OKAZAKI Shin

Activity information

Name and contact details

• Name

  オカザキ　シン, 岡崎　伸, OKAZAKI Shin

• Fax

  042-367-5847

• E-mail

  sokazakicc.tuat.ac.jp

Affiliation / Position

• Institute of Agriculture　Division of International Environmental and Agricultural Science, Professor

Other affiliation

• Graduate School of Agriculture　Department of International Environmental and Agricultural Science
• Institute of Global Innovation Research
• United Graduate School of Agricultural Science

Research History

• 　
  博士研究員（大阪大学理学部、奈良女子大学理学部）
  From 01 Apr. 2004, To 14 Sep. 2005
• 　
  日本学術振興会海外特別研究員（ドレスデン工科大学）
  From 15 Sep. 2005, To 14 Sep. 2007
• 　
  博士研究員（奈良女子大学理学部）
  From 01 Oct. 2007, To 31 Mar. 2008
• 　
  助教（奈良女子大学大学院人間文化研究科）
  From 01 Apr. 2008, To 31 Jan. 2012
• 　
  テニュアトラック助教（東京農工大学大学院農学研究院）
  From 01 Feb. 2012, To 31 Jan. 2017
• 　
  Associate Professor
  From 01 Feb. 2017, To 31 Jan. 2020
• 　
  Professor
  From 01 Feb. 2020

Education

• Tohoku University
  Faculty of Agriculture
  To Mar. 1998, graduated
• Tohoku University
  Graduate School, Division of Agriculture
  To Mar. 2000, completed, master course
• Tohoku University
  Graduate School, Division of Agriculture
  To Mar. 2004, completed, doctor course

Degree

• Doctor of Agriculture

Research Areas

• Life Science, Plant nutrition and soil science
• Life Science, Molecular biology

Research Interests

• Plant-Microbe symbiosis, soil microorganisms, rhizobia, endophytes, arbuscular mycorrhiza, genome analysis

Teaching Experience

• アグリバイオ実験
  2022, 専門科目等
• 化学実験・生物学実験
  2022, 専門科目等
• 生物生産学原論
  2022, 専門科目等
• 生物生産学英語入門
  2022, 専門科目等
• 国際環境農学
  2022, 専門科目等
• Experiment Course on Agro-Environmental Science(3学期集中・集中・農学部)
  2022, 教養科目等
• Plant Microbiology(3学期・金4・農学部)
  2022, 専門科目等
• Plant Microbiology(3学期集中・集中・農学部)
  2022, 専門科目等
• 国際イノベーション農学概論Ⅱ(3学期・火1・農学府)
  2022, 専門科目等
• 国際生物生産資源学Ⅱ(1学期・月4・農学府)
  2022, 専門科目等
• 国際生物生産資源学Ｉ(1学期・火4・農学府)
  2022, 専門科目等
• 農業微生物学(1学期・火3・農学部)
  2022, 専門科目等

Grants-in-Aid for Scientific Research

• 基盤研究(C)
  イネ根圏に共生するBradyrhizobium属細菌の共生シグナルの解析
  From 2022, To 2022
• 挑戦的研究（萌芽）
  放電が土壌化学性・土壌生物性および植物生育に及ぼす影響とその機構の解析
  From 2022, To 2022
• 国際共同研究加速基金（国際共同研究強化(B)）
  半乾燥熱帯アフリカ畑作地における持続可能な集約化のための混作技術革新
  From 2021, To 2021
• 国際共同研究加速基金（国際共同研究強化(B)）
  半乾燥熱帯アフリカ畑作地における持続可能な集約化のための混作技術革新
  From 2020, To 2020
• 挑戦的研究（萌芽）
  イネ科植物への窒素固定根粒形成
  From 2019, To 2022
• 基盤研究(B)
  根粒菌エフェクターの宿主標的分子同定と共生シグナル活性化機構
  From 2019, To 2021
• 国際共同研究加速基金（国際共同研究強化(B)）
  半乾燥熱帯アフリカ畑作地における持続可能な集約化のための混作技術革新
  From 2019, To 2019
• 国際共同研究加速基金（国際共同研究強化(B)）
  半乾燥熱帯アフリカ畑作地における持続可能な集約化のための混作技術革新
  From 2018, To 2018
• 基盤研究(B)海外学術調査
  ベトナムで発生するイネ白化病の発生状況調査と病原体の解析
  From 2017, To 2022
• 基盤研究(B)
  根粒菌エフェクターによるマメ科植物新規共生経路の解明
  From 2016, To 2018
• 国際共同研究加速基金（国際共同研究強化）
  マメ科植物-根粒菌共生における新しい共生経路の解明（国際共同研究強化）
  From 2016, To 2018
• 基盤研究(C)
  マメ科植物-根粒菌共生における新しい共生経路の解明
  From 2013, To 2015
• 若手研究(B)
  根粒菌3型分泌系によるマメ科植物共生シグナルの活性化機構
  From 2011, To 2012
• 基盤研究(C)
  イネ根圏に共生するBradyrhizobium属細菌の共生シグナルの解析
  From 2023, To 2023
• 挑戦的研究（萌芽）
  放電が土壌化学性・土壌生物性および植物生育に及ぼす影響とその機構の解析
  From 2023, To 2023
• 基盤研究(B)
  根粒菌エフェクターによる新規共生経路の分子基盤解明
  From 2023, To 2026

