Papers - YAMAMOTO Akihiro
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Nitawaki Yoshikazu, Yasukochi Takaaki, Naono Shinya, Yamamoto Akihiro, Saeki Yuichi
Microbes and Environments 39 ( 4 ) ME24023 2024.12
Language：English Publishing type：Research paper (scientific journal) Publisher：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
We herein investigated the effects of salt (NaCl) stress on soybean nodulation by rhizobial strains. We specifically examined: (1) the effects of NaCl on nodule maturity and positioning by inoculating three rhizobial strains (<i>Bradyrhizobium diazoefficiens</i> USDA110<sup>T</sup>, <i>Bradyrhizobium elkanii</i> USDA31, and <i>Sinorhizobium fredii</i> USDA191) onto soybean variety CNS, (2) the effects of the NaCl treatment on isoflavones (daidzein and genistein) secretion by CNS, (3) the effects of the NaCl treatment on gene expression induced by daidzein and genistein in rhizobia, and (4) the effects of the NaCl treatment on rhizobial growth. The results obtained were as follows: (1) the NaCl treatment delayed nodule development and reduced nodulation on the primary root following the USDA110<sup>T</sup> inoculation, minimal sensitivity regarding nodule formation in the USDA 31 inoculation, and significantly increased the mature nodule number and nodules on the primary root following the USDA 191 inoculation. (2) The NaCl treatment significantly reduced the secretion of daidzein from soybean roots, but did not significantly affect that of genistein. (3) NaCl treatment induced a significant decrease in genistein-induced <i>nodC</i> expression in USDA110<sup>T</sup>, but not in USDA31, and also caused a significant reduction in daidzein-induced <i>nodC</i> expression, but not genistein-induced expression, in USDA191. (4) NaCl treatment reduced survivability under acidic conditions, but increased survivability under saline-alkaline conditions for USDA191 than bradyrhizobia. These results indicate that saline conditions give <i>S. fredii</i> a competitive advantage over <i>Bradyrhizobium</i> during soybean infection.
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Effect of Drought Stress and Short-term Recovery on Proline and Polyamine Metabolism in Lotus japonicus Reviewed International coauthorship
Lee Y., Yamamoto A., Ragaey M., Hashiguchi M., Akashi R., Saeki Y.
Agricultural Research 2024.12
Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Agricultural Research
Environmental issues, particularly drought and soil salinity, severely limit plant productivity. This study aimed to examine the general reaction of legumes, specifically Lotus japonicus, against drought stress and their recovery following rehydration. After a 5-week culturing period, drought stress was simulated by withholding irrigation for 7 days. Stress response and recovery were evaluated through bioassays, and measurements of chlorophyll, proline and polyamine (stress reactants), and hydrogen peroxide and malondialdehyde (oxidative stress indices). Drought stress inhibited overall growth and decreased relative water content, but a recovery to control levels was observed after 8 h of re-watering. Hydrogen peroxide and malondialdehyde levels increased under drought stress, but showed no significant difference from control levels upon recovery. The accumulation of proline and polyamines was also observed, suggesting that they are effective responses to drought stress in plants. Furthermore, gene expression of key enzymes involved in proline and polyamine metabolism was regulated by stress conditions. By a short 8-h recovery period, the expression levels of metabolism-related genes of proline and polyamine returned to the pre-stress level, but the accumulation of functional substances was not induced. This study provides insight into the physiological and biochemical changes that occur in plants under drought stress and highlights the importance of proline and polyamine metabolism in plant adaptation to drought stress.
