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During dismantling and relocation of the Takamatsuzuka Tumulus stone chamber, many Cladophialophora and chaetothyrialean black fungi, such as Exophiala and Phialophora, were isolated from samples taken from the joints between the stone walls. However, inside the stone chamber of the Kitora Tumulus, after intermittent UV irradiation in 2009, these black fungi were also isolated from samples taken from the stone walls. Molecular phylogenetic analyses based on only nrLSU and the concatenated (nrLSU D1/D2 + ITS) sequences revealed that the 35 Takamatsuzuka and Kitora Tumuli isolates of Cladophialophora and the chaetothyrialean black fungi were divergent. Two new species of Cladophialophora are described herein: C. tumulicola from the viscous gels and various substrates on the stone walls of the Takamatsuzuka and Kitora Tumuli and C. tumbae from black substances on the plastic cover over the “thief hole,” soil and plaster pieces between the stone walls, and the exterior of the Takamatsuzuka Tumulus chamber. Also, molecular phylogenetic placements for the remaining eight Takamatsuzuka and Kitora Tumuli isolates of chaetothyrialean black fungi have been determined or suggested.

Phenotypic and genotypic characteristics of five isolates of Cephalotrichum and Sagenomella from various samples collected while dismantling the Takamatsuzuka Tumulus stone chamber were found to represent Cephalotrichum verrucisporum and Sagenomella striatispora. In addition to these, one isolate from the ceiling stone surface in the adjacent small room of the Kitora Tumulus was assignable to Sagenomella griseoviridis. Colonization on biodeteriorated plaster and stone walls as substrata or habitats of these fungi is noteworthy. Physiologically Sagenomella isolates solubilized CaCO3 and may be involved in the deterioration of the plaster walls inside the stone chamber. Cephalotrichum verrucisporum is a new addition to Japan.

Two achlorophyllous microalgal strains were isolated from the soil and white moldy colony collected inside the stone chamber of the Takamatsuzuka Tumulus in Japan. Phylogenetic analyses of the small subunit ribosomal RNA (SSU rRNA) and Dl/D2 large subunit ribosomal RNA (LSU rRNA) gene sequences, and concatenated gene sequences of the SSU and D1/D2 LSU rRNA genes indicated that our two isolates were the members of the non-photosynthetic, yeast-like microalgal Chlorellaceous genus Prototheca (Chlorellales, Trebouxiophyceae, Chlorophyta) but well distinguished from known species. Based on phenotypic and genotypic characteristics, isolates T6713-13-10T and T61213-7-11 are proposed to represent a novel species in Prototheca, P. tumulicola, with the type strain JCM 31123T (isolate T6713-13-10T).

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 culture-independent 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.

Analysis of D1/D2 large-subunit (LSU) rRNA gene sequences predicted that 17 yeast isolates, mainly from viscous gels (biofilms) taken from the stone chamber interior of the Kitora tumulus in Nara, Japan, were placed in the Yamadazyma and Zygoascus clades. Polyphasic characterization, including morphological, physiological and chemotaxonomic characteristics, multigene sequence divergence and DNA-DNA hybridization, strongly suggested the assignment of one novel species to each of the clades; these are Yamadazyma kitorensis f.a., sp. nov., with the type strain JCM 31005T (ex-type CBS 14158T=isolate K8617-6-8T), and Zygoascus biomembranicola f.a., sp. nov., with the type strain JCM 31007T (ex-type CBS 14157T=isolate K61208-2-11T). Furthermore, the transfer of five known species of the genus Candida as novel combinations to the genera Yamadazyma and Zygoascus is proposed; these are Yamadazyma olivae f.a., comb. nov. (type strain CBS 11171T=ATCC MYA-4568T), Yamadazyma tumulicola f.a., comb. nov. (type strain JCM 15403T=ex-type CBS 10917T=isolate T6517-9-5T), Yamadazyma takamatsuzukensis f.a., comb. nov. (type strain JCM 15410T=CBS 10916T = isolate T4922-1-1T), Zygoascus polysorbophila f.a., comb. nov. (type strain NRRL Y-27161T=CBS 7317T) and Zygoascus bituminiphila f.a., comb. nov. (type strain CBS 8813T=MUCL 41424T).

