Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

Abstract

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

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  

<p>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 <i>mcrA</i> genes in six methanogenic archaeal groups and “<i>Candidatus</i> 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 <i>Methanomicrobiales</i> and <i>Methanobrevibacter</i> 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.</p>

DOI： 10.1264/jsme2.me24097

Open Access

Web of Science

Scopus

PubMed

CiNii Research

Language：English   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  

<p>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 (<i>Oryza sativa</i> L. subsp. <i>japonica</i> cv. Nipponbare, <i>O. sativa</i> L. subsp. <i>indica</i> cv. Muha, and Tupa 121-3), in which twelve MOB isolates, two <i>Methylomonas</i> sp., three <i>Methylocystis</i> sp., and seven <i>Methylosinus</i> 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 <i>Methylomonas</i> or <i>Methylocystis</i> 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.</p>

DOI： 10.1264/jsme2.me25012

Open Access

Scopus

PubMed

CiNii Research

Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

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

Language：Japanese   Publisher：CROP SCIENCE SOCIETY OF JAPAN  

<p>For barley pearling in Japan, glassy grain rate is an important quality factor. However, the relationship between glassy grain rate and temperature has not been clarified. We investigated the effects of moderately high daytime and nighttime temperatures during the ripening period on the glassy grain rate of barley using phytotrons. The barley variety ‘Shunrai’ was tested under three conditions: high daytime temperature (HD: 25°C / 9°C), high nighttime temperature (HN: 20°C / 14°C), and control (CT: 20°C / 9°C) in 2016/2017 and 2017/2018. The HD group showed an increase in the glassy grain rate. This was possibly due to the decrease in grain weight and increase in grain protein content. The HN group did not show any decrease in grain weight or increase in grain protein content, and the glassy grain rate was similar to that in the CT group. Based on these results, we investigated the trends of starch, soluble sugars, N, and C content in the seed during the ripening process in the HD and CT groups in 2019/2020. Accumulation of starch and N was accelerated during the first half of ripening in the HD group, but the final starch synthesis per individual plant was reduced because the ripening period was shortened. The ratio of change in N content to C content (ΔN/ΔC) from flowering to physiological maturity increased. Protein content per grain increased in the HD group. Furthermore, electron microscopic observation of the endosperm in the HD group revealed that large starch granules became larger while small starch granules became smaller. These results suggest that the increase in glassy grain rate due to high daytime temperatures is mainly due to changes in the accumulation pattern of starch and cytoplasmic proteins in the endosperm and the accumulation of more cytoplasmic proteins. This study may serve as a stepping stone to understanding the factors that increase the glassy grain rate in barley production sites.</p>

DOI： 10.1626/jcs.92.19

CiNii Research

Language：Japanese   Publishing type：Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)  

CiNii Research

Presentation type：Oral presentation (general)  

Presentation type：Poster presentation  

Presentation type：Poster presentation  

Presentation type：Oral presentation (general)