Background and aim Rice and duckweed are two monocotyledonous plants that naturally coexist in paddy fields. While the presence of duckweed in paddy fields significantly improves rice productivity, the interplay between soil microbes and the two plant hosts in this agroecosystem remains unexplored. Methods We compared the bacterial community structure between duckweed, rice and soil from multiple rice paddies. We also isolated bacteria from these communities and characterized their modes of bacterial colonization and plant growth-promotion using model plants. Results Our data indicate that host-specific and tissue-dependent factors reproducibly orchestrate the bacterial community structure associated with their plant hosts. This is corroborated by results from culture-dependent approaches in which the dominant genus Pantoea isolated from rice aerial tissues can strongly attach and colonize gnotobiotic duckweed in spite of the low representation of this bacterial genus in the natural duckweed microbiome. Our study identified a core of 254 bacterial taxa that are consistently found in all rice and duckweed tissue samples from rice paddy fields. Furthermore, characterizing auxin-producing bacteria isolates from both plant species identified potential plant growth-promoting bacteria that may improve growth for both duckweed and rice in paddy fields. Conclusions Results from this work provide evidence for the importance of the host tissue and species context in determining plant colonization by microbes in the paddy field system. The resources generated in this study could facilitate the agronomic deployment of microbes for more sustainable rice production.

中文翻译：

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传统稻田生态系统中微生物群落结构的宿主特异性和组织依赖性协调

背景与目的水稻和浮萍是两种天然共生于稻田的单子叶植物。虽然稻田中浮萍的存在显着提高了水稻的生产力，但土壤微生物与该农业生态系统中两种植物宿主之间的相互作用仍未得到探索。方法我们比较了来自多个稻田的浮萍、水稻和土壤之间的细菌群落结构。我们还从这些群落中分离出细菌，并使用模型植物表征了它们的细菌定植和植物生长促进模式。结果我们的数据表明宿主特异性和组织依赖性因素可重复地协调与其植物宿主相关的细菌群落结构。这得到了依赖培养方法的结果的证实，其中从水稻地上组织中分离出的优势属 Pantoea 可以强烈附着和定植于无菌浮萍，尽管这种细菌属在天然浮萍微生物组中的代表性较低。我们的研究确定了 254 个细菌分类群的核心，这些分类群始终存在于来自稻田的所有水稻和浮萍组织样本中。此外，对从两种植物中分离的生长素产生细菌进行表征，确定了潜在的植物促生长细菌，这些细菌可能会改善稻田中浮萍和水稻的生长。结论 这项工作的结果为宿主组织和物种背景在确定稻田系统中微生物定植植物的重要性提供了证据。