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-5T. 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 T5916-2-1bT ( = JCM 30961T = NCIMB 15009T). Group B, which contained only one TT and one KT isolate, was closely related to [Pseudomonas] geniculata, [P.] hibiscicola, [P.] beteli, Stenotrophomonas maltophilia and Stenotrophomonas pavanii. The two isolates were genotypically and phenotypically assignable to S. maltophilia.

Integrated analysis of phenotypic and genotypic characteristics of 20 isolates of “black particles” (“Kuro-tsubu” in Japanese), that mainly appeared on the plaster wall of the ceiling tuff stone surface of the Kitora Tumulus stone chamber interior in Asuka village, Nara, Japan, has identified them as the bulbilliferous basidiomycetous anamorphic fungus Burgoa anomala. Our 28S rRNA gene D1/D2 (28S) and internal transcribed spacer (ITS) regions sequence-based phylogenies indicated that the 20 isolates displayed no genetic divergence and firmly clustered with the authentic strain B. anomala CBS 130.38. These isolates and B. anomala CBS 130.38 grouped together with species of the teleomorphic genus Sistotrema and its allies in the Cantharelloid clade. Colonization of biodeteriorated murals, plaster, and stone walls as the substrata or habitats by this fungus colonized, are noteworthy. Additionally, B. anomala is recorded for the first time from Japan.

Huge numbers of cultural objects were damaged by microorganisms after having been soaked with seawater from the tsunami that followed the Great East Japan Earthquake on March 11, 2011. Among the cultural objects that were damaged, paper-based objects in the tsunami area were severely affected. In the present study, a culture-based analysis and on-site investigations were carried out to determine the extent of the microbial deterioration of paper-based objects (i.e., administrative documents and historical documents). Dark-colored fungi were isolated from black-spotted paper as Stachybotrys chartarum , which was observed to grow significantly in mineral salt medium supplemented with cellulose as the sole nutrient source; growth was shown in 10% NaCl. Two isolates from light red-spotted paper were related to Streptomyces sp. and Myxotrichum sp., respectively. These isolates generated red pigments in the mycelia and on the culture plates. Penicillium -related isolates were dominant in the sample tested, and they showed a higher level of NaCl tolerance. From the results of our on-site investigations, a unique discoloration, mainly black- and light red-spotted alterations caused by microbes, was observed on many paper-based objects that had been left wet for several months. The adhesive tape method applied to the black-spotted and red-spotted areas on damaged documents, Stachybotrys , Chaetomium and Cladosporium , and Actinomycetales bacterium were observed, respectively. With regard to the discoloration found on tsunami-affected paper-based objects, Stachybotrys and Streptomyces sp. seem to be responsible for the black- and red-spotted paper alterations, respectively.

A Gram-stain-positive, facultatively anaerobic actinomycete, designated strain T6220-5-2bT, was isolated from a sample taken from a mouldy spot on the surface of a mural painting (the white tiger, Byakko) inside the stone chamber of Takamatsuzuka Tumulus in Asuka village, Nara Prefecture, Japan. Based on 16S rRNA gene sequence analysis of the isolate, it was closely related to the genus Promicromonospora , but formed of a novel lineage within the family Promicromonosporaceae . The closest related species to strain T6220-5-2bT was Promicromonospora flava , with which it shared 99.1 % 16S rRNA gene sequence similarity. The isoprenoid quinone systems were menaquinones MK-9(H2), MK-9(H0) and MK-9(H4). The predominant cellular fatty acids for the isolate were anteiso-C15 : 0 and iso-C15 : 0. The peptidoglycan contained glutamic acid, aspartic acid, alanine and lysine, with the last named being the diagnostic diamino acid. The cell-wall acyl type was acetyl. The major polar lipids of the isolate were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositolmannoside, two unknown phospholipids and an unknown phosphoglycolipid. Whole-cell sugars of the isolate were galactose, glucose and ribose. The DNA G+C content of the genomic DNA was 75.2 mol%. Based on the results of phylogenetic, physiological and biochemical analyses and DNA–DNA hybridization experiments, the isolate was considered to represent a novel species of a new genus in the family Promicromonosporaceae , for which the name Krasilnikoviella muralis gen. nov., sp. nov. is proposed. The type strain of Krasilnikoviella muralis is T6220-5-2bT (=JCM 28789T=NCIMB 15040T). The reclassification of Promicromonospora flava as Krasilnikoviella flava comb. nov. is also proposed with the emended description of this species.