Papers

• Isolation and characterization of Bradyrhizobium elkanii as a root nodule symbiont of red sword bean Canavalia gladiata var. gladiata
  Masuda, Wataru; Hatanaka, Yusuke; Mochizuki, Akimitsu; Okazaki, Shin; Ben Nanzai; Saito, Akihiro
  SOIL SCIENCE AND PLANT NUTRITION
  TAYLOR & FRANCIS LTD
  Bacterial strains were isolated from root nodules of red sword bean (Canavalia gladiata var. gladiata) cultivated in Shizuoka, Japan, in order to elucidate the taxonomy of the symbionts. Of the 52 bacterial isolates, 28 strains were identified as the genus Bradyrhizobium and 10 as Rhizobium, based on the nucleotide sequences of 16S rRNA genes. Nine Bradyrhizobium isolates, which were phylogenetically selected from the 28 strains, exhibited nucleotide sequences of ITS regions that were 99.9% or 100% identical with known B. elkanii strains. These nine strains shared more than 70% similarity with B. elkanii USDA 76 (T) or USDA 94 in DNA-DNA hybridization analysis, indicating that the strains are B. elkanii. In a nodule formation experiment using red sword bean seeds treated with mercury chloride solution, all of the plants which were inoculated with each of the B. elkanii strains (the isolate TI06 or MI08, or the type strain USDA 76 (T)) formed round-type root nodules (234-664 nodules per plant), while no nodules were observed in control plants that were cultivated without inoculating bacterial strains. The bacterial strains, which were isolated from the obtained nodules, exhibited nucleotide sequences of the ITS regions that were identical to those of the corresponding inoculated strains. The root nodules formed in the experiment exhibited acetylene-reducing activity, suggesting the nitrogen-fixation activity of the nodules. We thus conclude that B. elkanii is a root nodule symbiont of red sword bean.
  04 Jul. 2022, Research paper (scientific journal), joint, 68, 4, 0038-0768, DOI(公開)(r-map), 434, 441
• Type III effector provides a novel symbiotic pathway in legume-rhizobia symbiosis
  Ratu, Safirah Tasa Nerves; Amelia, Lidia; Okazaki, Shin
  BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
  OXFORD UNIV PRESS
  Rhizobia form nodules on the roots of legumes and fix atmospheric nitrogen into ammonia, thus supplying it to host legumes. In return, plants supply photosynthetic products to maintain rhizobial activities. In most cases, rhizobial Nod factors (NFs) and their leguminous receptors (NFRs) are essential for the establishment of symbiosis. However, recent studies have discovered a novel symbiotic pathway in which rhizobia utilize the type III effectors (T3Es) similar to the pathogenic bacteria to induce nodulation. The T3Es of rhizobia are thought to be evolved from the pathogen, but they have a unique structure distinct from the pathogen, suggesting that it might be customized for symbiotic purposes. This review will focus on the recent findings from the study of rhizobial T3Es, discussing their features on a symbiont and pathogen, and the future perspectives on the role of rhizobial T3Es in symbiosis control technology.
  21 Dec. 2022, Research paper (scientific journal), joint, 87, 1, 0916-8451, DOI(公開)(r-map), 28, 37
• Isolation and Characterization of Phosphate Solubilizing Bacteria from Paddy Field Soils in Japan
  Damo, Jean Louise Cocson; Ramirez, Maria Daniela Artigas; Agake, Shin-ichiro; Pedro, Mannix; Brown, Marilyn; Sekimoto, Hitoshi; Yokoyama, Tadashi; Sugihara, Soh; Okazaki, Shin; Ohkama-Ohtsu, Naoko
  MICROBES AND ENVIRONMENTS
  JAPANESE SOC MICROBIAL ECOLOGY, DEPT BIORESOURCE SCIENCE
  Phosphorus (P) is abundant in soil and is essential for plant growth and development; however, it is easily rendered insoluble in complexes of different types of phosphates, which may lead to P deficiency. Therefore, increases in the amount of P released from phosphate minerals using microbial inoculants is an important aspect of agriculture. The present study used inorganic phosphate solubilizing bacteria (iPSB) in paddy field soils to develop microbial inoculants. Soils planted with rice were collected from different regions of Japan. Soil P was sequentially fractionated using the Hedley method. iPSB were isolated using selective media supplemented with tricalcium phosphate (Ca-P), aluminum phosphate (Al-P), or iron phosphate (Fe-P). Representative isolates were selected based on the P solubilization index and soil sampling site. Identification was performed using 16S rRNA and rpoB gene sequencing. Effectiveness was screened based on rice cultivar Koshihikari growth supplemented with Ca-P, Al-P, or Fe-P as the sole P source. Despite the relatively homogenous soil pH of paddy field sources, three sets of iPSB were isolated, suggesting the influence of fertilizer management and soil types. Most isolates were categorized as ss-Proteobacteria (43%). To the best of our knowledge, this is the first study to describe the genera Pleomorphomonas, Rhodanobacter, and Trinickia as iPSB. Acidovorax sp. JC5, Pseudomonas sp. JC11, Burkholderia sp. JA6 and JA10, Sphingomonas sp. JA11, Mycolicibacterium sp. JF5, and Variovorax sp. JF6 promoted plant growth in rice supplemented with an insoluble P source. The iPSBs obtained may be developed as microbial inoculants for various soil types with different P fixation capacities.
  2022, Research paper (scientific journal), joint, 37, 2, 1342-6311, DOI(公開)(r-map)
• Microbiome and pathobiome analyses reveal changes in community structure by foliar pathogen infection in rice
  Dastogeer, Khondoker M. G.; Yasuda, Michiko; Okazaki, Shin
  FRONTIERS IN MICROBIOLOGY
  FRONTIERS MEDIA SA
  Increasing evidence suggests that the plant rhizosphere may recruit beneficial microbes to suppress soil-borne pathogens, but microbiome assembly due to foliar pathogen infection and ecological mechanisms that govern microbiome assembly and functions in the diseased host are not fully understood. To provide a comprehensive view of the rice-associated microbiome, we compared bacterial and fungal communities of healthy rice and those infected with Magnaporthe oryzae, the causal agent of blast disease. We found that the soil had a greater diversity of bacterial and fungal communities than plant endospheric communities. There was no significant dysbiosis of bacterial and fungal microbiome diversity due to disease, but it caused a substantial alteration of bacterial community structure in the root and rhizosphere compartments. The pathobiome analysis showed that the microbiome community structure of leaf and grain tissues was changed markedly at the pathogen infection site, although the alpha diversity did not change. Correspondingly, the relative abundances of some bacteria and fungi were clearly altered in symptomatic tissues. We noted an increase in Rhizobium bacteria and a decline of Tylospora, Clohesyomyces, and Penicillium fungi in the symptomatic leaf and grain tissues from both locations. According to the inferred microbial network, several direct interactions between M. oryzae and other microbes were identified. The majority of edges in the interaction network were positive in diseased samples; contrastingly, the number of edges was much lower in the healthy samples. With source tracking analysis, we observed a sharp contrast in the source of root endosphere bacteria due to Magnaporthe infection. Whereas the majority (71%) of healthy root bacteria could be tracked from the soil, only a very small portion (17%) could be tracked from the soil for diseased samples. These results advanced our understanding and provided potential ideas and a theoretical basis for studying pathobiome and exploiting the microbiome for sustainable agriculture.
  02 Aug. 2022, Research paper (scientific journal), joint, 13, DOI(公開)(r-map)
• Impact of Azospirillum sp. B510 on the Rhizosphere Microbiome of Rice under Field Conditions
  Yasuda, Michiko; Dastogeer, Khondoker M. G.; Sarkodee-Addo, Elsie; Tokiwa, Chihiro; Isawa, Tsuyoshi; Shinozaki, Satoshi; Okazaki, Shin
  AGRONOMY-BASEL
  MDPI
  There has been increasing attention toward the influence of biofertilizers on the composition of microbial communities associated with crop plants. We investigated the impact of Azospirillum sp. B510, a bacterial strain with nitrogen-fixing ability, on the structure of bacterial and fungal communities within rice plant rhizospheres by amplicon sequencing at two sampling stages (the vegetative and harvest stages of rice). Principal coordinate analysis (PCoA) demonstrated a significant community shift in the bacterial microbiome when the plants were inoculated with B510 at the vegetative stage, which was very similar to the effect of chemical N-fertilizer application. This result suggested that the inoculation with B510 strongly influenced nitrogen uptake by the host plants under low nitrogen conditions. Least discriminant analysis (LDA) showed that the B510 inoculation significantly increased the N-2-fixing Clostridium, Aeromonas and Bacillus populations. In contrast, there was no apparent influence of B510 on the fungal community structure. The putative functional properties of bacteria were identified through PICRUSt2, and this hinted that amino acid, sugar and vitamin production might be related to B510 inoculation. Our results indicate that B510 inoculation influenced the bacterial community structure by recruiting other N-2-fixing bacteria in the absence of nitrogen fertilizer.
  Jun. 2022, Research paper (scientific journal), joint, 12, 6, DOI(公開)(r-map)
• Isolation and Functional Characterization of Culture-Dependent Endophytes Associated with Vicia villosa Roth
  Taheri, Parisa; Kaida, Rumi; Dastogeer, Khondoker M. G.; Appiah, Kwame Sarpong; Yasuda, Michiko; Tanaka, Keisuke; Korrani, Hossein Mardani; Azizi, Majid; Okazaki, Shin; Fujii, Yoshiharu
  AGRONOMY-BASEL
  MDPI
  In a natural ecosystem, endophytic fungi in the internal tissues of plants help to improve the growth of the host plants and to decrease the negative effects of biotic and abiotic stresses without having adverse effects. In Japan, Vicia villosa (hairy vetch), a legume plant with a high capacity to fix nitrogen, is usually used as a cover crop before soybeans to enhance the fertility and structure of the soil. This study aimed to isolate endophytic fungi associated with different tissues of hairy vetch and to evaluate their potential for growth-promoting and biocontrol effects in plants. Thirty-three fungal endophytes belonging to Ascomycota and Basidiomycota were isolated from the leaf, stem, and root tissues of hairy vetch grown under both greenhouse and field conditions. The highest colonization frequency in both the greenhouse and field-grown hairy vetch plants was obtained from the root tissues. All isolates were checked for indole-3-acetic acid (IAA) and siderophore production. The maximum IAA content in the culture filtrate (4.21 mu g mL(-1)) was produced by the isolate hvef7 (Cladosporium cladosporioides), followed by hvef18 (Penicillium simplicissimum) (3.02 mu g mL(-1)) and hvef1 (Cladosporium pseudocladosporioides) (2.32 mu g mL(-1)). Nineteen isolates among a total of thirty-three isolates produced siderophores. Moreover, some of the isolated strains could solubilize phosphate and potassium. Most of the isolates showed antagonistic potential against Calonectria ilicicola. The results of this study show that endophytic fungi isolated from hairy vetch have the potential for application as plant growth promotion fungi (PGPF) to promote plant growth and control disease in sustainable agriculture.
  Oct. 2022, Research paper (scientific journal), joint, 12, 10, DOI(公開)(r-map)
• Genetic and Physiological Characterization of Soybean-Nodule-Derived Isolates from Bangladeshi Soils Revealed Diverse Array of Bacteria with Potential Bradyrhizobia for Biofertilizers
  Mortuza, Md Firoz; Djedidi, Salem; Ito, Takehiro; Agake, Shin-ichiro; Sekimoto, Hitoshi; Yokoyama, Tadashi; Okazaki, Shin; Ohkama-Ohtsu, Naoko
  MICROORGANISMS
  MDPI
  Genetic and physiological characterization of bacteria derived from nodules of leguminous plants in the exploration of biofertilizer is of paramount importance from agricultural and environmental perspectives. Phylogenetic analysis of the 16S rRNA gene of 84 isolates derived from Bangladeshi soils revealed an unpredictably diverse array of nodule-forming and endosymbiotic bacteria-mostly belonging to the genus Bradyrhizobium. A sequence analysis of the symbiotic genes (nifH and nodD1) revealed similarities with the 16S rRNA gene tree, with few discrepancies. A phylogenetic analysis of the partial rrn operon (16S-ITS-23S) and multi-locus sequence analysis of atpD, glnII, and gyrB identified that the Bradyrhizobium isolates belonged to Bradyrhizobium diazoefficiens, Bradyrhizobium elkanii, Bradyrhizobium liaoningense and Bradyrhizobium yuanmingense species. In the pot experiment, several isolates showed better activity than B. diazoefficiens USDA110, and the Bho-P2-B2-S1-51 isolate of B. liaoningense showed significantly higher acetylene reduction activity in both Glycine max cv. Enrei and Binasoybean-3 varieties and biomass production increased by 9% in the Binasoybean-3 variety. Tha-P2-B1-S1-68 isolate of B. diazoefficiens significantly enhanced shoot length and induced 10% biomass production in Binasoybean-3. These isolates grew at 1-4% NaCl concentration and pH 4.5-10 and survived at 45 degrees C, making the isolates potential candidates for eco-friendly soybean biofertilizers in salty and tropical regions.
