著者

Wataru Suda Asami Nagasaki Masahiro Shishido

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.24, no.3, pp.217-223, 2009 (Released:2009-09-04)

参考文献数

40

被引用文献数

20 45

---

To investigate changes in bacterial communities associated with a fungal foliar disease, epiphytic bacteria from powdery mildew-infected and uninfected leaves of cucumber and Japanese spindle were analyzed using both culture-dependent and -independent methods. Dilution plate counting suggested that powdery mildew-infected leaves likely accommodated larger populations of phyllosphere bacteria than uninfected leaves. Community-level physiological profiles (CLPP) also indicated that functional diversity, richness, and evenness of bacterial communities were significantly greater in the phyllosphere of powdery mildew-infected leaves. Genotype diversity and richness based on band patterns of denaturing gradient gel electrophoresis (DGGE) of the phyllosphere bacterial community were greater for leaves infected by powdery mildew. A principle component analysis of CLPP and DGGE patterns revealed a clear difference between infected and uninfected leaves of both plant species. These results suggest that powdery mildew-infection results in larger bacterial populations, and greater diversity and richness, and also changes the structure of the phyllosphere bacterial community. Furthermore, DNA sequences of the DGGE bands that showed greater intensity in the infected than uninfected leaves, differed between cucumber and Japanese spindle. This suggests that specific bacteria are associated with the plant species accompanying this fungal infection.

著者

Chandan Lall K. Vinod Kumar R. Vimal Raj K. Vedhagiri P. Vijayachari

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME15149, (Released:2016-03-03)

被引用文献数

1 17

---

Leptospirosis is an emerging disease around the globe. South Andaman Island is an endemic region for leptospirosis. We herein compared the prevalence of leptospires in urban and rural areas of South Andaman Island. The PCR detection and isolation of Leptospira revealed that pathogenic leptospires were prevalent in sewage water and household drainage water in urban areas and in paddy fields, vegetable field water, and stream water in rural areas. These results demonstrate that intermediates are ubiquitously present in the environment and may be responsible for asymptomatic infections, and also provide an insight into disease ecology.

著者

KAZUKO OHMORI MASAKI HIROSE MASAYUKI OHMORI

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.13, no.1, pp.23-27, 1998-03-31 (Released:2009-10-05)

参考文献数

9

被引用文献数

1 2 1

著者

Nobuyasu Yamaguchi Michael Roberts Sarah Castro Cherie Oubre Koichi Makimura Natalie Leys Elisabeth Grohmann Takashi Sugita Tomoaki Ichijo Masao Nasu

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME14031, (Released:2014-08-12)

被引用文献数

8 81 1

---

Previous space research conducted during short-term flight experiments and long-term environmental monitoring on board orbiting space stations suggests that the relationship between humans and microbes is altered in the crewed habitat in space. Both human physiology and microbial communities adapt to spaceflight. Microbial monitoring is critical to crew safety in long-duration space habitation and the sustained operation of life support systems on space transit vehicles, space stations, and surface habitats. To address this critical need, space agencies including NASA(National Aeronautics and Space Administration), ESA (European Space Agency), and JAXA (Japan Aerospace Exploration Agency) are working together to develop and implement specific measures to monitor, control, and counteract biological contamination in closed-environment systems. In this review, the current status of microbial monitoring conducted in the International Space Station (ISS) as well as the results of recent microbial spaceflight experiments have been summarized and future perspectives are discussed.