Ten strains of Gram-stain-negative, rod-shaped, non-spore-forming bacteria were isolated from the burial mound soil collected before the dismantling and samples collected during the dismantling work on the Takamatsuzuka Tumulus in Asuka village, Nara Prefecture, Japan in 2007. On the basis of the 16S rRNA gene sequence analysis of the isolates, they were accommodated in the genus Gluconacetobacter (class Alphaproteobacteria ) and can be separated into four groups within the cluster containing the genus Gluconacetobacter . One of the groups demonstrated a phylogenetic position identical to that of Gluconacetobacter asukensis , which was isolated from small holes on plaster walls of the stone chamber interior of Kitora Tumulus in Asuka village, Nara Prefecture, Japan. The remaining three groups consisted of novel lineages within the genus Gluconacetobacter . A total of four isolates were selected from each group and carefully identified using a polyphasic approach. The isolates were characterized on the basis of their possessing Q-10 as the major ubiquinone system and C18 : 1ω7c (58.5–65.2 %) as the predominant fatty acid. A DNA–DNA hybridization test was used to determine that the three lineages represented novel species, for which the names Gluconacetobacter tumulisoli sp. nov., Gluconacetobacter takamatsuzukensis sp. nov. and Gluconacetobacter aggeris sp. nov. are proposed. The type strains are T611xx-1-4aT ( = JCM 19097T = NCIMB 14861T), T61213-20-1aT ( = JCM 19094T = NCIMB 14859T) and T6203-4-1aT ( = JCM 19092T = NCIMB 14860T), respectively.

The Kitora tumulus, which is thought to have been built around the late seventh to early eighth century, has beautiful mural paintings which were executed directly on a very thin layer of plaster in the stone chamber. When the paintings were found, the plaster was partly detached from the stone wall and the murals were therefore considered to be likely to fall off the wall with a casual touch or stimulation. Therefore, it was decided to detach the mural paintings and to store them flat and under controlled environmental conditions. This was initiated immediately after the excavation of the tumulus in 2004. However, fungal growth and biofilm development were observed within the stone chamber during the relocation work. In 2005, small holes containing black substances were observed on certain areas of the ceiling plaster, and following investigation an acetic acid bacterium, Gluconacetobacter sp., was isolated from the black substances. The bacterium was also isolated from the ceiling, floor, and ea...

Using an integrated analysis of phenotypic and genotypic characterizations, a total of 18 isolates of “bristle-like” fungal colonizers of the Kitora and Takamatsuzuka Tumuli, which had been provisionally identified as Phialocephala phycomyces, were here determined to be Kendrickiella phycomyces (Auersw.) K. Jacobs & M. J. Wingf. The 18 isolates consisted of 10 from stone surfaces or viscous gels (biofilms) of the stone chamber interior and adjacent small room, and air in the adjacent small room of the Kitora Tumulus, and 8 from viscous gels on the stone surfaces of the stone chamber interior, plant roots, and soil in the adjacent space or stone wall interspaces (interstices) in the stone chamber of the Takamatsuzuka Tumulus. Plaster and stone walls in both tumuli were recorded as novel substrates of this fungus. Our 18S sequence-based phylogeny indicated that K. phycomyces and species of the leotiomycetous anamorph genera Chaetomella, Pilidium, Sphaerographium, and Synchaetomella formed a monophyletic lineage distant from the core taxa of the Leotiomycetes (Pezizomycotina, Ascomycota). The relationship between the physicochemical characteristics of these isolates on GYC agar plates, i.e., soluble brownish pigments and dissolution of calcium carbonate (CaCO3), and the biodeterioration of the plaster and plaster walls of both tumuli, are briefly discussed.