  Nov. 2022, Research paper (scientific journal), joint, 10, 11, DOI(公開)(r-map)
• Seasonal Changes in the Plant Growth-Inhibitory Effects of Rosemary Leaves on Lettuce Seedlings
  Appiah, Kwame Sarpong; Omari, Richard Ansong; Onwona-Agyeman, Siaw; Amoatey, Christiana Adukwei; Ofosu-Anim, John; Smaoui, Abderrazak; Ben Arfa, Abdelkarim; Suzuki, Yoko; Oikawa, Yosei; Okazaki, Shin; Katsura, Keisuke; Isoda, Hiroko; Kawada, Kiyokazu; Fujii, Yoshiharu
  PLANTS-BASEL
  MDPI
  Plant biodiversity has been studied to explore allelopathic species for the sustainable management of weeds to reduce the reliance on synthetic herbicides. Rosemary (Rosmarinus officinalis L., syn Salvia rosmarinus Spenn.), was found to have plant growth-inhibitory effects, and carnosic acid was reported as an allelochemical in the plant. In this study, the effects of seasonal variation (2011-2012) on the carnosic acid concentration and phytotoxicity of rosemary leaves from two locations in Tunisia (Fahs and Matmata) were investigated. The carnosic acid concentration in rosemary leaves was determined by HPLC, and lettuce (Lactuca sativa L.) was used as the receptor plant in the phytotoxicity bioassay. The highest carnosic acid concentration was found in rosemary samples collected in June 2011, which also had the highest inhibitory activity. Furthermore, a significant inverse correlation (r = -0.529; p < 0.01) was found between the inhibitory activity on lettuce hypocotyl and the carnosic acid concentration in rosemary leaves. Both temperature and elevation had a significant positive correlation with carnosic acid concentration, while rainfall showed a negative correlation. The results showed that the inhibitory effects of rosemary leaf samples collected in summer was highest due to their high carnosic acid concentration. The phytotoxicity of rosemary needs to be studied over time to determine if it varies by season under field conditions.
  Mar. 2022, Research paper (scientific journal), joint, 11, 5, DOI(公開)(r-map)
• Rhizobia use a pathogenic-like effector to hijack leguminous nodulation signalling
  Ratu, Safirah Tasa Nerves; Teulet, Albin; Miwa, Hiroki; Masuda, Sachiko; Nguyen, Hien P.; Yasuda, Michiko; Sato, Shusei; Kaneko, Takakazu; Hayashi, Makoto; Giraud, Eric; Okazaki, Shin
  SCIENTIFIC REPORTS
  NATURE PORTFOLIO
  Legume plants form a root-nodule symbiosis with rhizobia. This symbiosis establishment generally relies on rhizobium-produced Nod factors (NFs) and their perception by leguminous receptors (NFRs) that trigger nodulation. However, certain rhizobia hijack leguminous nodulation signalling via their type III secretion system, which functions in pathogenic bacteria to deliver effector proteins into host cells. Here, we report that rhizobia use pathogenic-like effectors to hijack legume nodulation signalling. The rhizobial effector Bel2-5 resembles the XopD effector of the plant pathogen Xanthomonas campestris and could induce nitrogen-fixing nodules on soybean nfr mutant. The soybean root transcriptome revealed that Bel2-5 induces expression of cytokinin-related genes, which are important for nodule organogenesis and represses ethylene- and defense-related genes that are deleterious to nodulation. Remarkably, Bel2-5 introduction into a strain unable to nodulate soybean mutant affected in NF perception conferred nodulation ability. Our findings show that rhizobia employ and have customized pathogenic effectors to promote leguminous nodulation signalling.
  21 Jan. 2021, Research paper (scientific journal), joint, 11, 1, 2045-2322, DOI(公開)(r-map), 2034
• The Bradyrhizobium diazoefficiens type III effector NopE modulates the regulation of plant hormones towards nodulation in Vigna radiata
  Piromyou, Pongdet; Nguyen, Hien P.; Songwattana, Pongpan; Boonchuen, Pakpoom; Teamtisong, Kamonluck; Tittabutr, Panlada; Boonkerd, Nantakorn; Tantasawat, Piyada Alisha; Goettfert, Michael; Okazaki, Shin; Teaumroong, Neung
  SCIENTIFIC REPORTS
  NATURE PORTFOLIO
  Host-specific legume-rhizobium symbiosis is strictly controlled by rhizobial type III effectors (T3Es) in some cases. Here, we demonstrated that the symbiosis of Vigna radiata (mung bean) with Bradyrhizobium diazoefficiens USDA110 is determined by NopE, and this symbiosis is highly dependent on host genotype. NopE specifically triggered incompatibility with V. radiata cv. KPS2, but it promoted nodulation in other varieties of V. radiata, including KPS1. Interestingly, NopE1 and its paralogue NopE2, which exhibits calcium-dependent autocleavage, yield similar results in modulating KPS1 nodulation. Furthermore, NopE is required for early infection and nodule organogenesis in compatible plants. Evolutionary analysis revealed that NopE is highly conserved among bradyrhizobia and plant-associated endophytic and pathogenic bacteria. Our findings suggest that V. radiata and B. diazoefficiens USDA110 may use NopE to optimize their symbiotic interactions by reducing phytohormone-mediated ETI-type (PmETI) responses via salicylic acid (SA) biosynthesis suppression.
  16 Aug. 2021, Research paper (scientific journal), joint, 11, 1, 2045-2322, DOI(公開)(r-map)
• Genetic Diversity and Characterization of Symbiotic Bacteria Isolated from Endemic Phaseolus Cultivars Located in Contrasting Agroecosystems in Venezuela
  Ramirez, Maria Daniela Artigas; Espana, Mingrelia; Sekimoto, Hitoshi; Okazaki, Shin; Yokoyama, Tadashi; Ohkama-Ohtsu, Naoko
  MICROBES AND ENVIRONMENTS
  JAPANESE SOC MICROBIAL ECOLOGY, DEPT BIORESOURCE SCIENCE
  Phaseolus vulgaris is a grain cultivated in vast areas of different countries. It is an excellent alternative to the other legumes in the Venezuelan diet and is of great agronomic interest due to its resistance to soil acidity, drought, and high temperatures. Phaseolus establishes symbiosis primarily with Rhizobium and Ensifer species in most countries, and this rhizobia-legume interaction has been studied in Asia, Africa, and the Americas. However, there is currently no evidence to show that rhizobia nodulate the endemic cultivars of P. vulgaris in Venezuela. Therefore, we herein investigated the phylogenetic diversity of plant growth-promoting and N-2-fixing nodulating bacteria isolated from the root nodules of P. vulgaris cultivars in a different agroecosystem in Venezuela In comparisons with other countries, higher diversity was found in isolates from P. vulgaris nodules, ranging from alpha- and beta-proteobacteria. Some isolates belonging to several new phylogenetic lineages within Bradyrhizobium, Ensifer, and Afesorhizobium species were also specifically isolated at some topographical regions. Additionally, some isolates exhibited tolerance to high temperature, acidity, alkaline pH, salinity stress, and high Al levels; some of these characteristics may be related to the origin of the isolates. Some isolates showed high tolerance to Al toxicity as well as strong plant growth-promoting and antifungal activities, thereby providing a promising agricultural resource for inoculating crops.
  05 Jun. 2021, Research paper (scientific journal), joint, 36, 2, 1342-6311, DOI(公開)(r-map)
• Leaf Bleaching in Rice: A New Disease in Vietnam Caused by Methylobacterium indicum, Its Genomic Characterization and the Development of a Suitable Detection Technique
  Lai, Khoa; Ngoc Thai Nguyen; Yasuda, Michiko; Dastogeer, Khondoker M. G.; Toyoda, Atsushi; Higashi, Koichi; Kurokawa, Ken; Nga Thi Thu Nguyen; Komatsu, Ken; Okazaki, Shin
  MICROBES AND ENVIRONMENTS
  JAPANESE SOC MICROBIAL ECOLOGY, DEPT BIORESOURCE SCIENCE
  A new disease in rice that is characterized by leaf bleaching was recently identified in some fields in the Mekong Delta region of Vietnam. The present study was the first to isolate and identify the pathogen of this disease. We confirmed that leaf bleaching symptoms were due to infection with Methylobacterium indicum bacteria using molecular biology approaches. A full-length genome analysis of pathogenic Methylobacterium strain VL1 revealed that it comprises a single chromosome and six plasmids, with a total size of 7.05 Mbp and GC content of 70.5%. The genomic features of VL1 were similar to those of the non-pathogenic M. indicum strain SE2.11(T); however, VL1 possessed additional unique genes, including those related to homoserine lactone biosynthesis. We established a loop-mediated isothermal amplification (LAMP) assay using the unique sequences of VL1 as target sequences for the rapid and simple detection of pathogenic M. indicum strains. Our initial evaluation demonstrated that the LAMP assay successfully distinguished between pathogenic and non-pathogenic strains infecting rice plants in a rapid and sensitive manner. The present results provide insights into the pathogenesis and development of control measures for novel rice diseases.
  03 Nov. 2021, Research paper (scientific journal), joint, 36, 4, 1342-6311, DOI(公開)(r-map)
• Multiple Domains in the Rhizobial Type III Effector Bel2-5 Determine Symbiotic Efficiency With Soybean
  Ratu, Safirah Tasa Nerves; Hirata, Atsushi; Kalaw, Christian Oliver; Yasuda, Michiko; Tabuchi, Mitsuaki; Okazaki, Shin
  FRONTIERS IN PLANT SCIENCE
  FRONTIERS MEDIA SA
  Bradyrhizobium elkanii utilizes the type III effector Bel2-5 for nodulation in host plants in the absence of Nod factors (NFs). In soybean plants carrying the Rj4 allele, however, Bel2-5 causes restriction of nodulation by triggering immune responses. Bel2-5 shows similarity with XopD of the phytopathogen Xanthomonas campestris pv. vesicatoria and possesses two internal repeat sequences, two ethylene (ET)-responsive element-binding factor-associated amphiphilic repression (EAR) motifs, a nuclear localization signal (NLS), and a ubiquitin-like protease (ULP) domain, which are all conserved in XopD except for the repeat domains. By mutational analysis, we revealed that most of the putative domains/motifs in Bel2-5 were essential for both NF-independent nodulation and nodulation restriction in Rj4 soybean. The expression of soybean symbiosis- and defense-related genes was also significantly altered by inoculation with the bel2-5 domain/motif mutants compared with the expression upon inoculation with wild-type B. elkanii, which was mostly consistent with the phenotypic changes of nodulation in host plants. Notably, the functionality of Bel2-5 was mostly correlated with the growth inhibition effect of Bel2-5 expressed in yeast cells. The nodulation phenotypes of the domain-swapped mutants of Bel2-5 and XopD indicated that both the C-terminal ULP domain and upstream region are required for the Bel2-5-dependent nodulation phenotypes. These results suggest that Bel2-5 interacts with and modifies host targets via these multiple domains to execute both NF-independent symbiosis and nodulation restriction in Rj4 soybean.
  07 Jun. 2021, Research paper (scientific journal), joint, 12, 1664-462X, DOI(公開)(r-map), 1046
• Distinct Root Microbial Communities in Nature Farming Rice Harbor Bacterial Strains With Plant Growth-Promoting Traits
  Sinong, Grace Flavyeliz; Yasuda, Michiko; Nara, Yoshiyuki; Lee, Chol Gyu; Dastogeer, Khondoker Mohammad Golam; Tabuchi, Hiroyasu; Nakai, Hirokazu; Djedidi, Salem; Okazaki, Shin
  FRONTIERS IN SUSTAINABLE FOOD SYSTEMS
  FRONTIERS MEDIA SA
  A nature farming system is an ecological farming practice that entails cultivating crops without using chemical fertilizers and pesticides. To understand the diversity and functions of root microbiomes associated with nature farming systems, we compared the root microbial community of rice under nature farming conditions with those under conventional farming conditions. High-throughput amplicon analysis demonstrated a higher abundance and greater diversity of the root microbiome under unfertilized nature farming conditions than under conventional conditions. The application of chemical fertilizers reduced the microbial diversity and abundance of some beneficial taxa important for plant growth and health. Subsequently, we isolated and identified 46 endo- and epiphytic bacteria from rice roots grown under nature farming conditions and examined their plant growth-promoting activity. Six potential isolates were selected for plant growth assessment in insoluble P- and K-containing media. Most of the isolates promoted rice growth, and Pseudomonas koreensis AEPR1 was able to enhance rice growth significantly in both insoluble P- and K-containing media. Our data indicated that nature farming systems create a distinct root microbiome that is comparatively more diverse and supports plant growth under low-input cultivation practices than under conventional practices. The potential isolates could be exploited as sources with potential applications in sustainable agriculture.