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Soybean gene expression correlated with symbiotic rhizobial nitrogen fixation activity Reviewed
Yano Shunichi, Takushima Teruya, Ezawa Tatsuhiro, Sugimura Yusaku, Yamamoto Akihiro, Saeki Yuichi
Plant Root 18 35 - 47 2024.12
Language：English Publishing type：Research paper (scientific journal) Publisher：Japanese Society for Root Research
Soybean (<i>Glycine max</i> L.) can establish a symbiotic relationship with rhizobia. However, little is known about the host plant genes that correlate with the nitrogen fixation activity of symbiotic rhizobia. In this study, we investigated soybean genes that correlate with bacterial symbiotic nitrogen fixation in two experiments. In the first experiment, soybean seeds were inoculated with two strains of soybean rhizobia exhibiting different nitrogen fixation activities and were grown in the field until the R1 stage. Subsequently, the roots and nodules were subjected to RNA-seq analysis to identify the expression of soybean genes related to bacterial nitrogen fixation. In the second experiment, to confirm host gene expressions dependent on bacterial nitrogen fixation activity, nod<sup><sup>+</sup></sup>/fix<sup><sup>－</sup></sup> (Δ<i>nif</i> gene) mutants and the wild type were inoculated into soybean, and gene expressions were evaluated by qRT-PCR. <i>GmNRT2.5</i>, a high-affinity nitrate transporter gene, was correlated with nitrogen fixation activity. qPCR analysis of roots and nodules inoculated with a nod<sup><sup>+</sup></sup>/fix<sup><sup>－</sup></sup> mutant revealed that <i>GmNRT2.5</i> on chromosome 8 (Glyma.08G284000: <i>GmNRT2.5</i> Chr8) was particularly correlated with nitrogen fixation activity in the root nodule section. Based on the results, it is suggested that <i>GmNRT2.5</i> Chr8 may function as a regulatory gene bridging nitrogen fixation and nitrate absorption from the soil. Therefore, <i>GmNRT2.5</i> Chr8 might be a useful host gene for estimating symbiotic nitrogen fixation activity.
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Land utilization types impacted the species diversity and population distribution of nodulating and non-nodulating rhizobia in the Philippines Reviewed International coauthorship
Mason M.L.T., De Guzman B.L.T., Mactal A.G., Yamamoto A., Saeki Y.
Rhizosphere 27 100743 2023.9
Language：English Publishing type：Research paper (scientific journal) Publisher：Rhizosphere
The influence of three land utilization types (LUT) on the diversity and population of soybean-nodulating rhizobia indicated how human activities affect the ecology of these microorganisms. This report revealed that based on LUT (LUT1-rice-based; LUT2-soybean-based; LUT3-legume-rice), different species of rhizobia can be more abundant than the other species. Targeting the 16S rRNA gene and the 16S-23S rRNA gene ITS region through Polymerase Chain Reaction - Restriction Fragment Length Polymorphisms (PCR-RFLP), it was found out that a majority of the nodulating rhizobia was classified under the genus Bradyrhizobium and the non-nodulating rhizobia was classified under the genus of Sinorhizobium. The species diversity of nodulating rhizobia on the LUT2 showed the lowest at 0.00 whereas the LUT1 showed the highest diversity at 0.87. Similarly, the lowest species diversity of the non-nodulating rhizobia was found on the LUT2 at 0.00 but the highest was obtained from the LUT3 at 0.69. These results suggest that the nodulating rhizobia in this study may have preference with rice-based cropping pattern than with the two cropping systems. On the other hand, the diversity of rhizobia observed on LUT2 indicated that soybean monocropping may have resulted to a lesser diversity of both nodulating and non-nodulating rhizobia. Thus, it can be stated that the change in land utilization even in an agriculture land-use, species diversification and population dominance of certain rhizobia may occur.
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Development of an effective method of human DNA extraction from soil as forensic evidence Reviewed International coauthorship
Hiroko Hirashima, Rinnosuke Hisazumi, Maria Luisa T. Mason, Akihiro Yamamoto, Yuichi Saeki
Forensic Science International 335 111284 2022.3
Language：English Publishing type：Research paper (scientific journal)
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Hafiz M.H.R., Salehin A., Adachi F., Omichi M., Saeki Y., Yamamoto A., Hayashi S., Itoh K.
