著者

Yunhong Kong James Kong Dingkang Wang Heping Huang Kaiyou Geng Yonxia Wang Yun Xia

出版者

公益財団法人 応用微生物学・分子細胞生物学研究奨励会

雑誌

The Journal of General and Applied Microbiology (ISSN:00221260)

巻号頁・発行日

pp.2016.08.002, (Released:2017-02-24)

参考文献数

37

被引用文献数

14

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In the present study, high throughput 16S rRNA gene sequencing was used to investigate soil invaded by the aggressive weed Ageratina adenophora to determine its effect on the species composition, distribution, and biodiversity of the bacterial communities. Soil samples from 12 micro-sites containing a monoculture of A. adenophora plants, mixtures of A. adenophora and different native plant species, and native species alone were studied. We found that the invasion of this weed resulted in a selection of bacteria belonging to phyla Acidobacteria and Verrucomicrobia and the lack of bacteria belonging to phyla Actinobacteria and Planctomycetes, but did not affect significantly the percentage abundances of members of other phyla. A similar bacterial population selection was also observed at genus or subgroup levels. The NO3–-N level was an important factor affecting soil bacterial communities and contributed to the dominance of A. adenophora. However, the numbers of total bacterial species, and the diversity and structure of soil bacterial microbiome did not (P > 0.05) change significantly following invasion by this weed.

著者

Ryudo Ohbayashi Hideto Akai Hirofumi Yoshikawa Wolfgang R. Hess Satoru Watanabe

出版者

公益財団法人 応用微生物学・分子細胞生物学研究奨励会

雑誌

The Journal of General and Applied Microbiology (ISSN:00221260)

巻号頁・発行日

pp.2016.02.002, (Released:2016-06-01)

参考文献数

32

被引用文献数

43

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Cyanobacteria are photosynthetic microorganisms that serve as experimental model organisms for the study of photosynthesis, environmental stress responses, and the production of biofuels. Genetic tools for bioengineering have been developed as a result of such studies. However, there is still room for improvement for the tight control of experimental protein expression in these microorganisms. Here, we describe an expression system controlled by a theophylline-responsive riboswitch that we have constructed in the cyanobacterium Synechocystis sp. PCC 6803. We demonstrate that, in response to different theophylline concentrations, this riboswitch can tightly control green fluorescence protein expression in Synechocystis. Thus, this system is useful as a tool for genetic engineering and the synthetic biology of cyanobacteria.

著者

Akihito Endo Sanae Okada Hidetoshi Morita

出版者

公益財団法人 応用微生物学・分子細胞生物学研究奨励会

雑誌

The Journal of General and Applied Microbiology (ISSN:00221260)

巻号頁・発行日

vol.53, no.3, pp.191-200, 2007 (Released:2007-08-29)

参考文献数

37

被引用文献数

8 31 32

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Diversity and compositions of the Lactobacillus, Streptococcus, and Bifidobacterium group in the feces of six healthy, actively racing horses (Thoroughbreds) were analyzed by using PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR with primer sets specific for each group. PCR-DGGE analysis of the feces showed that Lactobacillus equi, Lactobacillus johnsonii, a phylogenetic relative of Lactobacillus salivarius, a phylogenetic relative of Lactobacillus gastricus, and Weissella confusa were predominant in almost all of the feces tested, and Streptococcus bovis/Streptococcus equinus was predominant in the Streptococcus group. The Bifidobacterium group was not detected by single-PCR but atypical species of the group were found in three of the six Thoroughbreds tested by nested-PCR. Calculation and estimation of lactic acid bacteria and bifidobacteria revealed that lactic acid bacteria were predominant in the feces and bifidobacteria were minor. These results indicate that the community of lactic acid bacteria and bifidobacteria in horse feces are unique because of the presence of specific species for horse feces and a minority of the Bifidobacterium group. Repeated tests of the feces from the same horse over 3 months showed that the diversity and composition of lactic acid bacteria and bifidobacteria in the feces was basically stable throughout the test period.