  28 Jan. 2021, Research paper (scientific journal), joint, 4, DOI(公開)(r-map), 314
• Biofertilizer Activity of Azospirillum sp. B510 on the Rice Productivity in Ghana
  Sarkodee-Addo, Elsie; Tokiwa, Chihiro; Bonney, Patrick; Aboagye, Daniel Asiamah; Yeboah, Alex; Abebrese, Samuel Oppong; Bam, Ralph; Nartey, Eric Kwesi; Okazaki, Shin; Yasuda, Michiko
  MICROORGANISMS
  MDPI
  Rice production in Ghana has become unsustainable due to the extremely nutrient-poor soils. It is caused by inadequate soil fertility management, including the inefficient application of fertilizers. A practical solution could be the biofertilizers, Azospirillum sp. B510. We performed field trials in Ghana and Japan to compare the effects of B510 colonization on selected Ghanaian rice varieties grown. The B510 inoculation significantly enhanced the rice cultivars' growth and yield. The phenotypic characteristics observed in rice varieties Exbaika, Ex-Boako, AgraRice, and Amankwatia were mainly short length and high tillering capacity. These features are attributed to the host plant (cv. Nipponbare), from which the strain B510 was isolated. Furthermore, Azospirillum species has been identified as the dominant colonizing bacterium of rice rhizosphere across a diverse range of agroecologies in all major rice-growing regions in Ghana. Our results suggest that the utilization of B510 as a bio-fertilizer presents a promising way to improve rice growth, enhance soil fertility, and sustain rice productivity in Ghana.
  Sep. 2021, Research paper (scientific journal), joint, 9, 9, DOI(公開)(r-map)
• The rhizobial type III effector ErnA confers the ability to form nodules in legumes
  Teulet, Albin; Busset, Nicolas; Fardoux, Joel; Gully, Djamel; Chaintreuil, Clemence; Cartieaux, Fabienne; Jauneau, Alain; Comorge, Virginie; Okazaki, Shin; Kaneko, Takakazu; Gressent, Frederic; Nouwen, Nico; Arrighi, Jean-Francois; Koebnik, Ralf; Mergaert, Peter; Deslandes, Laurent; Giraud, Eric
  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
  NATL ACAD SCIENCES
  Several Bradyrhizobium species nodulate the leguminous plant Aeschynomene indica in a type III secretion system-dependent manner, independently of Nod factors. To date, the underlying molecular determinants involved in this symbiotic process remain unknown. To identify the rhizobial effectors involved in nodulation, we mutated 23 out of the 27 effector genes predicted in Bradyrhizobium strain ORS3257. The mutation of nopAO increased nodulation and nitrogenase activity, whereas mutation of 5 other effector genes led to various symbiotic defects. The nopM1 and nopP1 mutants induced a reduced number of nodules, some of which displayed large necrotic zones. The nopT and nopAB mutants induced uninfected nodules, and a mutant in a yet-undescribed effector gene lost the capacity for nodule formation. This effector gene, widely conserved among bradyrhizobia, was named ernA for ”effector required for nodulation-A.” Remarkably, expressing ernA in a strain unable to nodulate A. indica conferred nodulation ability. Upon its delivery by Pseudomonas fluorescens into plant cells, ErnA was specifically targeted to the nucleus, and a fluorescence resonance energy transfer-fluorescence lifetime imaging microscopy approach supports the possibility that ErnA binds nucleic acids in the plant nuclei. Ectopic expression of ernA in A. indica roots activated organogenesis of root- and nodule-like structures. Collectively, this study unravels the symbiotic functions of rhizobial type III effectors playing distinct and complementary roles in suppression of host immune functions, infection, and nodule organogenesis, and suggests that ErnA triggers organ development in plants by a mechanism that remains to be elucidated.
  22 Oct. 2019, Research paper (scientific journal), joint, 116, 43, 0027-8424, DOI(公開)(r-map), 21758, 21768
• Lotus Accessions Possess Multiple Checkpoints Triggered by Different Type III Secretion System Effectors of the Wide-Host-Range Symbiont Bradyrhizobium elkanii USDA61
  Kusakabe, Shohei; Higasitani, Nahoko; Kaneko, Takakazu; Yasuda, Michiko; Miwa, Hiroki; Okazaki, Shin; Saeki, Kazuhiko; Higashitani, Atsushi; Sato, Shusei
  MICROBES AND ENVIRONMENTS
  JAPANESE SOC MICROBIAL ECOLOGY, DEPT BIORESOURCE SCIENCE
  Bradyrhizobium elkanii, a rhizobium with a relatively wide host range, possesses a functional type III secretion system (T3SS) that is involved in symbiotic incompatibility against Rj4-genotype soybean (Glycine max) and some accessions of mung bean (Vigna radiata). To expand our knowledge on the T3SS-mediated partner selection mechanism in the symbiotic legume-rhizobia association we inoculated three Lotus experimental accessions with wild-type and T3SS-mutant strains of B. elkanii USDA61. Different responses were induced by T3SS in a host genotype-dependent manner. Lotus japonicus Gifu inhibited infection; L. burttii allowed infection, but inhibited nodule maturation at the post-infection stage; and L. burttii and L. japonicus MG-20 both displayed a nodule early senescence-like response. By conducting inoculation tests with mutants of previously reported and newly identified effector protein genes of B. elkanii USDA61, we identified NopF as the effector protein triggering the inhibition of infection,. and NopM as the effector protein triggering the nodule early senescence-like response. Consistent with these results, the B. elkanii USDA61 gene for NopF introduced into the Lotus symbiont Mesorhizobium japonicum induced infection inhibition in L. japonicus Gifu, but did not induce any response in L. burttii or L. japonicus MG-20. These results suggest that Lotus accessions possess at least three checkpoints to eliminate unfavorable symbionts, including the post-infection stage, by recognizing different T3SS effector proteins at each checkpoint.
  2020, Research paper (scientific journal), joint, 35, 1, 1342-6311, DOI(公開)(r-map)
• Plant Salinity Tolerance Conferred by Arbuscular Mycorrhizal Fungi and Associated Mechanisms: A Meta-Analysis
  Dastogeer, Khondoker M. G.; Zahan, Mst Ishrat; Tahjib-Ul-Arif, Md.; Akter, Mst Arjina; Okazaki, Shin
  FRONTIERS IN PLANT SCIENCE
  FRONTIERS MEDIA SA
  Soil salinity often hinders plant productivity in both natural and agricultural settings. Arbuscular mycorrhizal fungal (AMF) symbionts can mediate plant stress responses by enhancing salinity tolerance, but less attention has been devoted to measuring these effects across plant-AMF studies. We performed a meta-analysis of published studies to determine how AMF symbionts influence plant responses under non-stressed vs. salt-stressed conditions. Compared to non-AMF plants, AMF plants had significantly higher shoot and root biomass (p < 0.0001) both under non-stressed conditions and in the presence of varying levels of NaCl salinity in soil, and the differences became more prominent as the salinity stress increased. Categorical analyses revealed that the accumulation of plant shoot and root biomass was influenced by various factors, such as the host life cycle and lifestyle, the fungal group, and the duration of the AMF and salinity treatments. More specifically, the effect of Funneliformis on plant shoot biomass was more prominent as the salinity level increased. Additionally, under stress, AMF increased shoot biomass more on plants that are dicots, plants that have nodulation capacity and plants that use the C3 plant photosynthetic pathway. When plants experienced short-term stress (<2 weeks), the effect of AMF was not apparent, but under longer-term stress (>4 weeks), AMF had a distinct effect on the plant response. For the first time, we observed significant phylogenetic signals in plants and mycorrhizal species in terms of their shoot biomass response to moderate levels of salinity stress, i.e., closely related plants had more similar responses, and closely related mycorrhizal species had similar effects than distantly related species. In contrast, the root biomass accumulation trait was related to fungal phylogeny only under non-stressed conditions and not under stressed conditions. Additionally, the influence of AMF on plant biomass was found to be unrelated to plant phylogeny. In line with the greater biomass accumulation in AMF plants, AMF improved the water status, photosynthetic efficiency and uptake of Ca and K in plants irrespective of salinity stress. The uptake of N and P was higher in AMF plants, and as the salinity increased, the trend showed a decline but had a clear upturn as the salinity stress increased to a high level. The activities of malondialdehyde (MDA), peroxidase (POD), and superoxide dismutase (SOD) as well as the proline content changed due to AMF treatment under salinity stress. The accumulation of proline and catalase (CAT) was observed only when plants experienced moderate salinity stress, but peroxidase (POD) and superoxide dismutase (SOD) were significantly increased in AMF plants irrespective of salinity stress. Taken together, arbuscular mycorrhizal fungi influenced plant growth and physiology, and their effects were more notable when their host plants experienced salinity stress and were influenced by plant and fungal traits.
  09 Dec. 2020, Research paper (scientific journal), joint, 11, 1664-462X, DOI(公開)(r-map)
• Host Specificity of Endophytic Fungi from Stem Tissue of Nature Farming Tomato (Solanum lycopersicum Mill.) in Japan
  Dastogeer, Khondoker Mohammad Golam; Oshita, Yutaro; Yasuda, Michiko; Kanasugi, Makoto; Matsuura, Eri; Xu, Qicong; Okazaki, Shin
  AGRONOMY-BASEL
  MDPI
  To understand the distribution of the cultivable fungal community in plant tissues from nature farming tomato plants, we sampled plants of seven different tomato cultivars and recovered 1742 fungal isolates from 1895 stem tissues sampled from three sites in Japan. Overall, the isolation frequency was low (3-13%) and the isolation and colonization frequencies did not vary significantly as a function of the cultivar. The fungi were divided into 29 unique operational taxonomic units (OTUs) with 97% ITS gene sequence identity, the majority of which belong to Ascomycota (99.3%). The dominant genera of cultivable endophytic fungi wereFusarium(45.1%),Alternaria(12.8%),Gibberella(12.0%), andDipodascus(6.8%). The alpha diversity of the fungal endophytes varied among tomato cultivars. Ordination analysis performed to investigate patterns of endophyte community assemblages on the various cultivars revealed that host cultivars had a significant impact on the endophyte community assemblages in all the study sites. Some of the taxaFusarium, Alternaria,andPenicilliumwere found on all cultivars, while few were uniquely present in different cultivars. The dominant taxa may be adapted to the particular microecological and physiological conditions present in tomato stems.
  15 Jul. 2020, Research paper (scientific journal), joint, 10, 7, DOI(公開)(r-map)
• Exploring Rice Root Microbiome; The Variation, Specialization and Interaction of Bacteria and Fungi In Six Tropic Savanna Regions in Ghana
  Kanasugi, Makoto; Sarkodee-Addo, Elsie; Omari, Richard Ansong; Dastogeer, Khondoker Mohammad Golam; Fujii, Yoshiharu; Abebrese, Samuel Oppong; Bam, Ralph; Asuming-Brempong, Stella; Okazaki, Shin
  SUSTAINABILITY
  MDPI
  We investigated the root microbiomes of rice sampled from six major rice-producing regions in Ghana using Illumina MiSeq high-throughput amplicon sequencing analysis. The result showed that both bacterial and fungal community compositions were significantly varied across the regions. Bacterial communities were shaped predominantly by biotic factors, including root fungal diversity and abundance. In contrast, fungal communities were influenced by abiotic factors such as soil nitrate, total carbon and soil pH. A negative correlation between the diversity and abundance of root fungi with soil nitrate (NO3-) level was observed. It suggested that there were direct and indirect effects of NO(3)(-)on the root-associated bacterial and fungal community composition. The gradient of soil nitrate from North to South parts of Ghana may influence the composition of rice root microbiome. Bacterial community composition was shaped by fungal diversity and abundance; whereas fungal community composition was shaped by bacterial abundance. It suggested the mutualistic interaction of bacteria and fungi at the community level in the rice root microbiome. Specific bacterial and fungal taxa were detected abundantly in the 'Northern' regions of Ghana, which were very low or absent from the samples of other regions. The analysis of indicator species suggested that an 'ecological specialization' may have occurred which enabled specific microbial taxa to adapt to the local environment, such as the low-nitrate condition in the Northern regions.