著者

Kasthuri Venkateswaran Myron T. La Duc Gerda Horneck

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME14032, (Released:2014-08-12)

被引用文献数

6 23 1

---

The National Research Council (NRC) has recently recognized the International Space Station (ISS) as uniquely suitable for furthering the study of microbial species in closed habitats. Answering the NRC’s call for the study, in particular, of uncommon microbial species in the ISS, and/or of those that have significantly increased or decreased in number, space microbiologists have begun capitalizing on the maturity, speed, and cost-effectiveness of molecular/genomic microbiological technologies to elucidate changes in microbial populations in the ISS and other closed habitats. Since investigators can only collect samples infrequently from the ISS itself due to logistical reasons, Earth analogs, such as spacecraft-assembly clean rooms, are used and extensively characterized for the presence of microbes.Microbiologists identify the predominant, problematic, and extremophilic microbial species in these closed habitats and use the ISS as a testbed to study their resistance to extreme extraterrestrial environmental conditions. Investigators monitor the microbes exposed to the real space conditions in order to track their genomic changes in response to the selective pressures present in outer space (external to the ISS) and the spaceflight (in the interior of the ISS). In this review, we discussed the presence of microbes in space research-related closed habitats and the resistance of some microbial species to the extreme environmental conditions of space.

著者

Takashi Narihiro Aya Suzuki Kazuaki Yoshimune Tomoyuki Hori Tamotsu Hoshino Isao Yumoto Atsushi Yokota Nobutada Kimura Yoichi Kamagata

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.29, no.2, pp.154-161, 2014 (Released:2014-07-19)

参考文献数

64

被引用文献数

4 12

---

Metagenomic screening and conventional cultivation have been used to exploit microbial lipolytic enzymes in nature. We used an indigenous forest soil (NS) and oil-fed enriched soil (OS) as microbial and genetic resources. Thirty-four strains (17 each) of lipolytic bacteria were isolated from the NS and OS microcosms. These isolates were classified into the (sub)phyla Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria, all of which are known to be the main microbial resources of commercially available lipolytic enzymes. Seven and 39 lipolytic enzymes were successfully retrieved from the metagenomic libraries of the NS and OS microcosms, respectively. The screening efficiency (a ratio of positive lipolytic clones to the total number of environmental clones) was markedly higher in the OS microcosm than in the NS microcosm. Moreover, metagenomic clones encoding the lipolytic enzymes associated with Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Armatimonadetes, and Planctomycetes and hitherto-uncultivated microbes were recovered from these libraries. The results of the present study indicate that functional metagenomics can be effectively used to capture as yet undiscovered lipolytic enzymes that have eluded the cultivation-based method, and these combined approaches may be able to provide an overview of lipolytic organisms potentially present in nature.

著者

松浦 克美

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.13, no.4, pp.269-275, 1998-12-31 (Released:2009-10-05)

参考文献数

23

被引用文献数

1 1

---

Green filamentous bacteria (Chloroflexus) and cyanobacteria are commonly observed in bacterial mats of hot springs with the temperature range betwen 45 and 70°C and pH range between 6.5 and 9.0. Sulfide concentration is another factor which largely affects the distribution of thermophilic photosynthetic bacteria. Chloroflexus spp. are thought to maintain many characteristics of the oldest photosynthetic bacteria. Photosynthetic bacterial mats in hot springs are important for the studies on early stages of the evolution of photosynthesis.

著者

Yuki Sato-Takabe Koji Hamasaki Koji Suzuki

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.29, no.1, pp.100-103, 2014 (Released:2014-04-02)

参考文献数

17

被引用文献数

4 12

---

This paper describes the photosynthetic response of a Roseobacter strain of marine aerobic anoxygenic phototrophic bacteria to an organic substrate limitation. In batch cultures, higher values of the spheroidenone/bacteriochlorophyll a ratio were observed under substrate-deficient conditions. Interestingly, the maximum photochemical quantum efficiencies of the photosystem under substrate-deficient conditions using blue or green excitation were significantly higher than those under substrate-replete conditions. These results indicate that spheroidenone, which can absorb green light, may play an important role in their photosynthesis as a light-harvesting antenna pigment, and the photosynthetic competence of the Roseobacter strain can increase in an organic substrate-deficient environment.