著者

Yoon-Jong Nam Hyun Kim Jin-Hyung Lee Hyeokjun Yoon Jong-Guk Kim

出版者

公益財団法人 応用微生物学・分子細胞生物学研究奨励会

雑誌

The Journal of General and Applied Microbiology (ISSN:00221260)

巻号頁・発行日

vol.61, no.3, pp.67-74, 2015-06-30 (Released:2015-07-29)

参考文献数

61

被引用文献数

11

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Ulleungdo and Dokdo are volcanic islands that experience a characteristic marine climate, influenced by warm currents. The richness and diversity of the plant species, particularly vascular plants, are higher on Ulleungdo than on Dokdo. In contrast to the native plant life, little is known about the diversity of soil fungi living in the rhizosphere of these two islands. In this study, we utilized the barcoded pyrosequencing method to analyze rhizosphere soil fungi on Ulleungdo and Dokdo. In total, 768 operational taxonomic units (OTUs) were analyzed from the Ulleungdo samples, while 640 OTUs and 382 OTUs were analyzed from the Dongdo and Seodo (islets of Dokdo) samples, respectively. Species richness was considerably higher in the Ulleungdo samples than in the Dongdo and Seodo samples, while there was little difference in species diversity between the samples. The taxonomic composition analyses demonstrated that members of the phylum Basidiomycota dominated the Ulleungdo samples, whereas members of the phylum Ascomycota were predominant in the Dokdo samples. Ectomycorrhizal fungi belonging to the phylum Basidiomycota, in particular, were more abundant in the Ulleungdo samples. This finding suggests that the difference in the abundance of the ectomycorrhizal fungi in the rhizospheres of Ulleungdo and Dokdo may have been affected by species richness and diversity of the vascular plants. Our study is the first detailed report of the composition of soil fungal communities on the Ulleungdo and Dokdo islands. In addition, our findings provide a basis for understanding the ecological interactions between plants and fungi.

著者

KENKICHI KODAMA TADASHI KYONO SHOJIRO KODAMA

出版者

公益財団法人 応用微生物学・分子細胞生物学研究奨励会

雑誌

The Journal of General and Applied Microbiology (ISSN:00221260)

巻号頁・発行日

vol.8, no.1, pp.52-55, 1962 (Released:2006-08-11)

参考文献数

4

被引用文献数

2 5

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A new species of yeast belonging to the Genus Pichia Hansen was isolated from exudation of a tree stump, (Carpinus spec.) in Japan. The name Pichia saitoi was proposed for this microorganism. A characteristic feature of this species is in its unique shape of ascospores.

著者

Edward Alain B. Pajarillo Jong-Pyo Chae Marilen P. Balolong Hyeun Bum Kim Dae-Kyung Kang

出版者

公益財団法人 応用微生物学・分子細胞生物学研究奨励会

雑誌

The Journal of General and Applied Microbiology (ISSN:00221260)

巻号頁・発行日

vol.60, no.4, pp.140-146, 2014 (Released:2014-10-01)

参考文献数

47

被引用文献数

141

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The high level of genetic diversity in the microflora of the gastrointestinal tract has the potential to provide numerous beneficial functions to the host. Thus it is now acknowledged that the complexity in animal functioning is linked to the interacting microbiome in the gut. Despite the importance of gut microbiome, there is a lack of information concerning the microbial communities in the pig gut during the weaning transition. This study describes the fecal microbial shifts of healthy piglets during the weaning transition using barcoded pyrosequencing of the prokaryotic 16S rRNA gene. Fecal samples were obtained from 15 piglets during the pre-weaning period (fourth week after birth) and post-weaning (sixth week after birth) and were subjected to community genomic DNA extraction for pyrosequencing analysis. As the piglets underwent the weaning transition a trend toward increased bacterial diversity was observed, based on species abundance as measured by the Shannon-Weaver index. Firmicutes (54.0%) and Bacteroidetes (59.6%) were the most dominant phyla during pre-weaning and post-weaning, respectively. During the weaning transition a distinct shift from Bacteroides to Prevotella as the most abundant genus was observed. Additionally, we detected a number of abundant gut bacterial species that have not been reported previously. Clostridium rectum, C. clostridioforme, C. lactatifermentans and Butyricimonas virosa were uniquely detected prior to weaning while Roseburia cecicola and Blautia wexlerae were detected during the post-weaning period only.