  05 Jul. 2020, Research paper (scientific journal), joint, 12, 14, DOI(公開)(r-map)
• Identification ofBradyrhizobium elkaniiUSDA61 Type III Effectors Determining Symbiosis withVigna mungo
  Nguyen, Hien P.; Ratu, Safirah T. N.; Yasuda, Michiko; Teaumroong, Neung; Okazaki, Shin
  GENES
  MDPI
  Bradyrhizobium elkaniiUSDA61 possesses a functional type III secretion system (T3SS) that controls host-specific symbioses with legumes. Here, we demonstrated thatB. elkaniiT3SS is essential for the nodulation of several southern AsiaticVigna mungocultivars. Strikingly, inactivation of either Nod factor synthesis or T3SS inB. elkaniiabolished nodulation of theV. mungoplants. Among the effectors, NopL was identified as a key determinant for T3SS-dependent symbiosis. Mutations of other effector genes, such asinnB,nopP2, andbel2-5, also impacted symbiotic effectiveness, depending on host genotypes. ThenopLdeletion mutant formed no nodules onV. mungo,but infection thread formation was still maintained, thereby suggesting its pivotal role in nodule organogenesis. Phylogenetic analyses revealed that NopL was exclusively conserved amongBradyrhizobiumandSinorhizobium(Ensifer) species and showed a different phylogenetic lineage from T3SS. These findings suggest thatV. mungoevolved a unique symbiotic signaling cascade that requires both NFs and T3Es (NopL).
  May 2020, Research paper (scientific journal), joint, 11, 5, DOI(公開)(r-map)
• Arbuscular Mycorrhizal Fungi Associated with Rice (Oryza sativa L.) in Ghana: Effect of Regional Locations and Soil Factors on Diversity and Community Assembly
  Sarkodee-Addo, Elsie; Yasuda, Michiko; Lee, Chol Gyu; Kanasugi, Makoto; Fujii, Yoshiharu; Omari, Richard Ansong; Abebrese, Samuel Oppong; Bam, Ralph; Asuming-Brempong, Stella; Dastogeer, Khondoker Mohammad Golam; Okazaki, Shin
  AGRONOMY-BASEL
  MDPI
  Understanding the community composition and diversity of arbuscular mycorrhizal fungi (AMF) in an agricultural ecosystem is important for exploiting their potential in sustainable crop production. In this study, we described the genetic diversity and community structure of indigenous AMF in rain-fed rice cultivars across six different regions in Ghana. The morphological and molecular analyses revealed a total of 15 different AMF genera isolated from rice roots. Rhizophagus and Glomus were observed to be predominant in all regions except the Ashanti region, which was dominated by the genera Scutellospora and Acaulospora. A comparison of AMF diversity among the agroecological zones revealed that Guinea Savannah had the highest diversity. Permutational Multivariate Analysis of Variance (PERMANOVA) analysis indicated that the available phosphorus (AP) in the soil was the principal determining factor for shaping the AMF community structure (p < 0.05). We report, for the first time, AMF diversity and community structure in rice roots and how communities are affected by the chemical properties of soil from different locations in Ghana.
  12 Apr. 2020, Research paper (scientific journal), joint, 10, 4, DOI(公開)(r-map)
• Multiphase characterization of wild Vigna associated root nodule bacteria from Japanese subtropical islands unveiled novel high temperature resistant Bradyrhizobium strains having high symbiotic compatibility with soybean and mungbean
  Mortuza, Md Firoz; Tomooka, Norihiko; Habib, Safiullah; Akatsu, Tetsuya; Djedidi, Salem; Naito, Ken; Sekimoto, Hitoshi; Okazaki, Shin; Ohkama-Ohtsu, Naoko; Yokoyama, Tadashi
  SOIL SCIENCE AND PLANT NUTRITION
  TAYLOR & FRANCIS LTD
  Vigna riukiuensis plant - a rare type of vigna, found only in Taiwan and the islands of Okinawa prefecture, Japan - possesses intrinsic property of high level of salt and heat tolerance. To understand the diversity and identify suitable rhizobia, multiphase characterization of root nodule bacteria associated with V. riukiuensis grown in Ishigaki and Iriomote Islands of Okinawa prefecture was performed. Multigene phylogenetic analysis of housekeeping genes based on 16S rRNA gene sequences, 16S-23S rRNA gene internal transcribed spacer (ITS) and 23S rRNA gene sequences identified three main groups closely similar to Bradyrhizobium japonicum, B. elkanii and B. jicamae family. However, analysis of symbiotic nifH and nodD1 genes and their phylogenetic trees showed similar topology, having only few discrepancies in comparison to the housekeeping gene phylogeny. Interestingly, for some of the isolates having similarity with B. elkanii, growth was observed at 40 degrees C, which exceed the highest record for B. elkanii to the best of our knowledge. All the isolates were observed to have the capability of forming root nodules and fix nitrogen in their original host plant V. riukiuensis and two other crops: soybean and mungbean. Most of the isolates showed similar or higher nitrogen-fixing capability in comparison with B. diazoefficiens USDA110 in V. riukiuensis and V. radiata (mungbean), and Iri 5/6 in V. riukiuensis, Iri 5/12 in soybean and Ishi 7/2 in mungbean showed highest acetylene reduction assay (in mu mol/h/gm nodule dry weight) activity, which was significantly higher than B. diazoefficiens USDA110. In addition, six isolates attained higher soybean biomass production compared with B. diazoefficiens USDA110, suggesting high symbiotic compatibility with soybean. Among them, Iri 5/7 of B. elkanii group contributed 29% higher soybean biomass production than B. diazoefficiens USDA110 and could grow at 40 degrees C, hence it could be a promising soybean inoculant in the tropics.
  03 Mar. 2020, Research paper (scientific journal), joint, 66, 2, 0038-0768, DOI(公開)(r-map), 285, 298
• Novel rhizobia exhibit superior nodulation and biological nitrogen fixation even under high nitrate concentrations
  Nguyen, Hien P.; Miwa, Hiroki; Obirih-Opareh, Jennifer; Suzaki, Takuya; Yasuda, Michiko; Okazaki, Shin
  FEMS MICROBIOLOGY ECOLOGY
  OXFORD UNIV PRESS
  Legume-rhizobium symbiosis leads to the formation of nitrogen-fixing root nodules. However, externally applied chemical nitrogen fertilizers (nitrate and ammonia) strongly inhibit nodule formation and nitrogen fixation. Here, we isolated several rhizobial strains exhibiting a superior nodulation and nitrogen fixation with soybean at high nitrate concentrations. The nodulation of soybean symbiont Bradyrhizobium diazoefficiens USDA110 was significantly inhibited at 12.5 mM nitrate; however, three isolates (NKS4, NKM2 and NKTG2) were capable of forming nitrogen-fixing nodules, even at 20 mM nitrate. These isolates exhibited higher nodulation competitiveness and induced larger nodules with higher nitrogen-fixation activity than USDA110 at 5 mM nitrate. Furthermore, these isolates induced more nodules than USDA110 even in nitrate-free conditions. These isolates had a distant lineage within the Bradyrhizobium genus; though they were relatively phylogenetically close to Bradyrhizobium japonicum, their morphological and growth characteristics were significantly different. Notably, in the presence of nitrate, expression of the soybean symbiosis-related genes (GmENOD40 and GmNIN) was significantly higher and expression of GmNIC1 that is involved in nitrate-dependent nodulation inhibition was lower in the roots inoculated with these isolates in contrast with inoculation of USDA110. These novel rhizobia serve as promising inoculants for soybeans cultivated in diverse agroecosystems, particularly on nitrate-applied soils.
  01 Feb. 2020, Research paper (scientific journal), joint, 96, 2, 0168-6496, DOI(公開)(r-map)
• Diversity of Methylobacterium spp. in the Rice of the Vietnamese Mekong Delta
  Lai, Khoa; Nguyen, Ngoc Thai; Miwa, Hiroki; Yasuda, Michiko; Hiep Huu Nguyen; Okazaki, Shin
  MICROBES AND ENVIRONMENTS
  JAPANESE SOC MICROBIAL ECOLOGY, DEPT BIORESOURCE SCIENCE
  The Vietnamese Mekong delta is one of the largest rice-producing areas globally. Methylobacterium spp. are persistent colonizers of the rice plant and exert beneficial effects on plant growth and health. Sixty-one Methylobacterium strains belonging to seven species were predominantly isolated from the phyllosphere of rice cultivated in six Mekong delta provinces. Inoculation tests revealed that some strains exhibited plant growth-promoting activity. Moreover, three strains possessed the novel characteristics of inducing leaf bleaching and killing rice seedlings. These results revealed the complex diversity of Methylobacterium in Mekong delta rice and that healthy and productive rice cultivation requires a proper balance of Methylobacterium.
  23 Jan. 2020, Research paper (scientific journal), joint, 35, 1, 1342-6311, DOI(公開)(r-map)
• Phylogenetic Analysis of Symbiotic Bacteria Associated with Two Vigna Species under Different Agro-Ecological Conditions in Venezuela
  Artigas Ramirez, Maria Daniela; Espana, Mingrelia; Lewandowska, Sylwia; Yuan, Kun; Okazaki, Shin; Ohkama-Ohtsu, Naoko; Yokoyama, Tadashi
  MICROBES AND ENVIRONMENTS
  JAPANESE SOC MICROBIAL ECOLOGY, DEPT BIORESOURCE SCIENCE
  Vigna is a genus of legumes cultivated in specific areas of tropical countries. Species in this genus are important crops worldwide. Vigna species are of great agronomic interest in Venezuela because Ligna beans are an excellent alternative to other legumes. However, this type of crop has some cultivation issues due to sensitivity to acidic soils, high temperatures, and salinity stress, which are common in Venezuela. Vigna species establish symbioses mainly with Bradvrhizobium and Ensifer, and Vigna-rhizobia interactions have been examined in Asia, Africa, and America. However, the identities of the rhizobia associated with V radiata and V unguiculata in Venezuela remain unknown. In the present study, we isolated Venezuelan symbiotic rhizobia associated with Vigna species from soils with contrasting agroccosystcms or from fields in Venezuela. Several types of soils were used for bacterial isolation and nodules were sampled from environments characterized by abiotic stressors, such as high temperatures, high concentrations of NaCI, and acidic or alkaline pH. Venezuelan Vigna-rhizobia were mainly fast-growing. Sequencing of several housekeeping genes showed that in contrast to other continents, Venezuelan Vigna species were nodulated by rhizobia genus including Burkholderia, containing bacteria from several new phylogenetic lineages within the genus Bradyrhizobium. Some Rhizobium and Bradyrhizobium isolates were tolerant of high salinity and Al toxicity. The stress tolerance of strains was dependent on the type of rhizobia. soil origin, and cultivation history'. An isolate classified as R. phaseoli showed the highest plant biomass, nitrogen fixation. and excellent abiotic stress response, suggesting a novel promising inoculant for Vigna cultivation in Venezuela.
  11 Jan. 2020, Research paper (scientific journal), joint, 35, 1, 1342-6311, DOI(公開)(r-map)
• Complete Genome Sequence of Plant Growth-Promoting Bacillus pumilus TUAT1
  Okazaki S, Sano N, Yamada T, Ishii K, Kojima K, Djedidi S, Artigas Ramírez MD, Yuan K, Kanekatsu M, Ohkama-Ohtsu N, Hirose Y, Oshima K, Hattori M, Yokoyama T.
  Microbiol Resour Announc.
  23 May 2019, Research paper (scientific journal), joint, 8, 21, DOI(公開)(r-map), 1, 2
• InnB, a Novel Type III Effector of Bradyrhizobium elkanii USDA61, Controls Symbiosis With Vigna Species
  Nguyen, Hien P.; Ratu, Safirah T. N.; Yasuda, Michiko; Goettfert, Michael; Okazaki, Shin
  Frontiers in Microbiology
  FRONTIERS MEDIA SA
  Bradyrhizobium elkanii USDA61 is incompatible with mung bean (Vigna radiata cv. KPS1) and soybean (Glycine max cv. BARC2) and unable to nodulate either plant. This incompatibility is due to the presence of a functional type III secretion system (T3SS) that translocates effector protein into host cells. We previously identified five genes in B. elkanii that are responsible for its incompatibility with KPS1 plants. Among them, a novel gene designated as innB exhibited some characteristics associated with the T3SS and was found to be responsible for the restriction of nodulation on KPS1. In the present study, we further characterized innB by analysis of gene expression, protein secretion, and symbiotic phenotypes. The innB gene was found to encode a hypothetical protein that is highly conserved among T3SS-harboring rhizobia. Similar to other rhizobial T3SS-associated genes, the expression of innB was dependent on plant flavonoids and a transcriptional regulator Ttsl. The InnB protein was secreted via the T3SS and was not essential for secretion of other nodulation outer proteins. In addition, T3SS-dependent translocation of InnB into nodule cells was confirmed by an adenylate cyclase assay. According to inoculation tests using several Vigna species, InnB promoted nodulation of at least one V mungo cultivar. These results indicate that innB encodes a novel type III effector controlling symbiosis with Vigna species.
  18 Dec. 2018, Research paper (scientific journal), joint, 9, 1664-302X, DOI(公開)(r-map)