著者

Dong Han Choi Jae Hoon noH Jung-Hyun Lee

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.29, no.1, pp.17-22, 2014 (Released:2014-04-02)

参考文献数

36

被引用文献数

2 10

---

Synechococcus are distributed throughout the world’s oceans and are composed of diverse genetic lineages. However, as they are much less abundant than Prochlorococcus in oligotrophic open oceans, their in-depth genetic diversity cannot be investigated using commonly used primers targeting both Prochlorococcus and Synechococcus. Thus, in this study, we designed a primer specific to the 16S–23S rRNA internal transcribed spacer (ITS) of the Synechococcus subcluster 5.1. Using the primer, we could selectively amplify Synechococcus sequences in oligotrophic seawater samples. Further, we showed that a barcoded amplicon pyrosequencing method could be applicable to investigate Synechococcus diversity using sequences retrieved in GenBank and obtained from environmental samples. Allowing sequence analyses of a large number of samples, this high-throughput method would be useful to study global biodiversity and biogeographic patterns of Synechococcus in marine environments.

著者

Kazuo Isobe Nobuhito Ohte

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.29, no.1, pp.4-16, 2014 (Released:2014-04-02)

参考文献数

143

被引用文献数

17 105

---

Nitrogen (N) cycles have been directly linked to the functional stability of ecosystems because N is an essential element for life. Furthermore, the supply of N to organisms regulates primary productivity in many natural ecosystems. Microbial communities have been shown to significantly contribute to N cycles because many N-cycling processes are microbially mediated. Only particular groups of microbes were implicated in N-cycling processes, such as nitrogen fixation, nitrification, and denitrification, until a few decades ago. However, recent advances in high-throughput sequencing technologies and sophisticated isolation techniques have enabled microbiologists to discover that N-cycling microbes are unexpectedly diverse in their functions and phylogenies. Therefore, elucidating the link between biogeochemical N-cycling processes and microbial community dynamics can provide a more mechanistic understanding of N cycles than the direct observation of N dynamics. In this review, we summarized recent findings that characterized the microbes governing novel N-cycling processes. We also discussed the ecological role of N-cycling microbial community dynamics, which is essential for advancing our understanding of the functional stability of ecosystems.

著者

Francesc Codony Mariana Fittipaldi Esther López Jordi Morató Gemma Agustí

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.27, no.4, pp.529-532, 2012 (Released:2012-12-07)

参考文献数

20

被引用文献数

9 20

---

Waddlia chondrophila is an emerging pathogen considered as a potential agent of abortion in humans and bovines, and is related with human respiratory disease. Despite these findings, the infection source and transmission pathways have not been identified. The evidence of growth into amoeba suggests water as a possible environmental source. The presence of Waddlia chondrophila was determined in drinking and well water samples (n=70) by quantitative PCR (Q-PCR). Positive results were observed in 10 (25%) of the 40 well samples analyzed; therefore, well water could be a potential reservoir and possible infection source of Waddlia chondrophila in animals and humans.

著者

Dong Han Choi Jae Hoon Noh Jung-Hyun Lee

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME13063, (Released:2013-12-28)

被引用文献数

2 10

---

Synechococcus are distributed throughout the world’s oceans and are composed of diverse genetic lineages. However, as they are much less abundant than Prochlorococcus in oligotrophic open oceans, their in-depth genetic diversity cannot be investigated using commonly used primers targeting both Prochlorococcus and Synechococcus. Thus, in this study, we designed a primer specific to the 16S-23S rRNA internal transcribed spacer (ITS) of the Synechococcus subcluster 5.1. Using the primer, we could selectively amplify Synechococcus sequences in oligotrophic seawater samples. Further, we showed that a barcoded amplicon pyrosequencing method could be applicable to investigate Synechococcus diversity using sequences retrieved in GenBank and obtained from environmental samples. Allowing sequence analyses of a large number of samples, this high-throughput method would be useful to study global biodiversity and biogeographic patterns of Synechococcus in marine environments.