著者

Ye-Eun Kim Hyeokjun Yoon Miae Kim Yoon-Jong Nam Hyun Kim Yeonggyo Seo Gyeong-Min Lee Young Ja Kim Won-Sik Kong Jong-Guk Kim Young-Bae Seu

出版者

公益財団法人 応用微生物学・分子細胞生物学研究奨励会

雑誌

The Journal of General and Applied Microbiology (ISSN:00221260)

巻号頁・発行日

vol.60, no.2, pp.65-74, 2014 (Released:2014-05-22)

参考文献数

47

被引用文献数

14

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Dokdo, located east of the mainland of South Korea, is a volcanic island designated as a natural monument of South Korea due to its ecological value. Dokdo is divided into Dongdo and Seodo, islands with geological differences. The soil bacterial communities on Dokdo (Dongdo and Seodo) were analyzed using the pyrosequencing method. There were 1,693 and 1,408 operational taxonomic units (OTU) from Dongdo and Seodo, respectively. The statistical analyses (rarefaction curves as well as Chao1, Shannon, and Simpson indices) showed that bacterial diversity was slightly higher in Dongdo than Seodo. From results of a BLASTN search against the EzTaxon-e database, the validated reads (obtained after sequence preprocessing) were almost all classified at the phylum level. From the phylum level down to the species level, the number of classified reads considerably decreased due to the absence of information concerning unculturable or unidentified bacteria to date. Among the 36 phyla identified, three phyla (Proteobacteria, Actinobacteria and Acidobacteria) accounted for around 74.64%. The taxonomic composition was similar at the higher ranks (family and above) between Dongdo and Seodo, but a little different at the genus level. There were also various differences in the relative abundance of taxonomic ranks between Dongdo and Seodo. In particular, the proportion of the genus Acidobacterium (of the phylum Acidobacteria) was about six times higher in Seodo than Dongdo. In addition, the percentage of the genus Mycobacterium (of the phylum Actinobacteria) was nearly three times higher in Seodo than Dongdo, and the proportion of the genus Gaiella was about 3.7 times higher in Dongdo than Seodo. Overall, through the metagenomic analysis, the number of species identified in Dongdo and Seodo was 1,239 and 1,055, respectively. This information on the numerous culturable and unculturable bacteria is expected to help in the screening of new species in Dokdo.

著者

Samson Viulu Kohei Nakamura Akihiro Kojima Yuki Yoshiyasu Sakiko Saitou Kazuhiro Takamizawa

出版者

公益財団法人 応用微生物学・分子細胞生物学研究奨励会

雑誌

The Journal of General and Applied Microbiology (ISSN:00221260)

巻号頁・発行日

vol.59, no.5, pp.325-334, 2013 (Released:2013-11-08)

参考文献数

49

被引用文献数

21

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An ethanol-utilizing Fe(III)-reducing bacterial strain, OSK2AT, was isolated from a lotus field in Aichi, Japan. Phylogenetic analysis of the 16S rRNA gene sequences of OSK2AT and related strains placed it within Geobacter sulfurreducens PCAT. Strain OSK2AT was shown to be a Gram-negative, motile, rod-shaped bacterium, strictly anaerobic, 0.76−1.65 µm long and 0.28−0.45 μm wide. Its growth occurred at 20−40℃, pH 6.0−8.1, and it tolerated up to 1% NaCl. The G+C content of the genomic DNA was 61.2 mol% and DNA-DNA hybridization value with Geobacter sulfurreducens PCAT was 60.7%. The major respiratory quinone was MK-8. The major fatty acids were 16:1 ω7c, 16:0, 14:0, 15:0 iso, 16:1 ω5c, and 18:1 ω7c. Strain OSK2AT could utilize H2, ethanol, acetate, lactate, pyruvate, and formate as substrates with Fe(III)-citrate as electron acceptor. Amorphous Fe(III) hydroxide, Fe(III)-NTA, fumarate, malate, and elemental sulfur were utilized as electron acceptors with either acetate or ethanol as substrates. Results obtained from physiological, DNA-DNA hybridization, and chemotaxonomic tests support genotypic and phenotypic differentiation of strain OSK2AT from its closest relative. The isolate is assigned as a novel subspecies with the name Geobacter sulfurreducens subsp. ethanolicus, subsp. nov. (type strain OSK2AT=DSMZ 26126T=JCM 18752T).