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.

Ten strains of Gram-stain-negative, non-spore-forming, non-motile coccobacilli were isolated from the plaster wall surface of 1300-year-old mural paintings inside the stone chamber of the Takamatsuzuka tumulus in Asuka village (Asuka-mura), Nara Prefecture, Japan. Based on 16S rRNA gene sequence analysis of the isolates, they belonged to the proteobacterial genusBordetella(classBetaproteobacteria) and could be separated into three groups representing novel lineages within the genusBordetella.Three isolates were selected, one from each group, and identified carefully using a polyphasic approach. The isolates were characterized by the presence of Q-8 as their major ubiquinone system and C16 : 0(30.0–41.8 %), summed feature 3 (C16 : 1ω7cand/or C16 : 1ω6c; 10.1–27.0 %) and C17 : 0cyclo (10.8–23.8 %) as the predominant fatty acids. The major hydroxy fatty acids were C12 : 02-OH and C14 : 02-OH. The DNA G+C content was 59.6–60.0 mol%. DNA–DNA hybridization tests confirmed that the isolates represented three separate novel species, for which the namesBordetella muralissp. nov. (type strain T6220-3-2bT = JCM 30931T = NCIMB 15006T),Bordetella tumulicolasp. nov. (type strain T6517-1-4bT = JCM 30935T = NCIMB 15007T) andBordetella tumbaesp. nov. (type strain T6713-1-3bT = JCM 30934T = NCIMB 15008T) are proposed. These results support previous evidence that members of the genusBordetellaexist in the environment and may be ubiquitous in soil and/or water.

Fumigant effects on protein-based materials were examined and compared with those of non-chemical pest-eradicating measures. The responses to six fumigants – methyl bromide, methyl iodide, ethylene oxide, methyl bromide/ethylene oxide mixture, propylene oxide and sulfuryl fluoride – were examined with two controlled atmospheres and a range of thermal treatments, using protein electrophoresis, Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry (DSC), thermal microscopy (Tmic), thermal gravimetric analysis (TGA), amino acid analysis and X-ray fluorescence (XRF) spectrometry. A model soft-tissue protein, freeze-dried chicken muscle, was shown to be affected by some fumigants, especially methyl bromide, methyl iodide and sulfuryl fluoride (Vikane®). This is the first detailed evidence of chemical alterations of a protein material by fumigants under the common treatment conditions for museum use, especially showing a possibility of protein modification by purer grade sulf...

Unidentified black spots (or stains) appeared on the plaster walls of the Takamatsuzuka and Kitora Tumuli in the village of Asuka, Nara Prefecture, Japan. Public attention was drawn to the biodeterioration of the colorful 1,300-year-old murals. A total of 46 isolates of Acremonium sect. Gliomastix were obtained from various samples (mainly black spots) of the Takamatsuzuka Tumulus (TT) (sampling period, May 2004–December 2006) and the Kitora Tumulus (KT) (June 2004–May 2007). These isolates were assignable to four known taxa and a new species in the ‘series Murorum’ sensu W. Gams as inferred from the integrated analysis of phenotypic and genotypic (i.e., ITS and 28S rDNA-D1/D2 sequences) characters: these were Acremonium masseei, A. murorum, A. felinum comb. nov. with the neotype designation, A. polychromum, and A. tumulicola sp. nov., which have been accommodated in the validated series Murorum in the section Gliomastix. The black spots on the murals of the TT and KT were caused mainly by A. masseei and A. murorum, respectively.