Horticulturae 7 ( 2 ) 1 - 12 2021.2
Language：English Publishing type：Research paper (scientific journal) Publisher：Horticulturae
© 2021 by the authors. Licensee MDPI, Basel, Switzerland. A species-specific latitudinal distribution of soybean rhizobia has been reported; Bradyrhi-zobium japonicum and B. elkanii dominate in nodules in northern and southern areas, respectively. The aim of this study was to elucidate whether temperature-dependent proliferation in soil or infection is more reliable for determining the latitudinal characteristic distribution of soybean-nodulating rhizobia under local climate conditions. Three study locations, Fukagawa (temperate continental climate), Matsue and Miyazaki (humid sub-tropical climate), were selected in Japan. Each soil sample was transported to the other study locations, and soybean cv. Orihime (non-Rj) was pot-cultivated using three soils at three study locations for two successive years. Species composition of Bradyrhi-zobium in the nodules was analyzed based on the partial 16S rRNA and 16S–23S rRNA ITS gene sequences. Two Bradyrhizobium japonicum (Bj11 and BjS10J) clusters and one B. elkanii (BeL7) cluster were phylogenetically sub-grouped into two (Bj11-1-2) and four clusters (BjS10J-1-4) based on the ITS sequence. In the Fukagawa soil, Bj11-1 dominated (80–87%) in all study locations. In the Matsue soil, the composition was similar in the Matsue and Miyazaki locations, in which BeL7 dominated (70–73%), while in the Fukagawa location, BeL7 decreased to 53% and Bj11-1 and BjS10J-3 increased. In the Miyazaki soil, BeL7 dominated at 77%, and BeL7 decreased to 13% and 33% in the Fukagawa and Matsue locations, respectively, while BjS10J-2 and BjS10J-4 increased. It was supposed that the B. japonicum strain preferably proliferated in the Fukagawa location, leading to its nodule domi-nancy, while in the Miyazaki location, temperature-dependent infection would lead to the nodule dominancy of B. elkanii, and both factors would be involved in the Matsue location.
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Mason M.L.T., De Guzman B.L.T., Yamamoto A., Saeki Y.
Symbiosis 83 ( 1 ) 55 - 63 2021.1
Language：English Publishing type：Research paper (scientific journal) Publisher：Symbiosis
© 2020, Springer Nature B.V. This report aimed to evaluate the ability of the dominant indigenous strains of bradyrhizobia obtained from different locations in the Philippines in terms of their symbiosis, N-fixation and nodulation with various soybean cultivars harboring different Rj genotypes. This was done to select the most efficient and effective strain that can be used as an inoculant under the Philippines’ local condition. Two soybean cultivars from the Philippines and three cultivars from Japan and Brazil were used and inoculated with 12 indigenous strains and the reference strain Bradyrhizobium diazoefficiens USDA110. Culture pots were grown inside a growth chamber for four weeks with 33 °C for 16 h as daytime and 28 °C for 8 h as night time. All the strains formed nodules on all soybean cultivars, except for B. elkanii BO-4, which only formed nodules on Philippines’ cultivars. Among the indigenous strains, B. elkanii IS-2 is significantly the most efficient and effective N-fixer than the other strains for the Philippines’ cultivars. In contrast, B. diazoefficiens SK-5 was found to be the most efficient and effective N-fixer for cultivars from Japan and Brazil. Additionally, a positive correlation was observed between the symbiotic efficiency and the nitrogenase activity indicating an efficient N-fixation by the indigenous strains. Thus, we were able to identify the most promising indigenous bradyrhizobia that could be used as an inoculant to increase the soybean yield in the Philippines and provided insights on soybean inoculation.
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Effect of salt stress on soybean growth and nodulation under inoculation with soybean rhizobia Reviewed
Nitawaki Y., Kitabayashi H., Mason M.L.T., Yamamoto A., Saeki Y.
Soil Science and Plant Nutrition 2020.12
Language：English Publishing type：Research paper (scientific journal) Publisher：Soil Science and Plant Nutrition
© 2020 Japanese Society of Soil Science and Plant Nutrition. Salinity is one of the major problems when it comes to soil fertility and agricultural productivity. In this regard, this study aimed to elucidate the influence of four salinity levels (0, 20, 50, 100 mM NaCl) on the soybean growth and the nodulation by rhizobia inoculated on the soybean variety CNS. Additionally, the compatibility of soybean varieties with the seven representative strains of rhizobia was also investigated. Through the compatibility test, it was revealed that the Sinorhizobium (Ensifer) fredii USDA 191 and the three bradyrhizobia (Bradyrhizobium japonicum USDA 6T, B. elkanii USDA 31, and B. diazoefficiens USDA 110T) showed compatible nodulation with the Rfg1 genotype soybean, whereas, the S. fredii USDA 192, 193, and 205T showed incompatible nodulation. The inoculation tests with bradyrhizobia (USDA 31, 110T) and sinorhizobia (USDA 191, 192, 193) indicated a better growth of soybean for bradyrhizobia than the sinorhizobia until 50 mM NaCl. Note that even though the symbiotic efficiency at each strain was not different among 0, 20, and 50 mM NaCl treatments, the symbiotic efficiency of bradyrhizobia was higher than the sinorhizobia at each NaCl treatment. The result of the mix inoculation test indicated that the nodule occupancy rate of strain USDA 191 increased significantly along with the NaCl concentration but strain USDA 110T showed an opposite response. These results indicate a positive relationship between the soybean growth and the nitrogen fixation ability of the inoculant under salt-stress conditions. Furthermore, the results obtained from the mix inoculation test partly describe the dominance of sinorhizobia under saline conditions.
