著者

Takashi Okubo Takahiro Tsukui Hiroko Maita Shinobu Okamoto Kenshiro Oshima Takatomo Fujisawa Akihiro Saito Hiroyuki Futamata Reiko Hattori Yumi Shimomura Shin Haruta Sho Morimoto Yong Wang Yoriko Sakai Masahira Hattori Shin-ichi Aizawa Kenji V. P. Nagashima Sachiko Masuda Tsutomu Hattori Akifumi Yamashita Zhihua Bao Masahito Hayatsu Hiromi Kajiya-Kanegae Ikuo Yoshinaga Kazunori Sakamoto Koki Toyota Mitsuteru Nakao Mitsuyo Kohara Mizue Anda Rieko Niwa Park Jung-Hwan Reiko Sameshima-Saito Shin-ichi Tokuda Sumiko Yamamoto Syuji Yamamoto Tadashi Yokoyama Tomoko Akutsu Yasukazu Nakamura Yuka Nakahira-Yanaka Yuko Takada Hoshino Hideki Hirakawa Hisayuki Mitsui Kimihiro Terasawa Manabu Itakura Shusei Sato Wakako Ikeda-Ohtsubo Natsuko Sakakura Eli Kaminuma Kiwamu Minamisawa

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

pp.1203230372, (Released:2012-03-28)

参考文献数

1

被引用文献数

37 53

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Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.

著者

Shin-ichiro Agake Fernanda Plucani do Amaral Tetsuya Yamada Hitoshi Sekimoto Gary Stacey Tadashi Yokoyama Naoko Ohkama-Ohtsu

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.37, no.1, pp.ME21060, 2022 (Released:2022-01-27)

参考文献数

61

被引用文献数

3

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Spores are a stress-resistant form of Bacillus spp., which include species that are plant growth-promoting rhizobacteria (PGPR). Previous studies showed that the inoculation of plants with vegetative cells or spores exerted different plant growth-promoting effects. To elucidate the spore-specific mechanism, we compared the effects of viable vegetative cells, autoclaved dead spores, and viable spores of Bacillus pumilus TUAT1 inoculated at 107 CFU plant–1 on the growth of the C4 model plant, Setaria viridis A10.1. B. pumilus TUAT1 spores exerted stronger growth-promoting effects on Setaria than on control plants 14 days after the inoculation. Viable spores increased shoot weight, root weight, shoot length, root length, and nitrogen uptake efficiency 21 days after the inoculation. These increases involved primary and crown root formation. Additionally, autoclaved dead spores inoculated at 108 or 109 CFU plant–1 had a positive impact on crown root differentiation, which increased total lateral root length, resulting in a greater biomass and more efficient nitrogen uptake. The present results indicate that an inoculation with viable spores of B. pumilus TUAT1 is more effective at enhancing the growth of Setaria than that with vegetative cells. The plant response to dead spores suggests that the spore-specific plant growth-promoting mechanism is at least partly independent of symbiotic colonization.

著者

Tadashi YOKOYAMA Satoki SHINTAKU Naoki NISHIYAMA

出版者

Japan Association of Mineralogical Sciences

雑誌

Journal of Mineralogical and Petrological Sciences (ISSN:13456296)

巻号頁・発行日

pp.221107, (Released:2023-03-11)

被引用文献数

1

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Rocks have pores of various sizes. We investigated which pore sizes filled with water and in what order with the progression of water infiltration. The pore radii of the sandstone mainly ranges from a few µm to several tens of µm. Water was passed through the sandstone core at 25 °C, and water saturation, S, was adjusted to 63%, 67%, 71%, 87%, and 100%. At each S, the porewater radius distribution was measured using the water expulsion method, in which water in pores of a given pore radius was expelled by gas pressure. The results showed that the porewater radius distribution was approximately the same for S = 63-71%. As S increased from 71% to 100%, the pores with 4-10 µm and 10-20 µm radii were filled with water first, followed by pores with 20-52 µm radius. For S = 63-71%, water was considered to have entered via adsorption on the pore walls and capillary action at the corners of the pore. Because this water cannot be expelled by gas pressure, an increased amount of water was not detected by the water expulsion method. As for the results at S >71%, a theoretical model of the dissolution of entrapped air, assuming a cylindrical shape, showed that the length of the trapped air decreases faster in pores with small radii than in those with large radii. This may be a major explanation for the experimental result, which showed that pores with small radii fill with water more quickly than those with large radii.

