@article{sokel_samuel_suzuki_harada_2024, title={Differences in Early Root Endophytic Bacterial Communities between Japanese Sake Rice Cultivars and Table Rice Cultivars}, volume={14}, ISSN={["2073-4395"]}, DOI={10.3390/agronomy14081769}, abstractNote={Sake, which is produced mainly from japonica rice (Oryza sativa subsp. japonica), is one of the most important alcohol products in Japan. In this study, we aimed to investigate a hypothesis that the early root endophytic bacterial communities in Japanese sake rice cultivars would be distinct from those in table rice cultivars, comparing four sake rice cultivars and two table rice cultivars. Rice roots in the vegetative stage were collected 0, 3, and 6 weeks after transplanting, and 16S rRNA gene amplicon sequencing revealed significant differences in bacterial community composition diversity between the sake and table rice cultivars. The root endophytic bacterial communities at the transplanting differed significantly between the rice cultivars, indicating differences in each seed-derived endophytic community. After an overall dominance of Pantoea and Methylobacterium-Methylorubrum at the transplanting, the endophytic community was gradually replaced by soil-derived bacteria that varied by the rice cultivars. Notably, PERMANOVA results showed that the rice endophytic bacterial community composition differed significantly between the sake and table rice cultivars (p < 0.001). These results highlight the distinct root endophytic bacterial composition in the sake rice cultivars compared to those in the table rice cultivars, supporting our hypothesis.}, number={8}, journal={AGRONOMY-BASEL}, author={Sokel, Sibel and Samuel, Solomon Oloruntoba and Suzuki, Kazuki and Harada, Naoki}, year={2024}, month={Aug} }
 @article{bodur_samuel_suzuki_harada_asiloglu_2024, title={Nitrogen-based fertilizers differentially affect protist community composition in paddy field soils}, volume={6}, ISSN={["2662-2297"]}, DOI={10.1007/s42832-023-0221-3}, abstractNote={Protists are one of the most diverse and dominant microbial groups and they play critical roles in the soil ecosystem. Although nitrogen fertilizers have a profound impact on protist communities, still less is known about how different nitrogen fertilizer types affect protist community composition in different soil types. Here we investigated the effects of six inorganic nitrogen fertilizers (urea, ammonium nitrate, ammonium sulfate, potassium nitrate, ammonium chloride, and diammonium hydrogen phosphate) and an organic fertilizer (a mixture of rice husk and cow manure) on protist community composition in three paddy field soils using a high-throughput sequencing method. The effect of the fertilizers on the functional groups of protists, namely consumers (predators and decomposers), photoautotrophs, and parasites (plant pathogens and animal parasites) was also analyzed. The results showed that nitrogen fertilizers had distinctive effects on the beta diversity of the protists, while we also observed that the same fertilizer had slightly different effects depending on the soil type. Amoebozoa and Rhizaria were the most affected protist taxonomical groups, while predatory protists were the main functional groups that were affected by nitrogen fertilizers. Random forest analysis showed that most of the fertilizer-affected protists were predators, among which Cercozoa was the most affected taxa. In conclusion, our results provide important insights into the impact of nitrogen fertilizers on soil protist communities.}, number={3}, journal={SOIL ECOLOGY LETTERS}, author={Bodur, Seda Ozer and Samuel, Solomon Oloruntoba and Suzuki, Kazuki and Harada, Naoki and Asiloglu, Rasit}, year={2024}, month={Sep} }
 @article{asiloglu_bodur_samuel_aycan_murase_harada_2024, title={Trophic modulation of endophytes by rhizosphere protists}, volume={18}, ISSN={["1751-7370"]}, DOI={10.1093/ismejo/wrae235}, abstractNote={The plant-microbe interactions, which is crucial for plant health and productivity, mainly occur in rhizosphere: a narrow zone of soil surrounding roots of living plants. The rhizosphere hosts one of the most intense habitats for microbial prey-predator interactions, especially between predatory protists and bacteria. Here, based on two key facts, microbial predators modulate rhizobacterial community composition, and the rhizobacterial community is the primary source of root microbiome, endophytes; we hypothesized that predation upon rhizobacteria would modulate the community composition of endophytic bacteria. The effects of three taxonomically distinct axenic protist species (Acanthamoeba castellanii, Vermamoeba vermiformis, and Heteromita globosa) were tested in this study. To examine the robustness of the hypotheses, the experiments were conducted in three soil types characterized by distinct bacterial communities and physicochemical properties. The bacterial community compositions were analyzed with high throughput sequencing. Bacterial gene abundances were estimated with a real-time-PCR method. The results showed that protists modulated endophytic communities, which originated in the rhizosphere soil. The modulation of endophytic communities by protists showed chaotic patterns rather than a deterministic effect under different soil types. The observed chaotic dynamics were further confirmed with an additional experiment, in which chaos was triggered by changes in the dilution rates of soil nutrients. Furthermore, the presence of predators enhanced the root colonization of endophytes. Our findings identify a key mechanism for the modulation of root endophytes and enhance understanding of underground plant-microbe interactions, which can lead to open new avenues for modulating the root microbiome to enhance crop production.}, number={1}, journal={ISME JOURNAL}, author={Asiloglu, Rasit and Bodur, Seda Ozer and Samuel, Solomon Oloruntoba and Aycan, Murat and Murase, Jun and Harada, Naoki}, year={2024}, month={Dec} }