著者

Akira Kawaguchi

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.28, no.3, pp.306-311, 2013 (Released:2013-09-21)

参考文献数

27

被引用文献数

7 29

---

A nonpathogenic strain of Rhizobium vitis ARK-1 was tested as a biological control agent for grapevine crown gall. When grapevine roots were soaked in a cell suspension of strain ARK-1 before planting in the field, the number of plants with tumors was reduced. The results from seven field trials from 2009 to 2012 were combined in a meta-analysis. The integrated relative risk after treatment with ARK-1 was 0.15 (95% confidence interval: 0.07–0.29, P<0.001), indicating that the disease incidence was significantly reduced by ARK-1. In addition, the results from four field trials from 2007 to 2009 using R. vitis VAR03-1, a previously reported biological control agent for grapevine crown gall, were combined in a meta-analysis. The integrated relative risk after treatment with VAR03-1 was 0.24 (95% confidence interval: 0.11–0.53, P<0.001), indicating the superiority of ARK-1 in inhibiting grapevine crown gall over VAR03-1 under field conditions. ARK-1 did not cause necrosis on grapevine shoot explants. ARK-1 established populations on roots of grapevine tree rootstock and persisted inside roots for two years.

著者

Satoshi Kawaichi Norihiro Ito Takashi Yoshida Yoshihiko Sako

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME13048, (Released:2013-11-21)

被引用文献数

3 9

---

Physicochemical characteristics and archaeal and bacterial community structures in an iron-rich coastal hydrothermal field, where the temperature of the most active hot spot reaches above 100ーC, were investigated to obtain fundamental information on microbes inhabiting a coastal hydrothermal field. The environmental settings of the coastal hydrothermal field were similar in some degree to those of deep-sea hydrothermal environments because of its emission of H2, CO2, and sulfide from the bottom of the hot spot. The results of clone analyses based on the 16S rRNA gene led us to speculate the presence of a chemo-synthetic microbial ecosystem, where chemolithoautotrophic thermophiles, primarily the bacterial order Aquificales, function as primary producers using H2 or sulfur compounds as their energy source and CO2 as their carbon source, and the organic compounds synthesized by them support the growth of chemoheterotrophic thermophiles, such as members of the order Thermales and the family Desulfurococcaceae. In addition, the dominance of members of the bacterial genus Herbaspirillum in the high temperature bottom layer led us to speculate the temporal formation of mesophilic zones where they can also function as primary producing or nitrogen-fixing bacteria.

著者

Norisuke Ushiki Hirotsugu Fujitani Yoshiteru Aoi Satoshi Tsuneda

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.28, no.3, pp.346-353, 2013 (Released:2013-09-21)

参考文献数

29

被引用文献数

15 68

---

Nitrite oxidation is a key step in nitrogen removal in biological wastewater treatment plants. Recently, two phylogenetically different Nitrospira (sublineages I and II) have been recognized as the numerically dominant nitrite-oxidizing bacteria in wastewater treatment plants. However, Nitrospira sublineage II inhabiting activated sludge was not isolated and its detailed properties were unclear. In this study, we developed a new method for the isolation of Nitrospira forming micro-colonies using a cell sorter. We obtained a novel pure strain “Nitrospira japonica” from the activated sludge. Subsequently, phylogenetic and physiological analyses revealed that Nitrospira japonica belongs to sublineage II and grew in medium containing formate. This method has the potential to isolate other uncultured microorganisms forming micro-colonies.

著者

Indun Dewi Puspita Yoichi Kamagata Michiko Tanaka Kozo Asano Cindy H. Nakatsu

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.27, no.4, pp.356-366, 2012 (Released:2012-12-07)

参考文献数

144

被引用文献数

29 106

---

Many strategies have been used to increase the number of bacterial cells that can be grown from environmental samples but cultivation efficiency remains a challenge for microbial ecologists. The difficulty of cultivating a fraction of bacteria in environmental samples can be classified into two non-exclusive categories. Bacterial taxa with no cultivated representatives for which appropriate laboratory conditions necessary for growth are yet to be identified. The other class is cells in a non-dividing state (also known as dormant or viable but not culturable cells) that require the removal or addition of certain factors to re-initiate growth. A number of strategies, from simple to high throughput techniques, are reviewed that have been used to increase the cultivation efficiency of environmental samples. Some of the underlying mechanisms that contribute to the success of these cultivation strategies are described. Overall this review emphasizes the need of researchers to first understand the factors that are hindering cultivation to identify the best strategies to improve cultivation efficiency.