Penicillium appeared as the major dweller in the Takamatsuzuka Tumulus (TT) and Kitora Tumulus (KT) stone chambers, both located in the village of Asuka, Nara Prefecture, in relation to the biodeterioration of the 1,300-year-old mural paintings, plaster walls and ceilings. Of 662 Penicillium isolates from 373 samples of the TT (sampling period, May 2004-2007) and the KT (sampling period, June 2004-Sep 2007), 181 were phenotypically assigned as Penicillium sp. 1 which shared similar phenotypic characteristics of sect. Roqueforti in Penicillium subg. Penicillium. Fifteen representative isolates of Penicillium sp. 1, 13 from TT and 2 from KT, were selected for molecular phylogenetic analysis. The 28S rDNA D1/D2, ITS, beta-tubulin, and lys2 gene sequence-based phylogenies clearly demonstrated that the three known species P. roqueforti, P. carneum and P. paneum in sect. Roqueforti, and all TT and KT isolates grouped together. In addition to this, TT and KT isolates formed a monophyletic group with the ex-holotype strain CBS 101032 of P. paneum Frisvad with very strong bootstrap supports. So far, P. paneum has been isolated only from mouldy rye breads, other foods, and baled grass silage. Therefore, this is the first report of P. paneum isolation from samples relating to the biodeteriorated cultural properties such as mural paintings on plaster walls.

In an effort to clarify the cause of the deterioration of the colorfully painted murals that adorn the inner walls of the small stone chambers in the Takamatsuzuka and Kitora Tumuli in Japan, we enumerated the fungi that were isolated from moldy spots on the plaster walls collected between May 2004 and April 2005. The 262 fungal isolates from 79 samples of both tumuli were identified as approximately 100 species based on their phenotypic characters. Fusarium, Trichoderma, and Penicillium species were the predominant colonizers in the stone chamber interior and adjacent areas of both tumuli. In addition to the 28S phylogeny, neighbor-joining and Bayesian phylogenies of partial EF-1-alpha gene sequences revealed 24 genetically diverse fusaria in the Takamatsuzuka and Kitora Tumuli. Most of the fusaria were nested in clade 3 of the Fusarium solani species complex (FSSC); however, a few isolates were members of the F. oxysporum species complex (FOSC) clade or the F. avenaceum/F. tricinctum species complex clade. The FSSC isolates were compared with those detected in the Lascaux cave in France. In addition, a partial EF-1α gene phylogeny indicated that 13 Trichoderma isolates clustered in the Harzianum-Virens clade and 5 isolates in the Viride clade or Trichoderma sect. Longibrachiatum. Our analyses suggest that most of the fungi recovered from both tumuli are typically soil dwellers.

An International Symposium on the Conservation and Restoration of Cultural Property with a focus on microbial biodeterioration of cultural property was held in Tokyo, Japan on December 5–7, 2012. In addition to microbial deterioration of stone, paper and wood, available technologies and innovations in removal and protection of cultural property, monitoring fungal contamination and classification of the contamination level, this symposium showed results dealing with cultural property after earthquake and tsunami as the key issues affecting the artifacts and cultural property highlighted at this symposium. Interestingly, it was found that salt in water can control the growth of molds and fungi on documents and less growth was observed when salinity was higher. This has a greater implication when dealing with large amounts of documents after natural disaster. The papers derived from invited speakers and also posters are being published in a dedicated volume of book available to research scientists, conservationists, applied biologists and graduate students working on related subjects.

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 murals had changed to black, white or another tone, and from viscous gels (biofilms) on plaster walls. The 26S rDNA D1/D2 domain sequence-based phylogeny clearly indicates two groups of isolates. Polyphasic characterization, including morphological, physiological and chemotaxonomic characteristics, and sequence analysis of the 26S rDNA D1/D2 domain and ITS regions suggest that each group is assignable to one of two novel species within the Candida membranifaciens clade. Proposed herein are the names Candida tumulicola sp. nov. (originally T6517-9-5T; holotype JCM 15403T; isotypes CBS 10917T, NBRC 104392T) and Candida takamatsuzukensis sp. nov. (originally T4922-1-1T; holotype JCM 15410T; isotypes CBS 10916T, NBRC 104391T). The 26S rDNA D1/D2 domain sequence divergence indicates that C. tumulicola differs from Candida friedrichii NBRC 10277T, the type strain of the nearest species, in 15 nucleotides (3 %), whereas C. takamatsuzukensis differs from Candida insectorum NBRC 10283T and Pichia mexicana NBRC 10544T, the type strains of the nearest species, in 20 nucleotides (4 %). Both novel species are also clearly distinguishable from the species closest to them by various physiological characteristics.