  URL(公開)(r-map)
• Effects of Different Sources of Nitrogen on Endophytic Colonization of Rice Plants by Azospirillum sp B510
  Naher, Kamrun; Miwa, Hiroki; Okazaki, Shin; Yasuda, Michiko
  Microbes and Environments
  JAPANESE SOC MICROBIAL ECOLOGY, DEPT BIORESOURCE SCIENCE
  Azospirillum sp. B510, a free-living nitrogen-fixing bacterium isolated from the stems of rice (Oryza saliva cv. Nipponbare), was investigated to establish effective conditions for the colonization of rice plants. We analyzed the effects of the nitrogen sources KNO3,NH4Cl, urea (CO[NH2](2)), and NH4 NO3 at different concentrations (0.01-10 mM) on this colonization. Nitrogen promoted plant growth in a concentration-dependent manner, with minor differences being observed among the different nitrogen sources. Bacterial colonization was markedly suppressed on media containing NH4+ concentrations higher than 1 mM. Since concentrations of up to and including 10 mM NH4+ did not exhibit any antibacterial activity, we analyzed several factors affecting the NH4+-dependent inhibition of endophytic colonization, including the accumulation of the reactive oxygen species H2O2 and the secretion of the chemotactic substrate malic acid. The accumulation of H2O2 was increased in rice roots grown on 1 mM NH4Cl. The amounts of malic acid secreted from NH4 -grown rice plants were lower than those secreted from plants grown without nitrogen or with KNO3. Although the bacterium exhibited chemotactic activity, moving towards root exudates from plants grown without nitrogen and KNO3-grown plants, this activity was not observed with root exudates from NH(4)(+)grown plants. NH4+, but not NO3(-), caused the acidification of growth media, which inhibited plant bacterial colonization. These NH4+-dependent phenomena were markedly suppressed by the stabilization of medium pH using a buffer. These results demonstrate that the type and concentration of nitrogen fertilizer affects the colonization of rice plants by Azospirillum sp. B510.
  29 Sep. 2018, Research paper (scientific journal), joint, 33, 3, 1342-6311, DOI(公開)(r-map), 301, 308
• Identification of Bradyrhizobium elkanii genes involved in incompatibility with Vigna radiata
  Nguyen HP, Miwa H, Kaneko T, Sato S, Okazaki S.
  Genes
  Dec. 2017, Research paper (scientific journal), joint, 8, 12, DOI(公開)(r-map), E374
• Involvement of programmed cell death in suppression of the number of root nodules formed in soybean induced by Bradyrhizobium infection
  Li M, Yasuda M, Yamaya-Ito H, Maeda M, Sasaki N, Nagata M, Suzuki A, Okazaki S, Sekimoto H, Yamada T, Ohtsu N, Yokoyama T.
  Soil Science and Plant Nutrition
  Nov. 2017, Research paper (scientific journal), joint, 63, 6, 561, 577
• 根粒菌・エンドファイトと植物との共生
  岡崎伸
  アグリバイオ2017年9月号
  Sep. 2017, joint, 1, 9, 18, 22
• How effectors promote beneficial interactions
  Miwa, Hiroki; Okazaki, Shin
  Current Opinion in Plant Biology
  CURRENT BIOLOGY LTD
  Beneficial microbes such as rhizobia possess effector proteins that are secreted into the host cytoplasm where they modulate host-signaling pathways. Among these effectors, type 3 secreted effectors (T3Es) of rhizobia play roles in promoting nitrogen-fixing nodule symbiosis, suppressing host defenses and directly activating symbiosis-related processes. Rhizobia use the same strategy as pathogenic bacteria to suppress host defenses such as targeting the MAPK cascade. In addition, rhizobial T3E can promote root nodule symbiosis by directly activating Nod factor signaling, which bypasses Nod factor perception. The various strategies employed by beneficial microbes to promote infection and maintain viability in the host are therefore crucial for plant endosymbiosis.
  Aug. 2017, Research paper (scientific journal), joint, 38, 1369-5266, DOI(公開)(r-map), 148, 154
• Growth Rate of and Gene Expression in Bradyrhizobium diazoefficiens USDA110 due to a Mutation in blr7984, a TetR Family Transcriptional Regulator Gene
  Ohkama-Ohtsu N1, Honma H, Nakagome M, Nagata M, Yamaya-Ito H, Sano Y, Hiraoka N, Ikemi T, Suzuki A, Okazaki S, Minamisawa K, Yokoyama T
  Microbes and Environments
  Jul. 2016, Research paper (scientific journal), joint, 31, 249, 259
• Effector-triggered Immunity Determines Host Genotype-specific Incompatibility in Legume-Rhizobium Symbiosis
  Yasuda M, Miwa H, Masuda S, Takebayashi Y, Sakakibara H, *Okazaki S.
  Plant Cell Physiol.
  Jul. 2016, Research paper (scientific journal), joint, 57, 1791, 1800
• Genetic diversity and symbiotic phenotype of hairy vetch rhizobia in Japan
  Yuan K, Miwa H, Iizuka M, Yokoyama T, Fujii Y, *Okazaki S
  Microbes and Environment
  May 2016, Research paper (scientific journal), joint, 31, 121, 126
• Identification of Bradyrhizobium elkanii Genes Involved in Incompatibility with Soybean Plants Carrying the Rj4 Allele
  Omar F.M., Miwa H, Yasuda M, Fujii Y, Kaneko T, Sato S,*Okazaki S
  Appl. Environ. Microbiol.
  Jul. 2015, Research paper (scientific journal), joint, 81, 19, 6710, 6717
• Rhizobium-legume symbiosis in the absence of Nod factors : Two possible scenarios with or without the T3SS.
  Okazaki S, Tittabutr P, Teulet A, Thouin J, Fardoux J, Chaintreuil C, Gully D, Arrighi JF, Furuta N, Miwa H, Yasuda M, Nouwen N, Teaumroong N, *Giraud E.
  The ISME Journal
  10 Jul. 2015, Research paper (scientific journal), joint, DOI(公開)(r-map), 10:64–74
• Cyanamide Phytotoxicity in Soybean (Glycine max) Seedlings involves Aldehyde Dehydrogenase Inhibition and Oxidative Stress
  Maninang J, Okazaki S and *Fujii Y
  Natural Product Communications
  Jun. 2015, Research paper (scientific journal), joint, 10, 5, 743, 746
• Genome analysis of a novel Bradyrhizobium sp. DOA9 carrying a symbiotic plasmid
  *Okazaki S, Noisangiam R, Okubo T, Kaneko T, Oshima K, Hattori M, Teamtisong K, Songwattana P, Tittabutr P, Boonkerd N, Saeki K, Sato S, Uchiumi T, Minamisawa K, *Teaumroong N.
  PLOS ONE
  Feb. 2015, Research paper (scientific journal), joint, 10, 2, e0117392. doi:10.1371/journal.pone.0117392
• Microbiological and soil analysis of the growth-promotion effect of hairy vetch on velvet bean
  *Okazaki S, Yuan K, Iizuka M, Yasuda M, Oikawa Y, Bellingrath-Kimura SD and Fujii Y
  Acta Advanced in Agricultural Sciences
  Jan. 2015, Research paper (scientific journal), joint, 3, 1, 1, 10
• Divergent nod-containing Bradyrhizobium sp. DOA9 with a megaplasmid and its host range
  Teamtisong K, Songwattana P, Noisa-ngiam R, Piromyou P, Boonkerd N, Tittabutr P, Minamisawa K, Nantakit A, Okazaki S, Abe M, Uchiumi T, *Teaumroong N
  Microbes and Environment
  Dec. 2014, Research paper (scientific journal), joint, 29, 4, 370, 376
• Basic study of soybean cyst nematode control by enhanced expression of soybean genes
  Shin Okazaki
  Soy protein research, Japan
  Jun. 2014, Research paper (bulletin of university, research institution), only, 16, 173, 176
• Hijacking of leguminous nodulation signaling by the rhizobial type III secretion system.
  *Okazaki S, Kaneko T, Sato S, Saeki K
  Proc. Natl. Acad. Sci. USA
  Oct. 2013, Research paper (scientific journal), joint, 110, 42, 17131–17136
• Commonalities and differences among symbiosis islands of three Mesorhizobium loti strains.
  Kasai-Maita H, Hirakawa H, Nakamura Y, Kaneko T, Miki K, Maruya J, Okazaki S, Tabata S, *Saeki K, *Sato S
  Microbes and Environments
  May 2013, Research paper (scientific journal), joint, 28, 275, 278
• The type III secretion system of Bradyrhizobium japonicum USDA122 mediates symbiotic incompatibility with Rj2 soybean plants.
  Tsukui T, Eda S, Kaneko T, Sato S, Okazaki S, Kakizaki-Chiba K, Itakura M, Mitsui H, Yamashita A, Terasawa K, *Minamisawa K
  Appl. Environ. Microbiol.
  Jan. 2013, Research paper (scientific journal), joint, 79, 1048, 1051
• Identification and functional analysis of type III effector proteins in Mesorhizobium loti.
  Okazaki S, Okabe S, Higashi M, Shimoda Y, Sato S, Tabata S, Hashiguchi M, Akashi R, Göttfert M, *K. Saeki
  Molecular Plant-Microbe Interactions
  Feb. 2010, Research paper (scientific journal), joint, 23, 2, 223, 342
• Genetic organization and functional analysis of the type III secretion system of Bradyrhizobium elkanii
  Okazaki S, Zehner S, Hempel J, Lang K, *Göttfert M
  FEMS Microbiology Letters
  Apr. 2009, Research paper (scientific journal), joint, 95, 88, 95
• The Mesorhizobium loti purB gene is involved in infection thread formation and nodule development in Lotus japonicus.
  Okazaki S, Hattori Y., Saeki K
  Journal of Bacteriology
  Sep. 2007, Research paper (scientific journal), joint, 189, 22, 8347–8352
• Rhizobitoxine-induced chlorosis occurs in coincidence with methionine deficiency in soybeans
  Okazaki S, Sugawara M, Yuhashi K, Minamisawa K
  Annals of Botany
  May 2007, Research paper (scientific journal), joint, 100, 55, 59
• Rhizobitoxine production in Agrobacterium tumefaciens C58 by Bradyrhizobium elkanii rtxACDEFG genes
  Sugawara M, Haramaki R, Nonaka S, Ezura H, Okazaki S, Eda S, Mitsui H, Minamisawa K
  FEMS Microbiology Letters
  Jan. 2007, Research paper (scientific journal), joint, 269, 29, 35
• Rhizobitoxine modulates plant-microbe interactions by ethylene inhibition.
  Sugawara, M., Okazaki S., Nukui N., H. Ezura, Mitsui H., *Minamisawa K.
  Biotechnology Advances
  Mar. 2006, Research paper (scientific journal), joint, 24, 382, 388
• Rhizobial strategies to enhance symbiotic interactions: Rhizobitoxine and 1-aminocyclopropane- 1-carboxylate deaminase
  Okazaki S., Nukui N., Sugawara M., *Minamisawa K.
  Microbes and Environment
  Jun. 2004, Research paper (scientific journal), joint, 19, 2, 99, 111
• Bradyrhizobium elkanii rtxC gene is required for expression of symbiotic phenotypes in the final step of rhizobitoxine biosynthesis.
  Okazaki, S., Sugawara M., *Minamisawa K.
  Applied and Environmental Microbiology
  Jan. 2004, Research paper (scientific journal), joint, 70, 535, 541
• Quantitative and time-course evaluation of nodulation competitiveness of rhizobitoxine-producing Bradyrhizobium elkanii.
  Okazaki S., Yuhashi K., *Minamisawa K.
  FEMS Microbiology Ecology
  Jun. 2003, Research paper (scientific journal), joint, 45, 155, 160
• DNA sequence and mutational analysis of rhizobiotoxin biosynthesis genes in　Bradyrhizobium elkanii.
  Yasuta T, Okazaki S, Mitsui H, Yuhashi K, Ezura H, *Minamisawa K.
  Applied and Environmental Microbiology.
  Nov. 2001, Research paper (scientific journal), joint, 67, 11, 4999, 5009
• Widespread Bradyrhizobium distribution of diverse Type III effectors that trigger legume nodulation in the absence of Nod factor
  Camuel, Alicia; Teulet, Albin; Carcagno, Melanie; Haq, Fazal; Pacquit, Valerie; Gully, Djamel; Pervent, Marjorie; Chaintreuil, Clemence; Fardoux, Joel; Horta-Araujo, Natasha; Okazaki, Shin; Ratu, Safirah Tasa Nerves; Gueye, Fatou; Zilli, Jerri; Nouwen, Nico; Arrighi, Jean-Francois; Luo, Haiwei; Mergaert, Peter; Deslandes, Laurent; Giraud, Eric
  ISME JOURNAL
  SPRINGERNATURE
  The establishment of the rhizobium-legume symbiosis is generally based on plant perception of Nod factors (NFs) synthesized by the bacteria. However, some Bradyrhizobium strains can nodulate certain legume species, such as Aeschynomene spp. or Glycine max, independently of NFs, and via two different processes that are distinguished by the necessity or not of a type III secretion system (T3SS). ErnA is the first known type III effector (T3E) triggering nodulation in Aeschynomene indica. In this study, a collection of 196 sequenced Bradyrhizobium strains was tested on A. indica. Only strains belonging to the photosynthetic supergroup can develop a NF-T3SS-independent symbiosis, while the ability to use a T3SS-dependent process is found in multiple supergroups. Of these, 14 strains lacking ernA were tested by mutagenesis to identify new T3Es triggering nodulation. We discovered a novel T3E, Sup3, a putative SUMO-protease without similarity to ErnA. Its mutation in Bradyrhizobium strains NAS96.2 and WSM1744 abolishes nodulation and its introduction in an ernA mutant of strain ORS3257 restores nodulation. Moreover, ectopic expression of sup3 in A. indica roots led to the formation of spontaneous nodules. We also report three other new T3Es, Ubi1, Ubi2 and Ubi3, which each contribute to the nodulation capacity of strain LMTR13. These T3Es have no homology to known proteins but share with ErnA three motifs necessary for ErnA activity. Together, our results highlight an unsuspected distribution and diversity of T3Es within the Bradyrhizobium genus that may contribute to their symbiotic efficiency by participating in triggering legume nodulation.
  Sep. 2023, Research paper (scientific journal), joint, 17, 9, 1751-7362, DOI(公開)(r-map), 1416, 1429
• Apoplast-Localized β-Glucosidase Elevates Isoflavone Accumulation in the Soybean Rhizosphere
  Matsuda, Hinako; Yamazaki, Yumi; Moriyoshi, Eiko; Nakayasu, Masaru; Yamazaki, Shinichi; Aoki, Yuichi; Takase, Hisabumi; Okazaki, Shin; Nagano, Atsushi J.; Kaga, Akito; Yazaki, Kazufumi; Sugiyama, Akifumi
  PLANT AND CELL PHYSIOLOGY
  OXFORD UNIV PRESS
  Plant specialized metabolites (PSMs) are often stored as glycosides within cells and released from the roots with some chemical modifications. While isoflavones are known to function as symbiotic signals with rhizobia and to modulate the soybean rhizosphere microbiome, the underlying mechanisms of root-to-soil delivery are poorly understood. In addition to transporter-mediated secretion, the hydrolysis of isoflavone glycosides in the apoplast by an isoflavone conjugate-hydrolyzing beta-glucosidase (ICHG) has been proposed but not yet verified. To clarify the role of ICHG in isoflavone supply to the rhizosphere, we have isolated two independent mutants defective in ICHG activity from a soybean high-density mutant library. In the root apoplastic fraction of ichg mutants, the isoflavone glycoside contents were significantly increased, while isoflavone aglycone contents were decreased, indicating that ICHG hydrolyzes isoflavone glycosides into aglycones in the root apoplast. When grown in a field, the lack of ICHG activity considerably reduced isoflavone aglycone contents in roots and the rhizosphere soil, although the transcriptomes showed no distinct differences between the ichg mutants and wild-types (WTs). Despite the change in isoflavone contents and composition of the root and rhizosphere of the mutants, root and rhizosphere bacterial communities were not distinctive from those of the WTs. Root bacterial communities and nodulation capacities of the ichg mutants did not differ from the WTs under nitrogen-deficient conditions either. Taken together, these results indicate that ICHG elevates the accumulation of isoflavones in the soybean rhizosphere but is not essential for isoflavone-mediated plant-microbe interactions.
  15 May 2023, Research paper (scientific journal), joint, 64, 5, 0032-0781, DOI(公開)(r-map), 486, 500
• Diversity and function of soybean rhizosphere microbiome under nature farming
  Agyekum, Dominic V. A.; Kobayashi, Tatsuyuki; Dastogeer, Khondoker M. G.; Yasuda, Michiko; Sarkodee-Addo, Elsie; Ratu, Safirah T. N.; Xu, Qicong; Miki, Takaaki; Matsuura, Eri; Okazaki, Shin
  FRONTIERS IN MICROBIOLOGY
  FRONTIERS MEDIA SA
  Nature farming is a farming system that entails cultivating crops without using chemical fertilizers and pesticides. The present study investigated the bacterial and fungal communities in the rhizosphere of soybean grown in conventional and nature farming soils using wild-type and non-nodulating mutant soybean. The effect of soil fumigant was also analyzed to reveal its perturbation of microbial communities and subsequent effects on the growth of soybean. Overall, the wild-type soybean exhibited a better growth index compared to mutant soybean and especially in nature farming. Nodulation and arbuscular mycorrhiza (AM) fungi colonization were higher in plants under nature farming than in conventionally managed soil; however, fumigation drastically affected these symbioses with greater impacts on plants in nature farming soil. The rhizosphere microbiome diversity in nature farming was higher than that in conventional farming for both cultivars. However, the diversity was significantly decreased after fumigation treatment with a greater impact on nature farming. Principal coordinate analysis revealed that nature farming and conventional farming soil harbored distinct microbial communities and that soil fumigation significantly altered the communities in nature farming soils but not in conventional farming soils. Intriguingly, some beneficial microbial taxa related to plant growth and health, including Rhizobium, Streptomyces, and Burkholderia, were found as distinct microbes in the nature farming soil but were selectively bleached by fumigant treatment. Network analysis revealed a highly complex microbial network with high taxa connectivity observed under nature farming soil than in conventional soil; however, fumigation strongly broke it. Overall, the results highlighted that nature farming embraced higher microbial diversity and the abundance of beneficial soil microbes with a complex and interconnected network structure, and also demonstrated the underlying resilience of the microbial community to environmental perturbations, which is critical under nature farming where chemical fertilizers and pesticides are not applied.
  01 Mar. 2023, Research paper (scientific journal), joint, 14, DOI(公開)(r-map)
• The Application of Sulfur Influences Microbiome of Soybean Rhizosphere and Nutrient-Mobilizing Bacteria in Andosol
  Damo, Jean Louise Cocson; Shimizu, Takashi; Sugiura, Hinako; Yamamoto, Saki; Agake, Shin-ichiro; Anarna, Julieta; Tanaka, Haruo; Sugihara, Soh; Okazaki, Shin; Yokoyama, Tadashi; Yasuda, Michiko; Ohkama-Ohtsu, Naoko
  MICROORGANISMS
  MDPI
  This study aimed to determine the effect of sulfur (S) application on a root-associated microbial community resulting in a rhizosphere microbiome with better nutrient mobilizing capacity. Soybean plants were cultivated with or without S application, the organic acids secreted from the roots were compared. High-throughput sequencing of 16S rRNA was used to analyze the effect of S on microbial community structure of the soybean rhizosphere. Several plant growth-promoting bacteria (PGPB) isolated from the rhizosphere were identified that can be harnessed for crop productivity. The amount of malic acid secreted from the soybean roots was significantly induced by S application. According to the microbiota analysis, the relative abundance of Polaromonas, identified to have positive association with malic acid, and arylsulfatase-producing Pseudomonas, were increased in S-applied soil. Burkholderia sp. JSA5, obtained from S-applied soil, showed multiple nutrient-mobilizing traits among the isolates. In this study, S application affected the soybean rhizosphere bacterial community structure, suggesting the contribution of changing plant conditions such as in the increase in organic acid secretion. Not only the shift of the microbiota but also isolated strains from S-fertilized soil showed PGPB activity, as well as isolated bacteria that have the potential to be harnessed for crop productivity.
  03 May 2023, Research paper (scientific journal), joint, 11, 5, DOI(公開)(r-map)

