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>Since nitrogenase is intrinsically sensitive to oxygen (O₂), diverse aerobic diazotrophs need strategies to cope with nitrogenase damage by O₂. In the present study, we investigated the mechanisms by which aerobic methane-oxidizing bacteria (methanotrophs) enable the concurrent activities of methane monooxygenase, which uses O₂, and nitrogenase in the cytoplasm of the same cell. By using ¹⁵N labeling, we confirmed the capacity of alphaproteobacterial methanotroph <i>Methylosinus</i> sp. 3S-1 for nitrogen fixation and diazotrophic growth across a wide range of O₂ concentrations <20%. When the initial O₂ concentration was increased from 2 to 20% in a diazotrophic culture, similar decreases were observed in fixed nitrogen and NifH protein levels. In contrast, the mRNA levels of nitrogen fixation genes (<i>nif</i> genes) markedly increased and remained elevated for the duration of slow growth at high O₂ concentrations. This pattern of <i>nif</i> expression in response to O₂ may be attributed to the properties of the <i>nif</i>-specific transcriptional regulator NifA. The present results suggest that the increase in <i>nif</i> transcription is one of the strategies by which this methanotroph maintains nitrogen fixation on the background of aerobic methane oxidation.</p>

DOI： 10.1264/jsme2.me25032

Open Access

Web of Science

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：English   Publishing type：Research paper (scientific journal)   Publisher：Microbiology Society  

A novel methane-oxidizing bacterial strain SS37A-Re^T was isolated from surface soil of a rice paddy field in Japan. Cells were Gram-stain-negative, motile rods with single polar flagellum and type II intracytoplasmic membrane arrangement. The strain grew on methane or methanol as the sole carbon and energy source. It grew at 15–37 °C (optimum 25–30 °C), pH 6.0–9.0 (optimum 7.0–8.0) and with 0–0.1 % (w/w) NaCl (no growth at 0.5 % or above). Cells formed cysts, but not exospores. The results of sequence analysis of the 16S rRNA gene indicated that SS37A-Re^T represented a member of the family Methylocystaceae, with the highest similarity (98.9 %) to Methylocystis parva corrig. OBBP^T. Phylogenetic analysis of pmoA and mxaF genes and core genes in the genome indicated that the strain was closely related to the members of the genus Methylocystis, while the analysis of the mmoX gene indicated the close relationships with the genus Methylosinus. The values of genome relatedness between SS37A-Re^T and species of the genera Methylocystis and Methylosinus were 78.6–82.5% and 21.7–24.9 % estimated by the average nucleotide identity and digital DNA–DNA hybridisation, respectively, showing the highest values with Methylocystis echinoides LMG 27198^T. The DNA G+C content was 63.2 mol% (genome). The major quinone and fatty acids were Q-8 and, C_18 : 1 (C_18 : 1ω8t and C_18 : 1ω8c) and C_18 : 2, respectively. On the basis of the phenotypic and phylogenetic features, the strain represents a novel species of the genus Methylocystis, for which the name Methylocystis iwaonis sp. nov. is proposed. The type strain is SS37A-Re^T (=JCM 34278^T =NBRC 114996^T=KCTC 82710^T).

DOI： 10.1099/ijsem.0.005925

Open Access

Web of Science

Scopus

PubMed

Language：Japanese   Publisher：CROP SCIENCE SOCIETY OF JAPAN  

DOI： 10.14829/jcsproc.254.0_111

CiNii Research

Language：Japanese   Publisher：CROP SCIENCE SOCIETY OF JAPAN  

DOI： 10.14829/jcsproc.254.0_108

Open Access

CiNii Research

Publishing type：Part of collection (book)   Publisher：Springer Nature Singapore  

DOI： 10.1007/978-981-19-4906-7_16

Scopus

Language：English   Publishing type：Research paper (scientific journal)  

Enhancement of the nitrogen-fixing ability of endophytic bacteria in rice is expected to result in improved nitrogen use under low-nitrogen conditions. Endophytic nitrogen-fixing bacteria require a large amount of energy to fix atmospheric nitrogen. However, it is unknown which carbon source and bacteria would affect nitrogen-fixing activity in rice. Therefore, this study examined genotypic variations in the nitrogen-fixing ability of rice plant stem as affected by non-structural carbohydrates and endophytic bacterial flora in field-grown rice. In the field experiments, six varieties and 10 genotypes of rice were grown in 2017 and 2018 to compare the acetylene reduction activity (nitrogen-fixing activity) and non-structural carbohydrates (glucose, sucrose, and starch) concentration in their stems at the heading stage. For the bacterial flora analysis, two genes were amplified using a primer set of 16S rRNA and nitrogenase (NifH) gene-specific primers. Next, acetylene reduction activity was correlated with sugar concentration among genotypes in both years, suggesting that the levels of soluble sugars influenced stem nitrogen-fixing activity. Bacterial flora analysis also suggested the presence of common and genotype-specific bacterial flora in both 16S rRNA and nifH genes. Similarly, bacteria classified as rhizobia, such as Bradyrhizobium sp. (Alphaproteobacteria) and Paraburkholderia sp. (Betaproteobacteria), were highly abundant in all rice genotypes, suggesting that these bacteria make major contributions to the nitrogen fixation process in rice stems. Gammaproteobacteria were more abundant in CG14 as well, which showed the highest acetylene reduction activity and sugar concentration among genotypes and is also proposed to contribute to the higher amount of nitrogen-fixing activity.

DOI： 10.3389/fpls.2021.719259

Open Access

Web of Science

Scopus

PubMed

Language：Japanese   Publisher：CROP SCIENCE SOCIETY OF JAPAN  

DOI： 10.14829/jcsproc.251.0_82

CiNii Research

Presentation type：Oral presentation (general)  

Presentation type：Poster presentation