Plant colonization by bradyrhizobia is found not only in leguminous plants but also in nonleguminous species such as rice. To understand the evolution of the endophytic symbiosis of bradyrhizobia, the effect of the ecosystems of rice plantations on their associations was investigated. Samples were collected from various rice (Oryza sativa) tissues and crop rotational systems. The rice endophytic bradyrhizobia were isolated on the basis of oligotrophic properties, selective medium, and nodulation on siratro (Macroptilium atropurpureum). Six bradyrhizobial strains were obtained exclusively from rice grown in a crop rotational system. The isolates were separated into photosynthetic bradyrhizobia (PB) and nonphotosynthetic bradyrhizobia (non-PB). Thai bradyrhizobial strains promoted rice growth of Thai rice cultivars better than the Japanese bradyrhizobial strains. This implies that the rice cultivars possess characteristics that govern rice-bacterium associations. To examine whether leguminous plants in a rice plantation system support the persistence of rice endophytic bradyrhizobia, isolates were tested for legume nodulation. All PB strains formed symbioses with Aeschynomene indica and Aeschynomene evenia. On the other hand, non-PB strains were able to nodulate Aeschynomene americana, Vigna radiata, and M. atropurpureum but unable to nodulate either A. indica or A. evenia. Interestingly, the nodABC genes of all of these bradyrhizobial strains seem to exhibit low levels of similarity to those of Bradyrhizobium diazoefficiens USDA110 and Bradyrhizobium sp. strain ORS285. From these results, we discuss the evolution of the plant-bradyrhizobium association, including nonlegumes, in terms of photosynthetic lifestyle and nod-independent interactions. P lant infection and colonization by bradyrhizobia are found in not only leguminous plants but also nonleguminous species such as rice (1, 2). However, the symbiosis mechanisms governing the relationship between Bradyrhizobium bacteria and rice have been absolutely unclear although the evolution of the bradyrhizobium-rice association may have occurred earlier than the bradyrhizobium-legume symbiosis. In addition, rice is the most important food crop in Asia. High-yield rice production requires huge amounts of nitrogen fertilizers. Biological nitrogen fixation (BNF) from rice root-associated bacteria has a great potential to improve sustainable rice production. Rice-legume rotational cropping systems are useful for rice production since legumes can be planted after the rice season, and nitrogen from the legumes can be provided for rice. Bradyrhizobia are well recognized for their ability to fix atmospheric dinitrogen into ammonia in the nodules of legumes, thus providing ammonia to host plants. The bradyrhizobium-legume symbiosis has been reported to increase the legume productivity of agricultural farms (3-5).Bradyrhizobium has been well defined as an oligotrophic bacteria which can survive under nutrient-deprived conditions (6, 7). In addition, a renewed interest in endop...

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The relationships between biogeochemical processes and microbial functions in rice (Oryza sativa) paddies have been the focus of a large number of studies. A mechanistic understanding of methane–nitrogen (CH4–N) cycle interactions is a key unresolved issue in research on rice paddies. This minireview is an opinion paper for highlighting the mechanisms underlying the interactions between biogeochemical processes and plant-associated microbes based on recent metagenomic, metaproteomic, and isotope analyses. A rice symbiotic gene, relevant to rhizobial nodulation and mycorrhization in plants, likely accommodates diazotrophic methanotrophs or the associated bacterial community in root tissues under low-N fertilizer management, which may permit rice plants to acquire N via N2 fixation. The amount of N fixed in rice roots was previously estimated to be approximately 12% of plant N based on measurements of 15N natural abundance in a paddy field experiment. Community analyses also indicate that methanotroph populations in rice roots are susceptible to environmental conditions such as the microclimate of rice paddies. Therefore, CH4 oxidation by methanotrophs is a driving force in shaping bacterial communities in rice roots grown in CH4-rich environments. Based on these findings, we propose a hypothesis with unanswered questions to describe the interplay between rice plants, root microbiomes, and their biogeochemical functions (CH4 oxidation and N2 fixation).

Under paddy field conditions, biological sulfur oxidation occurs in the oxidized surface soil layer and rhizosphere, in which oxygen leaks from the aerenchyma system of rice plants. In the present study, we examined community shifts in sulfur-oxidizing bacteria associated with the oxidized surface soil layer and rice roots under different sulfur fertilization conditions based on the 16S ribosomal RNA (rRNA) gene in order to explore the existence of oligotrophic sulfur-oxidizing bacteria in the paddy rice ecosystem. Rice plants were grown in pots with no fertilization (control) or CaCO3 or CaSO4 fertilization. A principal-coordinates analysis (PCoA) showed that CaSO4 fertilization markedly affected bacterial communities associated with rice roots and soil, whereas no significant differences were observed in plant growth among the fertilizer treatments examined. In rice roots, the relative abundance of Acidobacteria, Alphaproteobacteria, Gammaproteobacteria, and TM7 was significantly higher in CaSO4-fertilized pots than in control pots. Alphaproteobacteria, Bradyrhizobiaceae, and Methylocystaceae members were significantly more abundant in CaSO4-fertilized roots than in control roots. On the other hand, the abundance of Actinobacteria and Proteobacteria was lower in CaSO4-fertilized soil than in control soil. These results indicate that the bacteria associated with rice roots and soil responded to the sulfur amendment, suggesting that more diverse bacteria are involved in sulfur oxidation in the rice paddy ecosystem than previously considered.

The creaming behavior of a turbid oil-in-water emulsion was observed via the processes of multiphoton ionization time-of-flight mass spectrometry (MPI-TOFMS) and ultraviolet–visible spectrophotometry (UV–vis), and the results were compared. The transmittance measurement by UV–vis showed that the turbidity of the toluene emulsion was decreased with time. However, non-negligible errors are common in the measurement of a sample with high turbidity. The online measurement by MPI-TOFMS detected many spikes in the time profile, which revealed the existence of toluene droplets in the emulsion. A smooth time profile suggested that the signal intensity had initially increased, and then decreased with time; the initial concentration of toluene was 3 g/L, which had decreased by half after 60 min. The signal behavior obtained using MPI-TOFMS differed only slightly from that obtained using UV–vis. Since a change in turbidity is not the same as a change in the local concentration of an oil component, MPI-TOFMS is useful for the analysis of a turbid emulsion and offers additional information concerning the creaming phenomenon of an emulsion.