著者

Katsuhiro Kojima Tadashi Yokoyama Naoko Ohkama-Ohtsu Suwat Saengkerdsub Manabu Itakura Hisayuki Mitsui Kiwamu Minamisawa Yasuhiro Arima

出版者

Japanese Society of Soil Microbiology

雑誌

土と微生物 (ISSN:09122184)

巻号頁・発行日

vol.66, no.1, pp.12-21, 2012-04-01 (Released:2017-05-31)

参考文献数

35

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Tetronic acid is a candidate for an inducer of nodulation (nod) gene expression in Mesorhizobium loti. However, there is no evidence that tetronic acid is secreted from Lotus species, the host plants of M. loti. This suggests that Lotus plants may produce other genuine nod gene inducers that differ from tetronic acid. In this study, M. loti cells harboring a nodA-lacZ fusion were enclosed in dialysis tubing and immersed in L. corniculatus culture solution. Significant β-galactosidase activities were detected in the M. loti cells, indicating that nod gene inducers were present in the seed and root exudates. β-galactosidase activities in M. loti cells were also determined after cells were exposed to seed and root exudates or tetronic acid in vitro. Seed and root exudates induced greater β-galactosidase activity in M. loti cells in 1 mM CaSO_4 solution than in YEM medium. In contrast, tetronic acid induced greater β-galactosidase activity in M. loti cells in YEM medium than in 1 mM CaSO_4 solution. Further, β-galactosidase activities induced by seed and root exudates and tetronic acid tended to decrease as the pH of the medium became neutral. In an LC-MS analysis, we could not detect tetronic acid in the concentrated seed and root exudates. These findings indicate that Lotus plants release genuine nod gene inducers for M. loti that differ from tetronic acid. Finally, seed exudates of L. corniculatus were fractionated according to molecular size and polarity, and it was clarified that a putative nod gene inducer in the seed exudates was a low molecular weight and high polarity substance.

著者

Sayed Ziauddin Hashami Hiroyuki Nakamura Naoko Ohkama-Ohtsu Katsuhiro Kojima Salem Djedidi Izumi Fukuhara Mohammad Daud Haidari Hitoshi Sekimoto Tadashi Yokoyama

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.34, no.1, pp.64-75, 2019 (Released:2019-03-30)

参考文献数

35

被引用文献数

9

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Legumes form root nodules and fix atmospheric nitrogen by establishing symbiosis with rhizobia. However, excessive root nodules are harmful to plants because of the resulting overconsumption of energy from photosynthates. The delay of an inoculation of the soybean super-nodulation mutant NOD1–3 with Bradyrhizobium diazoefficiens USDA110T by 5 d after an inoculation with several soil bacteria confirmed that one bacterial group significantly decreased root nodules throughout the study period. Moreover, no significant changes were observed in nitrogen fixation by root nodules between an inoculation with USDA 110T only and co-inoculation treatments. To clarify the potential involvement of PR proteins in the restriction of nodule formation in the plants tested, the relative expression levels of PR-1, PR-2, PR-5, and PDF1.2 in NOD1–3 roots were measured using real-time PCR. One group of soil bacteria (Gr.3), which markedly reduced nodule numbers, significantly induced the expression of PR-1, PR-5 and PDF1.2 genes by day 5 after the inoculation. By days 7, 10, and 20 after the inoculation, the expression levels of PR-2 and PR-5 were lower than those with the uninoculated treatment. Inoculations with this group of soil bacteria resulted in lower root nodule numbers than with other tested soil bacteria exerting weak inhibitory effects on nodulation, and were accompanied by the induction of plant defense-related genes. Thus, PR genes appear to play important roles in the mechanisms that suppresses nodule formation on soybean roots.

著者

Takuma Iwai Hiroshi Yoshida Tadashi Yokoyama Hiroshi Maruyama Seiji Suzuki Takeshi Matsutani Akira Matsushita Atsushi Hirakata Koji Sasajima Eiji Uchida

出版者

日本医科大学医学会

雑誌

Journal of Nippon Medical School (ISSN:13454676)

巻号頁・発行日

vol.78, no.3, pp.189-193, 2011 (Released:2011-06-30)

参考文献数

17

被引用文献数

3 5 3

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We describe a patient in whom a fish bone penetrated the duodenum and migrated into the right renal vein. The bone was successfully removed with surgery. The 75-year-old man was admitted to Nippon Medical School Tama Nagayama Hospital because of right upper abdominal pain persisting for 7 days. The patient's medical history was not relevant to the current disorder. Plain radiography showed no abnormalities. Computed tomography revealed a linear object of high intensity that had penetrated the duodenum and migrated into the right renal vein with thrombus. The object was surrounded by a low-density area, suggesting severe inflammation. The patient had eaten fish 1 day before the onset of abdominal pain. We diagnosed duodenal penetration caused by an ingested fish bone. Endoscopic examination showed erosion, but no fish bone or ulceration was detected in the duodenum. The patient was treated conservatively with fasting, peripheral parental nutrition, and intravenous antibiotics. Three days after admission, non-contrast-enhanced computed tomography showed no movement of the foreign body. The patient continued to have pain, and the decision was made to surgically explore the abdomen. Intraoperative ultrasonography showed that the foreign body had migrated completely into the right renal vein with thrombus. Severe inflammation of the right renal vein was observed. Because we could not remove the foreign body without seriously injuring the right renal vein, right nephrectomy was performed. Macroscopic examination of the surgical specimen confirmed the presence of a fish bone with thrombus in the right renal vein. The patient was discharged 9 days after operation, with no complications.