著者

Lahiru N. Jayakody Keisuke Tsuge Akihiro Suzuki Hitoshi Shimoi Hiroshi Kitagaki

出版者

公益財団法人 応用微生物学・分子細胞生物学研究奨励会

雑誌

The Journal of General and Applied Microbiology (ISSN:00221260)

巻号頁・発行日

vol.59, no.3, pp.227-238, 2013 (Released:2013-07-17)

参考文献数

35

被引用文献数

3

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Because of the growing market for sports drinks, prevention of yeast contamination of these beverages is of significant concern. This research was performed to achieve insight into the physiology of yeast growing in sports drinks through a genome-wide approach to prevent microbial spoilage of sports drinks. The genome-wide gene expression profile of Saccharomyces cerevisiae growing in the representative sports drink was investigated. Genes that were relevant to sulphate ion starvation response were upregulated in the yeast cells growing in the drink. These results suggest that yeast cells are suffering from deficiency of extracellular sulphate ions during growth in the sports drink. Indeed, the concentration of sulphate ions was far lower in the sports drink than in a medium that allows the optimal growth of yeast. To prove the starvation of sulphate ions of yeast, several ions were added to the beverage and its effects were investigated. The addition of sulphate ions, but not chloride ions or sodium ions, to the beverage stimulated yeast growth in the beverage in a dose-dependent manner. Moreover, the addition of sulphate ions to the sports drink increased the biosynthesis of sulphur-containing amino acids in yeast cells and hydrogen sulphide in the beverage. These results indicate that sulphate ion concentration should be regulated to prevent microbial spoilage of sports drinks.

著者

Takashi Iizuka Shigeru Yamanaka Tohru Nishiyama Akira Hiraishi

出版者

公益財団法人 応用微生物学・分子細胞生物学研究奨励会

雑誌

The Journal of General and Applied Microbiology (ISSN:00221260)

巻号頁・発行日

vol.44, no.1, pp.75-84, 1998 (Released:2005-08-24)

参考文献数

47

被引用文献数

21 65

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Free-living, aerobic, copiotrophic ultramicrobacteria (UMB) that passed through a 0.45 μm membrane filter and had a cell volume of less than 0.3 μm3 were isolated from polluted urban soil by using both the direct plating method and the membrane-filter enrichment technique. The efficiency of recovering UMB from the soil was much higher in the latter method than in the former. All of the UMB isolates grew well with a doubling time of less than 6 h either in a complex nutrient medium or a chemically defined medium. The average cell volumes of the UMB isolates, as measured by scanning electron microscopy and epifluorescent microscopy with an image analysis, ranged from 0.07 to 0.22 μm3. The cell size was larger at the exponential phase of growth than at the stationary growth stage in general. Ultrathin-section electron microscopy of representatives of the UMB isolates showed that they had complete cell wall structures like typical Gram-negative or -positive bacteria. Phenotypic studies and phylogenetic analyses on the basis of 16S rDNA sequences showed that the UMB isolates were classified into three major groups, the beta and gamma subdivisions of the Proteobacteria and the Actinobacteria (the high G+C DNA group of Gram-positives). However, none of these isolates were assigned to any previously known species. These results demonstrate that free-living, relatively fast-growing, copiotrophic UMB strains undescribed so far are widely distributed in terrestrial environments, including urban soil.