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

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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

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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

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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 59

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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

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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.

著者

Saito Asami Minamisawa Kiwamu

出版者

日本微生物生態学会

雑誌

Microbes and environments (ISSN:13426311)

巻号頁・発行日

vol.21, no.1, pp.23-35, 2006-03

被引用文献数

7 21

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To examine whether plant-derived clostridia and their consortium fix nitrogen in plants, an inoculation system was developed using the grass Miscanthus sinensis under aseptic conditions. Among 13 clostridial strains previously isolated from M. sinensis, Clostridium sp. strain Kas107-1 was selected as the best colonizer in the plant with the non-diazotrophic bacterium Entrobacter sp. strain B901-2. Nitrogen-fixing (acetylene-reducing) activity was not observed in the plants inoculated with Kas107-1 without a carbon source. On the other hand, nitrogenfixing activity was detected when carbon sources were supplied to the roots. To confirm the endophytic nitrogenfixing activity, we cloned nifH genes and monitored their expression in strain Kas107-1. Although this bacterium possessed at least two copies of nifH (nifH1 and nifH2), the nifH1 transcript was exclusively detected in free-living cells and endophytic cells in the plants by reverse transcription (RT)-PCR analysis. RT-PCR analysis of ribosomal RNA suggested the endophytic colonization of the plants by Kas107-1. These results indicate that Clostridium sp. strain Kas107-1 can potentially fix nitrogen in plants. A RT-PCR analysis targeting both functional gene transcripts and the ribosomal RNA molecule is useful for researching endophyte ecology, because their function and colonization in plants can be examined simultaneously with a single preparation of RNA.

著者

Branko Velimirov

出版者

Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.16, no.2, pp.67-77, 2001 (Released:2001-07-16)

参考文献数

66

被引用文献数

38 60

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Very small forms of bacteria have been reported from marine and freshwater systems as well as from soils, subsurface terrestrial environments' and more recently from samples of kidney stones. Also, such small cells could be obtained in the laboratory during starvation experiments, indicating that bacteria which survive periods of nutrient deprivation manifest a decrease of cell size. Even though the various reports brought about poorly defined designations for small bacteria, they have stimulated the discussion on how small a living bacterium could be. The information derived from the literature concerning starvation forms, ultramicrobacteria and nanobacteria is analysed in the light of own field and laboratory observations. It could be shown that despite conceptual shortcomings and problems with definitions of what is meant by "small", starvation forms and ultramicrobacteria are clearly distinguishable according to physiological characteristics, which could not be achieved for nanobacteria or nanobes. Furthermore, it is documented that ultramicrobacteria are not the smallest procaryotes and that the size of bacterial starvation forms are much closer to the calculated minimal sizes required to ensure independent viable life. A bacterial cell which is growing and dividing needs to be large enough to accommodate DNA and RNA, enzymes for replication transcription and translation, solvent for ubstances as well as a minimum set of proteins and plasamtic space to run the operations. Many authors assume that this requires a cell with a diameter not smaller than 200 nm and with a volume between 0.014 and 0.06 μm3. Most cells with diameters equal or below 0.2 μm are rods while cocci are numerically of minor importance in natural aquatic systems. It seems that the rod morphotype has more potential to produce viable cells with minimal volumes than spherical morhotypes. This supports the assumption that not only size but also cell shape is important to achieve functional minimum cell volumes. Many cell parameters can be estimated with relatively high precision, but one should remember that absolute calibration is still not possible. Even if we assume that there are errors involved in most biometric measurements, there is still a trend which indicates that rod shaped cells can function with diameters below 0.2 μm and cell volumes well below 0.02 μm3. Such dimensions could be an indication that the lower size limit of a viable bacterium may be close to the size of the smallest hypothetical living cell, indicating that there is still more to know about the minimal required cell components allowing a bacterium the remain viable.