Zhu Fangming, Kamiya Takehiro, Fujiwara Toru, Hashimoto Masayoshi, Gong Siyu, Wu Jindong, Nakanishi Hiromi, Fujimoto Masaru
Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan.
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan.
Microorganisms. 2024 Dec 29;13(1):41. doi: 10.3390/microorganisms13010041.
The assembly of plant root microbiomes is a dynamic process. Understanding the roles of root-associated microbiomes in rice development requires dissecting their assembly throughout the rice life cycle under diverse environments and exploring correlations with soil properties and rice physiology. In this study, we performed amplicon sequencing targeting fungal ITS and the bacterial 16S rRNA gene to characterize and compare bacterial and fungal community dynamics of the rice root endosphere and soil in organic and conventional paddy fields. Our analysis revealed that root microbial diversity and composition was significantly influenced by agricultural practices and rice developmental stages ( < 0.05). The root microbiome in the organic paddy field showed greater temporal variability, with typical methane-oxidizing bacteria accumulating during the tillering stage and the amount of symbiotic nitrogen-fixing bacteria increasing dramatically at the early ripening stage. Redundancy analysis identified ammonium nitrogen, iron, and soil organic matter as key drivers of microbial composition. Furthermore, correlation analysis between developmental stage-enriched bacterial biomarkers in rice roots and leaf mineral nutrients showed that highly mobile macronutrient concentrations positively correlated with early-stage biomarkers and negatively correlated with later-stage biomarkers in both paddy fields. Notably, later-stage biomarkers in the conventional paddy field tended to show stronger correlations with low-mobility nutrients. These findings suggest potential strategies for optimizing microbiome management to enhance productivity and sustainability.
植物根系微生物群落的组装是一个动态过程。了解根系相关微生物群落在水稻生长发育中的作用，需要剖析其在不同环境下水稻整个生命周期中的组装情况，并探索与土壤性质和水稻生理学的相关性。在本研究中，我们针对真菌ITS和细菌16S rRNA基因进行扩增子测序，以表征和比较有机稻田和常规稻田中水稻根内生菌和土壤的细菌和真菌群落动态。我们的分析表明，农业实践和水稻发育阶段对根系微生物多样性和组成有显著影响（<0.05）。有机稻田中的根系微生物群落表现出更大的时间变异性，典型的甲烷氧化细菌在分蘖期积累，共生固氮细菌的数量在早熟期急剧增加。冗余分析确定铵态氮、铁和土壤有机质是微生物组成的关键驱动因素。此外，水稻根系中发育阶段富集的细菌生物标志物与叶片矿质营养之间的相关性分析表明，在两个稻田中，高移动性大量元素浓度与早期生物标志物呈正相关，与晚期生物标志物呈负相关。值得注意的是，常规稻田中的晚期生物标志物往往与低移动性养分表现出更强的相关性。这些发现为优化微生物群落管理以提高生产力和可持续性提供了潜在策略。
