記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Plant and Cell Physiology  

Plants accommodate diverse microbial communities, termed the microbiome, which can change dynamically during plant adaptation to varying environmental conditions. However, the direction of these changes and the underlying mechanisms driving them, particularly in crops adapting to the field conditions, are not well understood. Here, we investigate the root endosphere microbiome of rice (Oryza sativa ssp. japonica) across four consecutive cultivation seasons in a high-yield, non-fertilized, and pesticide-free paddy field, compared with a neighboring fertilized and pesticide-treated field. Using 16S rRNA amplicon and metagenome sequencing, we analyzed three Japonica cultivars - Nipponbare, Hinohikari, and Kinmaze. Our findings reveal that the root endosphere microbiomes diverge based on fertilization regime and plant developmental stages, while the effects of cultivar variation are less significant. Machine learning model and metagenomic analysis of nitrogenase (nif) genes suggest enhanced nitrogen fixation activity in the non-fertilized field-grown roots, highlighting a potential role of diazotrophic, iron-reducing bacteria Telmatospirillum. These results provide valuable insights into the assembly of the rice root microbiome in nutrient-poor soil, which can aid in managing microbial homeostasis for sustainable agriculture.

DOI： 10.1093/pcp/pcaf045

Web of Science

Scopus

PubMed

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会 / 極限環境生物学会  

Digital PCR is a technique that quantifies target genes based on the absence or presence of the targets in PCR amplicons. The present study examined group-specific probes for the quantification of mcrA genes in six methanogenic archaeal groups and “Candidatus Methanoperedens” by digital PCR with the universal primers ML-f and ML-r. A digital PCR analysis of paddy field soil detected all the targets, with the dominant and minor groups being Methanomicrobiales and Methanobrevibacter spp., respectively (10⁷ and 10⁴ copies [g dry soil]^–1). This method has the potential to reveal the dynamics of specific methanogenic archaeal groups in the environment.

DOI： 10.1264/jsme2.me24097

Open Access

Web of Science

Scopus

PubMed

CiNii Research

記述言語：英語   出版者・発行元：日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会 / 極限環境生物学会  

Flooded rice fields are a major source of atmospheric methane, a strong greenhouse gas second only to carbon dioxide. Rice roots are one of the most important hotspots for methane oxidation in rice fields. However, limited information is available on the physiological and genomic characteristics of methane-oxidizing bacteria (MOB) inhabiting rice roots. In the present study, we isolated MOB from rice roots and characterized the strains phenotypically and genomically. We obtained 100 MOB-enriched cultures from the roots of three rice cultivars (Oryza sativa L. subsp. japonica cv. Nipponbare, O. sativa L. subsp. indica cv. Muha, and Tupa 121-3), in which twelve MOB isolates, two Methylomonas sp., three Methylocystis sp., and seven Methylosinus sp., were successfully purified. They showed different morphological features (types of flagellation) and colony formation potentials within the same group in some cases. A genome sequencing analysis revealed variations in the number of genes or the clusters of methane monooxygenase, methanol dehydrogenase, and nitrogenase. The number of plasmid DNAs also differed among the strains. Four strains belonging to the genus Methylomonas or Methylocystis represented putative novel species based on their phenotypic and genotypic characteristics. The present study largely expanded the eco-collection of MOB cultures inhabiting rice fields and rice roots.

DOI： 10.1264/jsme2.me25012

Open Access

Scopus

PubMed

CiNii Research

担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Environmental Microbiology Reports  

Aerobic methane-oxidizing bacteria (MOB) play an important role in mitigating methane emissions from paddy fields. In this study, we developed a differential quantification method for the copy number of pmoA genes of type Ia, Ib, and IIa MOB in paddy field soil using chip-based digital PCR. Three probes specific to the pmoA of type Ia, Ib, and IIa MOB worked well in digital PCR quantification when genomic DNA of MOB isolates and PCR-amplified DNA fragments of pmoA were examined as templates. When pmoA genes in the surface soil layer of a flooded paddy were quantified by digital PCR, the copy numbers of type Ia, Ib, and IIa MOB were 10⁵–10⁶, 10⁵–10⁶, and 10⁷ copies g⁻¹ dry soil, respectively, with the highest values in the top 0–2-mm soil layer. Especially, the copy numbers of type Ia and Ib MOB increased by 240% and 380% at the top layer after soil flooding, suggesting that the soil circumstances at the oxic–anoxic interfaces were more preferential for growth of type I MOB than type II MOB. Thus, type I MOB likely play an important role in the methane consumption at the surface paddy soil.

DOI： 10.1111/1758-2229.13155

Open Access

Web of Science

Scopus

PubMed

記述言語：日本語   出版者・発行元：日本作物学会  

<p>人工気象室を用いて登熟期間における昼間および夜間の高温がオオムギの硝子率に及ぼす影響を検討した．供試品種は「シュンライ」とし，2016年/2017年，2017年/2018年に昼間高温 （HD区：25℃/9℃），夜間高温 （HN区：20℃/14℃），標準気温 （CT区：20℃/9℃） の3区を設けて開花盛期から温度処理を行った．HD区では硝子率が上昇した．これは1粒重の減少およびタンパク質含有率の上昇が影響したためと考えられた．一方，HN区では1粒重の減少とタンパク質含有率の上昇はみられず，硝子率は同程度だった．この結果を受け，2019/2020年にHD区とCT区で登熟過程における子実中のデンプン・可溶性糖・窒素 （N） ・炭素 （C） 含有量の推移を調査した．HD区では登熟前半にデンプン・N蓄積が加速されるが，登熟期間が短縮するため最終的な個体当たりデンプン合成量が少なくなり，開花～成熟期のC含有量の変化量に対するN含有量の変化量の比（ΔN/ΔC）が高まった．また，HD区では1粒当たりタンパク質含有量が増加した．さらに，胚乳を走査型電子顕微鏡で観察した結果，HD区では大粒デンプンが大型化する一方で，小粒デンプンが小型化する現象がみられた．この結果から，昼間高温による硝子率の上昇は，胚乳のデンプンや細胞質タンパク質の蓄積パターンが変化するとともに，細胞質タンパク質が多く蓄積することが主要因と考えられた．本研究はオオムギの生産現場における硝子率の増加要因の解明の足掛かりとなると考えられる．</p>

DOI： 10.1626/jcs.92.19

CiNii Research

記述言語：日本語   掲載種別：記事・総説・解説・論説等（商業誌、新聞、ウェブメディア）  

CiNii Research

会議種別：口頭発表（一般）  

会議種別：ポスター発表  

会議種別：ポスター発表  

会議種別：口頭発表（一般）