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品評会における煎茶の評価と茶葉中無機元素含有量との関係 Reviewed
児﨑章憲，山本昭洋，佐伯雄一
茶業研究報告 ( 129 ) 19 - 26 2020.6
Language：Japanese Publishing type：Research paper (scientific journal)
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品評会における煎茶の評価とアミノ酸，カテキン類，テオガリン，没食子酸およびカフェインとの関係 Reviewed
児﨑章憲，山本昭洋，佐伯雄一
茶業研究報告 ( 129 ) 11 - 18 2020.6
Language：Japanese Publishing type：Research paper (scientific journal)
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Ramesh Raj Puri, Fumihiko Adachi, Masayuki Omichi, Yuichi Saeki, Akihiro Yamamoto, Shohei Hayashi, Md Arshad Ali, Kazuhito Itoh
World Journal of Microbiology and Biotechnology 35 176 2019.10
Language：English Publishing type：Research paper (scientific journal)
The aim of this study was to clarify effects of soil and climatic conditions on community structure of sweet potato bacterial
endophytes by applying locked nucleic acid oligonucleotide-PCR clamping technique and metagenomic analysis. For this
purpose, the soil samples in three locations were transferred each other and sweet potato nursery plants from the same farm
were cultivated for ca. 3 months. After removal of plastid, mitochondria and undefined sequences, the averaged numbers of
retained sequences and operational taxonomic units per sample were 20,891 and 846, respectively. Proteobacteria (85.0%),
Bacteroidetes (6.6%) and Actinobacteria (6.3%) were the three most dominant phyla, accounting for 97.9% of the reads, and
γ-Proteobacteria (66.3%) being the most abundant. Top 10 genera represented 81.2% of the overall reads in which Pseudomonas
(31.9–45.0%) being the most predominant. The overall endophytic bacterial communities were similar among the
samples which indicated that the soil and the climatic conditions did not considerably affect the entire endophytic community.
The original endophytic bacterial community might be kept during the cultivation period. -
Culture-dependent analysis of endophytic bacterial community of sweet potato (Ipomoea batatas) in different soils and climates Reviewed
Ramesh Raj Puri, Fumihiko Adachi, Masayuki Omichi, Yuichi Saeki, Akihiro Yamamoto, Shohei Hayashi, Kazuhito Itoh
Journal of Advances in Microbiology 13 ( 2 ) 1 - 12 2018.11
Language：English Publishing type：Research paper (scientific journal)
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Maria Luisa Tabing Mason, Baby Lyn Cortez Tabing, Akihiro Yamamoto, Yuichi Saeki
Heliyon 4 ( 11 ) 2018.11
Language：English Publishing type：Research paper (scientific journal) Publisher：Heliyon
© 2018 One of the strategies that is commonly used in the Philippines to improve the production of soybean is by inoculation. However, this technique often fails mainly due to the lack of information about the indigenous soybean rhizobia in the Philippines soil. In this study, the diversity of indigenous bradyrhizobia collected from the non-flooded and flooded soil conditions at 11 locations in the country was investigated using a local soybean cultivar as the host plant. The genetic variation among the 424 isolates was detected through Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) treatment and sequence analysis for 16S rRNA gene, 16S-23S rRNA internal transcribed spacer (ITS) region and rpoB housekeeping gene. All the isolates were classified under the Bradyrhizobium species namely B. elkanii, B. diazoefficiens, B. japonicum, B. yuanmingense and a considerable proportion of the isolates were clustered under Bradyrhizobium sp. The isolates which were classified under Bradyrhizobium sp. were thought to be endemic to Philippines soil as evidenced by their nucleotide divergence against the known rhizobia and the historical absence of rhizobia inoculation in the collection sites. The major influence on the distribution and diversity of soybean bradyrhizobia is attributed to the difference in the flooding period, followed by soil properties such as pH, soil type, and nutrient content. As determined, it is proposed that the major micro-symbiont of soybean in the Philippines are B. elkanii for non-flooded soils, then B. diazoefficiens and B. japonicum for flooded soils.