Books and Other Publications

• 土のひみつ ―食料・環境・生命―
  土壌肥料学会「土のひみつ」編集グループ 編
  朝倉書店
  Sep. 2015
• The Lotus japonicus Genome. Tabata S and Stougaard J edition.
  Nakagawa T, Okazaki S, Shibuya N
  Springer Berlin Heidelberg
  Sep. 2014, 978-3-662-44269-2
• 放射性Csを子実に蓄積しない水稲系統の探索とその育種への利用　「平成24年度「大学固有の生物資源を用いた放射性元素除去技術、バイオ肥料・植物保護技術開発」概要集（福島農業復興支援バイオ肥料プロ）」ISBN 978-4-9906944-0-1-C3045-\00000E
  岡崎伸、山田哲也、大津直子、横山正
  東京農工大学　農学部文部科学省特別経費プロ　バイオ肥料 出版者記号：9906944
  Mar. 2013
• Biological Nitrogen Fixation: Towards Poverty Alleviation through Sustainable Agriculture. F.D. Dakora et al. (Eds.)
  Okazaki, S., S. Zehner, K. Lang and M. Göttfert
  Springer
  Aug. 2008
• Nitrogen Fixation: Global Perspectives: T.M. Finan et al. (Eds.).
  Okazaki, S., Ezura, H., Yuhashi, K. and K. Minamisawa
  CABI Publishing
  May 2002

