mapping (plotting detection sites of isolates), we speculate on the possible origins and invasion routes whereby the major microbial colonizers invaded the TT stone chamber interior. Finally, concluding remarks, lessons, and future perspectives based on our microbiological surveys of these ancient tumuli, and similar treasures outside of Japan, are briefly presented. A list of the microbial taxa that have been identified and fully or briefly described by us as known and novel taxa for TT and KT isolates since 2008 is presented in Supplementary Materials. 64SUGIYAMA et al.

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“…Sugiyama et al, 2009;Tazato et al, 2012;Nishijima et al, 2013). We obtained 365 bacterial isolates from 64 samples of TT and 42 samples of KT collected between September 2005 and April 2007 ) and September 2005 and June 2006, respectively.…”

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confidence: 99%

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

Harita

Tazato

Nagatsuka

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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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 mouldy 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 Stenotrophomonas chelatiphaga LPM-5 T . Based on our analysis of the phenotypic (cultural, morphological, physiological and chemotaxonomic) characteristics and genotypic/molecular characteristics (DNA base composition, DNA-DNA relatedness, and 16S rRNA and gyrB gene sequences), the novel species name Stenotrophomonas tumulicola sp. nov. is proposed for the group A isolates with the type strain T5916-2-1b The Takamatsuzuka Tumulus (TT) and Kitora Tumulus (KT), which are thought to have been built sometime between the late 7th and early 8th centuries, are circular burial mounds located in Asuka-mura, Takaichi County, Nara Prefecture, Japan. TT and KT were excavated in 1972 and 2004, respectively, and Since the respective excavations, both stone chamber interiors have been exposed to microbial disturbances (e.g. moulds and bacteria) that eventually produced biofilms (or viscous gels) on the wall plaster of the chamber interiors (Kigawa et al., , 2015Sugiyama et al., 2009;Ishizaki & Kigawa, 2011). The stone walls of TT and KT have been relocated and the mural paintings are being repaired. and Stenotrophomonas acidaminiphila DSM 13117 T ) were cultivated on nutrient agar or in nutrient broth (Oxoid) at 30 8C for 24 h for all tests, except for analysis of the cellular fatty acid (CFA) profile. Among the Stenotrophomonas isolates used in this study, the selected isolates, including the type strain of a novel species, have been deposited in two public culture collections (JCM in Tsukuba, Japan, and NCIMB in Aberdeen, UK), and the reference strains of known Stenotrophomonas species used for this study are listed (Table S1).Almost-complete 16S rRNA gene sequences (1470 or 1472 bp) were determined according to previously described methods (Tazato et al., 2012) and these sequences were deposited in DDBJ (Table S1). The sequences were compared with those retrieved from DDBJ/ENA (EMBL)/GenBank by BLAST searches (Altschul et al., 1997). The sequences of the isolates and related species from GenBank were aligned using the MUSCLE program (Edgar, 2004). A phylogenetic tree was reconstructed by the neighbour-joining method with Kimura's two-parameter model using MEGA version 6.0 (Tamura et al., 2013). 16S rRNA gene sequences of the 17 representative isolates determined in this study wer...

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Gluconacetobacter tumulisoli sp. nov., Gluconacetobacter takamatsuzukensis sp. nov. and Gluconacetobacter aggeris sp. nov., isolated from Takamatsuzuka Tumulus samples before and during the dismantling work in 2007

Cited by 28 publications

References 15 publications

The Traits of the Plant Growth Promoting Acetic Acid Bacterium, Nguyenibacter Vanlangensis

The Traits of the Plant Growth Promoting Acetic Acid Bacterium, Nguyenibacter Vanlangensis

Polyphasic insights into the microbiomes of the Takamatsuzuka Tumulus and Kitora Tumulus

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

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