Background

Utilizating the plant microbiome to enhance pathogen resistance in crop production is an emerging alternative to the use of chemical pesticides. However, the diversity and structure of the microbiota, and the assembly mechanisms of root-associated microbial communities of plants are still poorly understood.

Results

We invstigated the microbiota of the root endosphere and rhizosphere soils of the rice cultivar Nipponbare (NPB) and its Piz-t-transgenic line (NPB-Piz-t) when infected with the filamentous fungus Magnaporthe oryzae (M. oryzae) isolate KJ201, using 16S rRNA and internal transcribed spacer 1 (ITS1) amplicon sequencing. The rhizosphere soils showed higher bacterial and fungal richness and diversity than the endosphere except for fungal richness in the rhizosphere soils of the mock treatment. Bacteria richness and diversity increased in the endospheric communities of NPB and Piz-t under inoculation with KJ201 (referred to as ‘NPB-KJ201’ and ‘Piz-t-KJ201’, respectively) compared with the corresponding mock treatments, with the NPB-KJ201 showing the highest diversity in the four bacterial endocompartments. In contrast, fungal richness and diversity decreased in the endospheric communities of NPB-KJ201 and Piz-t-KJ201, relative to the corresponding mock treatments, with NPB-KJ201 and Piz-t-KJ201 having the lowest richness and diversity, respectively, across the four fungal endocompartments. Principal component analysis (PCA) indicated that the microbiota of Piz-t-KJ201 of root endophytes were mostly remarkablely distinct from that of NPB-KJ201. Co-occurrence network analysis revealed that the phyla Proteobacteria and Ascomycota were the key contributors to the bacterial and fungal communities, respectively. Furthermore, a comparative metabolic analysis showed that the contents of tryptophan metabolism and indole alkaloid biosynthesis were significantly lower in the Piz-t-KJ201 plants.

Conclusions

In this study, we compared the diversity, composition, and assembly of microbial communities associated with the rhizosphere soils and endosphere of Piz-t-KJ201 and NPB-KJ201. On the basis of the different compositions, diversities, and assemblies of the microbial communities among different compartments, we propose that the host genotype and inoculation pattern of M. oryzae played dominant roles in determining the microbial community assemblage. Further metabolomics analysis revealed that some metabolites may influence changes in bacterial communities. This study improves our understanding of the complex interactions between rice and M. oryzae, which could be useful in developing new strategies to improve rice resistance through the manipulation of soil microorganisms.

中文翻译：

---

水稻基因型与稻瘟病菌之间的相互作用调节水稻根部相关微生物群的组装

 背景

利用植物微生物组来增强作物生产中的病原体抗性是使用化学农药的新兴替代方案。然而，人们对微生物群的多样性和结构以及植物根部相关微生物群落的组装机制仍然知之甚少。

 结果

我们研究了水稻品种日本晴 (NPB) 及其 Piz-t 转基因品系 (NPB-Piz-t) 在感染丝状真菌米霉( M. oryzae ) 分离株 KJ201 时根内圈和根际土壤的微生物群，使用 16S rRNA 和内部转录间隔区 1 (ITS1) 扩增子测序。除了模拟处理的根际土壤中的真菌丰富度外，根际土壤表现出比内圈更高的细菌和真菌丰富度和多样性。与相应的模拟处理相比，接种 KJ201（分别称为“NPB-KJ201”和“Piz-t-KJ201”）的 NPB 和 Piz-t 内层群落的细菌丰富度和多样性有所增加。 KJ201 在四个细菌内室中显示出最高的多样性。相反，与相应的模拟处理相比，NPB-KJ201 和 Piz-t-KJ201 的内层群落的真菌丰富度和多样性有所下降，其中 NPB-KJ201 和 Piz-t-KJ201 的丰富度和多样性分别最低。四个真菌内室。主成分分析（PCA）表明，Piz-t-KJ201的根内生菌微生物群与NPB-KJ201的微生物群大多显着不同。共现网络分析表明，变形菌门和子囊菌门分别是细菌和真菌群落的关键贡献者。此外，比较代谢分析表明，Piz-t-KJ201植物的色氨酸代谢和吲哚生物碱生物合成含量显着降低。

 结论

在本研究中，我们比较了与 Piz-t-KJ201 和 NPB-KJ201 的根际土壤和内圈相关的微生物群落的多样性、组成和组装。基于不同区室中微生物群落的组成、多样性和组合不同，我们提出米霉的宿主基因型和接种模式在决定微生物群落组合中起主导作用。进一步的代谢组学分析表明，一些代谢物可能影响细菌群落的变化。这项研究提高了我们对水稻和米霉之间复杂相互作用的理解，这可能有助于制定通过操纵土壤微生物来提高水稻抗性的新策略。