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Mason M., Matsuura S., Domingo A., Yamamoto A., Shiro S., Sameshima-Saito R., Saeki Y.
Plant and Soil 417 ( 1-2 ) 349 - 362 2017.8
Language：English Publishing type：Research paper (scientific journal) Publisher：Plant and Soil
© 2017, Springer International Publishing Switzerland. Aims: Understanding the factors that influence the diversity of soybean-nodulating rhizobia is important before doing inoculation. Since studies about this topic in tropical regions are limited, this could lay the groundwork for related research particularly on Bradyrhizobium elkanii. Methods: To determine the genetic diversity of B. elkanii in different regions, we conducted Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) and sequence analysis of 16S rRNA gene, internal transcribed spacer (ITS) region and rpoB gene. Also, sequence analysis of symbiotic nifD and nodD1 genes was conducted. Results: Analysis of the rpoB gene revealed a higher genetic diversity than the ITS region, and possible endemic B. elkanii strains were observed. Meanwhile, no variation was detected among the strains in both nifD and nodD1 phylogenies. Through rpoB gene analysis, variations in the ITS-rpoB type of B. elkanii strains were distinguished and differentiated with that of the closest reference strains. We identified potential soybean inoculants which possess symbiotic efficiency regardless of the Rj genotypes used, suggesting broad host-range of the strains. Conclusions: We show how the genetic diversity of soybean-nodulating B. elkanii strains in subtropical and tropical regions might be influenced by temperature and soil pH and, provided some insights between the symbiotic genes and Rj genotypes.
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Effect of flooding and the nosZ gene in bradyrhizobia on bradyrhizobial community structure in the soil Reviewed
Yuichi Saeki, Misato Nakamura, Maria Luisa T. Mason, Tsubasa Yano, Sokichi Shiro, Reiko Sameshima-Saito, Manabu Itakura, Kiwamu Minamisawa, Akihiro Yamamoto
Microbes and Environments 32 154 - 163 2017.6
Language：English Publishing type：Research paper (scientific journal)
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Inhibition of putrescine biosynthesis enhanced salt stress sensitivity and decreased spermidine concentration in rice seedlings. Reviewed
Akihiro Yamamoto, Ie-Sung Shim, Shinsuke Fujihara
Biologia Plantarum 61 ( 2 ) 385 - 388 2017.6
Language：English Publishing type：Research paper (scientific journal)
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Identification and Characterization of the Human Cytosolic Sulfotransferases Mediating the Sulfation of Clioquinol and Iodoquinol Reviewed
Akihiro Yamamoto, Maame Debrah-Pinamang, Nicholas J. DiModica, Katsuhisa Kurogi, Ali A. Naqvi, Ying Hui, Yoichi Sakakibara, Masahito Suiko, Ming-Cheh Liu
Drug Metabolism Letters 10 ( 3 ) 200 - 205 2016.9
Language：English Publishing type：Research paper (scientific journal)
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Human Cytosolic Sulfotransferase SULT1A3 Mediates the Sulfation of Dextrorphan Reviewed
Akihiro Yamamoto, Katsuhisa Kurogi, Isaac Thomas Schiefer, Ming-Yih Liu, Yoichi Sakakibara, Masahito Suiko, Ming-Cheh Liu
Biological and Pharmaceutical Bulletin 39 ( 9 ) 1432 - 1436 2016.9
Language：English Publishing type：Research paper (scientific journal)
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The relationship between salt gland density and sodium accumulation/secretion in a wide selection from three Zoysia species Reviewed
Akihiro Yamamoto, Masatsugu Hashiguchi, Ryo Akune, Takahito Masumoto, Melody Muguerza, Yuichi Saeki, Ryo Akashi
Australian Journal of Botany 64 ( 4 ) 277 - 284 2016.6
Language：English Publishing type：Research paper (scientific journal)
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Temperature-dependent expression of nodC and community structure of soybean-nodulating bradyrhizobia Reviewed
Sokichi Shiro, Chika Kuranaga, Akihiro Yamamoto, Reiko Sameshima-Saito, Yuichi Saeki
Microbes and Environments 31 ( 1 ) 27 - 32 2016.3
Language：English Publishing type：Research paper (scientific journal)