著者

Akira Kawaguchi

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME13014, (Released:2013-05-24)

被引用文献数

7 29

---

A nonpathogenic strain of Rhizobium vitis ARK-1 was tested as a biological control agent for grapevine crown gall. When grapevine roots were soaked in a cell suspension of strain ARK-1 before planting in the field, the number of plants with tumors was reduced. The results from seven field trials from 2009 to 2012 were combined in a meta-analysis. The integrated relative risk after treatment with ARK-1 was 0.15 (95% confidence interval: 0.07–0.29, P<0.001), indicating that the disease incidence was significantly reduced by ARK-1. In addition, the results from four field trials from 2007 to 2009 using R. vitis VAR03-1, a previously reported biological control agent for grapevine crown gall, were combined in a meta-analysis. The integrated relative risk after treatment with VAR03-1 was 0.24 (95% confidence interval: 0.11–0.53, P<0.001), indicating the superiority of ARK-1 in inhibiting grapevine crown gall over VAR03-1 under field conditions. ARK-1 did not cause necrosis on grapevine shoot explants. ARK-1 established populations on roots of grapevine tree rootstock and persisted inside roots for two years.

著者

Mitsuro Hyakumachi Mitsuyoshi Nishimura Tatsuyuki Arakawa Shinichiro Asano Shigenobu Yoshida Seiya Tsushima Hideki Takahashi

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.28, no.1, pp.128-134, 2013 (Released:2013-03-12)

参考文献数

54

被引用文献数

12 61

---

Bacillus thuringiensis is a naturally abundant Gram-positive bacterium and a well-known, effective bio-insecticide. Recently, B. thuringiensis has attracted considerable attention as a potential biological control agent for the suppression of plant diseases. In this study, the bacterial wilt disease-suppressing activity of B. thuringiensis was examined in tomato plants. Treatment of tomato roots with B. thuringiensis culture followed by challenge inoculation with Ralstonia solanacearum suppressed the development of wilt symptoms to less than one third of the control. This disease suppression in tomato plants was reproduced by pretreating their roots with a cell-free filtrate (CF) that had been fractionated from B. thuringiensis culture by centrifugation and filtration. In tomato plants challenge-inoculated with R. solanacearum after pretreatment with CF, the growth of R. solanacearum in stem tissues clearly decreased, and expression of defense-related genes such as PR-1, acidic chitinase, and β-1,3-glucanase was induced in stem and leaf tissues. Furthermore, the stem tissues of tomato plants with their roots were pretreated with CF exhibited resistance against direct inoculation with R. solanacearum. Taken together, these results suggest that treatment of tomato roots with the CF of B. thuringiensis systemically suppresses bacterial wilt through systemic activation of the plant defense system.

著者

Suguru Okunishi Naoaki Yoshimura Hiroto Maeda Takeshi Yoshikawa Taizo Sakata

出版者

日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.17, no.3, pp.148-152, 2002 (Released:2002-10-02)

参考文献数

26

被引用文献数

2 3

---

A new cyanophage, strain S-KM1, infecting a phycoerythrin-rich Synechococcus sp., strain KFM001, was isolated from seawater of Kagoshima Bay. Transmission electron micrography of negative-stained specimens revealed that the phage isolate has an isometric head with a diameter of 83 nm and a contractile tail 166 nm in length and that it belongs to the family Cyanomyoviridae. The cyanophage was apparently virulent to the host strain KFM001 with a burst size of less than 70-80. The cyanophage may affect the population structure of the dominant picoplankton species in Kagoshima Bay.