Presentations

• Novel symbiotic pathway by rhizobial effector proteins in legume-rhizobium symbiosis
  日本農芸化学会
  16 Mar. 2022, Symposium workshop panel(nominated)
• 和食の主役：大豆と微生物
  土壌微生物学会　市民公開シンポジウム
  19 Jun. 2021, Public discourse, seminar, tutorial, course, lecture and others
• マメ科植物との共生を司る根粒菌のIII型分泌エフェクター
  日本細菌学会総会シンポジウム
  19 Feb. 2020, Symposium workshop panel(public)
• Type III effector of Bradyrhizobium elkanii hijacks soybean nodulation signaling
  21th International Congress on Nitrogen Fixation
  11 Oct. 2019, Oral presentation(general)
• Rhizobium utilizes a pathogenic effector to hijack leguminous nodulation signaling
  5th Asian Conference on Plant-Microbe Symbiosis & Nitrogen Fixation
  16 May 2019, Oral presentation(invited, special)
• Bel2-5, a type III effector of Bradyrhizobium elkanii hijacking soybean nodulation signaling
  5th Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation
  16 May 2019, Poster presentation
• Infection mechanism of Bradyrhizobium elkanii by type III secretion system
  2018 JSME annual meeting & 10th ASME
  12 Jul. 2018, Poster presentation
• A novel T3 effector of Bradyrhizobium elkanii plays a dual function in symbiosis with legumes
  2018 JSME annual meeting & 10th ASME
  12 Jul. 2018, Poster presentation
• Diversity and community composition of native arbuscular mycorrhizal fungi associated with different rice cultivars in Ghana
  2018 JSME annual meeting & 10th ASME
  12 Jul. 2018, Poster presentation
• マメ科植物との共生における根粒菌 III型分泌系の機能解析
  2017年度生命科学系学会合同年次大会
  07 Dec. 2017, Poster presentation
• santopine分解能を有する根粒菌の探索とその代謝遺伝子の同定
  植物微生物研究会第27回研究交流会
  21 Sep. 2017, Poster presentation
• The effect of different concentration of nitrogen source on endophytic colonization of Azospirillum sp. B510 in rice plant
  植物微生物研究会第27回研究交流会
  21 Sep. 2017, Poster presentation
• A novel type III effector of Bradyrhizobium elkanii abolishing infection and nodule development in Vigna radiate
  植物微生物研究会第27回研究交流会
  21 Sep. 2017, Poster presentation
• 施肥管理の異なる低リン酸圃場におけるイネ共生菌根菌の群集構造解析
  植物微生物研究会第27回研究交流会
  21 Sep. 2017, Poster presentation
• Molecular mechanisms underlying Vigna radiata-rhizobia interactions
  20th International Congress on Nitrogen Fixation
  05 Sep. 2017, Poster presentation
• Symbiotic roles of rhizobial type III effectors
  20th International Congress on Nitrogen Fixation
  05 Sep. 2017, Oral presentation(invited, special)
• マメ科植物との共生を司る根粒菌のIII型分泌系
  平成29年度植物感染生理談話会
  29 Jul. 2017, Oral presentation(invited, special)
• Genetic diversity and symbiotic phenotype of hairy vetch Rhizobia in Japan
  4th Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation
  18 Oct. 2016, Poster presentation
• Rhizobial type 3 effector proteins regulate nodulation of Lotus japonicus GIFU
  4th Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation
  18 Oct. 2016, Poster presentation
• Bradyrhizobium elkanii Genes Involved In Symbiotic Incompatibility With Vigna radiata cv. KPS1 And Rj4 Soybean
  4th Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation
  18 Oct. 2016, Poster presentation
• Dual Roles of Rhizobial Type III Secretion System in Soybean Nodulation
  4th Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation
  18 Oct. 2016, Poster presentation
• マメ科植物との共生を司る根粒菌のIII型分泌系
  日本細菌学会関東支部総会ワークショップ
  08 Oct. 2016, Oral presentation(invited, special)
• バイオ肥料微生物Bacillus pumilus TUAT1株のゲノム解析
  日本土壌肥料学会2016年度佐賀大会
  06 Sep. 2016, Oral presentation(general)
• Symbiotic roles of the type III secretion system in Bradyrhizobium elkanii
  12th European Nitrogen Fixation Conference
  27 Aug. 2016, Oral presentation(general)
• Rhizobial type III secretion system and symbiosis with legumes
  17th Congress for the International Society for Molecular Plant-Microbe Interactions
  20 Jul. 2016, Oral presentation(invited, special)
• Molecular genetic analysis of Bradyrhizobium elkanii mutants with altered symbiotic compatibility with Vigna radiata
  Japan-Taiwan-Korea (JTK) International Symposium - JSME 2015
  19 Oct. 2015, Poster presentation
• Bradyrhizobium elkanii の3型分泌系によるミヤコグサ根粒形成の制御
  日本微生物生態学会第30回大会
  19 Oct. 2015, Poster presentation
• Characterization of transposon mutants of Bradyrhizobium elkanii USDA61 that formed effective nodule on Rj4 soybean cv. BARC2
  Japan-Taiwan-Korea (JTK) International Symposium - JSME 2015
  19 Oct. 2015, Poster presentation
• Determination of a suitable condition for Azospirillum sp. B510 infection and colonization in rice plant and observation of the colonization
  Japan-Taiwan-Korea (JTK) International Symposium - JSME 2015
  19 Oct. 2015, Poster presentation
• Genetic diversity and plant growth promotion of methylobacterium spp. isolated from rice in Vietnam
  Japan-Taiwan-Korea (JTK) International Symposium - JSME 2015
  19 Oct. 2015, Poster presentation
• Rj4遺伝子保有ダイズとの非親和性を決定する根粒菌3型エフェクター
  日本微生物生態学会第30回大会
  19 Oct. 2015, Poster presentation
• The Nod factor-independent and T3SS-dependent nodulation in Rhizobium–legume symbiosis
  日本微生物生態学会第30回大会
  19 Oct. 2015, Other
• Rhizobial type III secretion system activates leguminous nodulation signaling in the absence of Nod factor
  19th International Congress on Nitrogen Fixation Conference
  04 Oct. 2015, Oral presentation(invited, special)
• Isolation and characterization of Bradyrhizobium elkanii mutants with altered nodulation compatibility with Vigna radiata
  第25回植物微生物研究交流会
  15 Sep. 2015, Poster presentation
• 根粒菌 3 型分泌系による根粒形成の制御機構
  第25回植物微生物研究交流会
  15 Sep. 2015, Poster presentation
• Cytokinin response during Nod-independent nodulation in soybean
  The 3rd Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation (3APMNF)
  28 Oct. 2014, Poster presentation
• Genetic diversity of rhizobia associated with hairy vetch in Japan
  The 3rd Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation (3APMNF)
  28 Oct. 2014, Poster presentation
• Profiling the novel symbiotic pathway of Bradyrhizobium sp. ORS278 by RNA-Seq analysis
  The 3rd Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation (3APMNF)
  28 Oct. 2014, Poster presentation
• Putative type III effector proteins of Bradyrhizobium elkanii USDA61 cause Incompatibility with Rj4 soybean
  The 3rd Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation (3APMNF)
  28 Oct. 2014, Poster presentation
• Rhizobial type III secretion system controls host-dependent nodulation on soybean
  The 3rd Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation (3APMNF)
  28 Oct. 2014, Other
• Role of the type III secretion system of Bradyrhizobium elkanii in the symbiotic incompatibility with Rj4 soybean
  The 3rd Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation (3APMNF)
  28 Oct. 2014, Poster presentation
• Molecular analysis of nodulation incompatibility between Rj4 soybean and Bradyrhizobium elkanii
  日本土壌肥料学会2014年度大会
  09 Sep. 2014, Poster presentation
• Genetic diversity of rhizobia associated with hairy vetch in Japan
  日本土壌肥料学会2014年度大会
  09 Sep. 2014, Poster presentation
• Hijacking of leguminous nodulation signaling by the rhizobial type III secretion system
  11th European Nitrogen Fixation Conference
  08 Sep. 2014, Oral presentation(invited, special)
• ヘアリーベッチ前作によるハッショウマメの生育促進機構の解析
  日本雑草学会第53回大会
  30 Mar. 2014, Other
• Hijacking of leguminous nodulation signaling by the rhizobial type III secretion system
  18th International Congress on Nitrogen Fixation
  17 Oct. 2013, Other
• The type III section system of Bradyrhizobium elkanii mediates symbiotic incompatibility with Rj4 soybean
  18th International Congress on Nitrogen Fixation
  16 Oct. 2013, Poster presentation
• Isolation and characterization of Tn5 mutants of Bradyrhizobium elkanii with altered compatibility with Rj4-soybean and Vigna radiata
  18th International Congress on Nitrogen Fixation
  16 Oct. 2013, Poster presentation
• III型分泌機構による根粒菌の新規感染機構とその応用
  日本土壌肥料学会2013年度名古屋大会
  13 Sep. 2013, Other
• Molecular analysis of nodulation incompatibility between Rj4 soybean and Bradyrhizobium elkanii USDA61
  日本土壌肥料学会2013年度名古屋大会
  11 Sep. 2013, Poster presentation
• マメ科植物との共生を決定づける根粒菌III型分泌機構
  第86回日本細菌学会総会ワークショップ
  18 Mar. 2013, Oral presentation(general)
• Genome sequence of a novel Bradyrhizobium strain isolated from Aeschynomene americana
  The 2nd Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation
  30 Oct. 2012, Poster presentation
• エダウチクサネムから分離した新規Bradyrhizobium属細菌のゲノム配列
  植物微生物研究会第22回研究交流会プログラム
  26 Sep. 2012, Poster presentation
• Activation of the Host Symbiosis Signaling by Rhizobial Type III Secretion System
  XV International Congress of Molecular Plant-Microbe Interactions
  30 Jul. 2012, Other

External funds

• 奨学寄附金
  donation, From 2020, To 2020
• 奨学寄附金
  donation, From 2019, To 2019
• 奨学寄附金
  donation, From 2019, To 2019
• 奨学寄附金
  donation, From 2019, To 2019
• 奨学寄附金
  donation, From 2018, To 2018
• 奨学寄附金
  donation, From 2018, To 2018
• クサネムとダイズにおける3型分泌系依存的根粒形成機構の比較解析
  cooperative research, From 01 Apr. 2016, To 31 Mar. 2017
• リョクトウ根粒多着変異株の解析とタイにおける接種効果の解析
  cooperative research, From 01 Apr. 2016, To 31 Mar. 2017
• エンドファイトのイネへの定着および生理作用における窒素肥料の影響の解析
  cooperative research, From 01 Apr. 2016, To 31 Mar. 2017
• 奨学寄附金
  donation, From 2012, To 2012

Committee Memberships

• アジア原子力協力フォーラム
  放射線加工部門運営委員
  From 20220401, To 20230331
• Microbes and Environment
  Associate Editor
  From 202204, To 202303
• 植物微生物研究会
  2021年度大会実行委員長
  From 20210401, To 20210910
• 土壌微生物学会
  編集委員会委員
  From 20210401, To 20220331
• アジア原子力協力フォーラム
  放射線加工部門運営委員
  From 20210401, To 20220331
• 土壌微生物学会
  編集委員会委員
  From 20200401, To 20210331
• 植物微生物研究会
  運営委員
  From 20200401, To 20210331
• 植物微生物研究会
  運営委員
  From 20190401, To 20200331
• アジア原子力協力フォーラム
  バイオ肥料部門運営委員
  From 20190401, To 20200331
• 植物微生物研究会
  運営委員
  From 20180401, To 20190331
• アジア原子力協力フォーラム
  バイオ肥料部門運営委員
  From 20180401, To 20190331
• 植物微生物研究会
  運営委員
  From 20170401, To 20180331
• アジア原子力協力フォーラム
  バイオ肥料部門運営委員
  From 20170401, To 20180331

Media Coverage

• 拓く・研究人（７５）東京農工大学大学院農学研究員助教・岡崎伸氏（３９歳）
  日刊工業新聞
  From 27 May 2015, To 27 May 2015
• 根粒菌に新規共生経路
  日刊工業新聞
  From 22 Oct. 2013, To 22 Oct. 2013

Professional Memberships

• Japanese Society of Soil Science and Plant Nutrition
• 　
• Japanese Society of Plant Microbe Interactions
• Society of Genome Microbiology, Japan

Awards

• Poster award（5th Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation）
  Bel2-5, a type III effector of Bradyrhizobium elkanii hijacking soybean nodulation signaling
  17 May 2019
• Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation
  Poster Award（4th Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation）
  Rhizobial type 3 effector proteins regulate nodulation of Lotus japonicus GIFU
  18 Oct. 2016
• Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation
  Poster Award（4th Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation）
  Genetic diversity and symbiotic phenotype of hairy vetch Rhizobia in Japan
  18 Oct. 2016