Type-specific quantification of particulate methane monooxygenase gene of methane-oxidizing bacteria at the oxic-anoxic interface of a surface paddy soil by digital PCR.

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.

Genotypic Variation of Endophytic Nitrogen-Fixing Activity and Bacterial Flora in Rice Stem Based on Sugar Content.

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.

Mass-producible disposable needle-type ion-selective electrodes for plant research.

Easily mass-producible needle-type Na+ and K+ ion-selective electrodes (ISEs) were developed for the direct and indirect measurement of Na+ and K+ ion concentrations in live plants. A polyimide strip with a silver layer on one side and Ag/AgCl formed at one end was used to construct two types of ISEs. For the type I ISE, an electrolyte layer was formed on the layer of silver and Ag/AgCl, which was then covered with a protecting layer. Subsequently, an ion-selective membrane (ISM) was formed at the truncated end with Ag/AgCl. For the type II ISE, a syringe needle was used as a container and an ISM was formed at the sharp end. Then, the polyimide strip with Ag/AgCl at one end was inserted and an electrolyte solution was injected to complete the ISE. Reference electrodes (REs) with similar structures were fabricated by forming a liquid junction instead of the ISM. The electrode responses and the relationship between the ISE potential and the Na+/K+ ion concentration agreed with those predicted by the Nernst equation. The Na+ and K+ ion concentrations in different parts of the rice plant (Oryza sativa L.) were measured using the Na+ and K+ ISEs, respectively. The results obtained using these devices agreed well with those obtained using inductively coupled plasma atomic emission spectrometry, thus confirming the practical applicability of the developed ISEs.

Draft Genome Sequence of Burkholderia vietnamiensis Strain RS1, a Nitrogen-Fixing Endophyte Isolated from Sweet Potato.

Burkholderia vietnamiensis strain RS1 is an endophytic bacterium with nitrogen-fixing ability that was isolated from tuberous roots of sweet potato. Here, we present its draft genome of 6,542,727 bases that contains a cluster of genes associated with nitrogen fixation. This genome sequence will provide important insights into the plant growth-promoting potential of endophytic bacteria.

Complete Genome Sequence of Kosakonia sacchari Strain BO-1, an Endophytic Diazotroph Isolated from a Sweet Potato.

The complete genome sequence of the endophytic diazotroph Kosakonia sacchari, isolated from a sweet potato, was analyzed. The 4,902,106-bp genome with 53.7% G+C content comprises 4,638 open reading frames, including nif genes, 84 tRNAs, and seven complete rRNAs in a circular chromosome.