DataSheet_1_Diversity and assembly of root-associated microbiomes of rubber trees.docx

IntroductionUnderstanding the diversity and assembly of the microbiomes of plant roots is crucial to manipulate them for sustainable ecosystem functioning. However, there are few reports about microbial communities at a continuous fine-scale of roots for rubber trees.
MethodsWe investigate the structure, diversity, and assembly of bacterial and fungal communities for the soil (non-rhizosphere), rhizosphere, and rhizoplane as well as root endosphere of rubber trees using the amplicon sequencing of 16S ribosomal ribonucleic acid (rRNA) and Internally Transcribed Spacer (ITS) genes.
ResultsWe show that 18.69% of bacterial and 20.20% of fungal operational taxonomic units (OTUs) in the rhizoplane derived from the endosphere and 20.64% of bacterial and 20.60% of fungal OTUs from the soil. This suggests that the rhizoplane microbial community was a mixed community of soil and endosphere microbial communities and that microorganisms can disperse bidirectionally across different compartments of the plant root. On the other hand, in the absence of an enrichment or depletion of core bacterial and fungal OTUs in the rhizosphere, little differences in microbial composition as well as a more shared microbial network structure between the soil and the rhizosphere support the theory that the rhizosphere microbial community is a subset of the soil community. A large number of functional genes (such as nitrogen fixation and nitrite reduction) and more enriched core OTUs as well as a less stable but more complex network structure were observed in the rhizoplane of rubber tree roots. This demonstrated that the rhizoplane is the most active root compartment and a hotspot for plant–soil–environment interactions. In addition, bacterial and fungal communities in the rhizoplane were more stochastic compared to the rhizosphere and soil.
DiscussionOur study expands our understanding of root-associated microbial community structure and function, which may provide the scientific basis for sustainable agriculture through biological process management.

引言
解析植物根系微生物组的多样性与组装机制，对于通过调控微生物组以实现生态系统可持续功能至关重要。然而，目前针对橡胶树根系连续精细尺度下的微生物群落的研究报道较为匮乏。

方法
本研究以橡胶树的非根际土壤（non-rhizosphere）、根际（rhizosphere）、根面（rhizoplane）及根内体（root endosphere）为研究对象，通过16S核糖体核糖核酸（16S ribosomal ribonucleic acid, 16S rRNA）与内部转录间隔区（Internally Transcribed Spacer, ITS）基因的扩增子测序技术，解析其细菌与真菌群落的结构、多样性及组装模式。

结果
研究结果显示，橡胶树根面菌群中18.69%的细菌操作分类单元（operational taxonomic units, OTUs）与20.20%的真菌OTUs来源于根内体，另有20.64%的细菌OTUs与20.60%的真菌OTUs来源于非根际土壤。这表明根面微生物群落是土壤与根内体微生物群落的混合群落，且微生物可在植物根系的不同生境间双向扩散。
另一方面，根际并未出现核心细菌与真菌OTUs的显著富集或耗竭，且土壤与根际的微生物群落组成差异微小，二者共享更为相似的微生物网络结构，这支持了“根际微生物群落是土壤微生物群落子集”的理论。
橡胶树根面中存在大量功能基因（如固氮、亚硝酸盐还原相关基因）、更多富集的核心OTUs，且其微生物网络结构虽稳定性更低但更为复杂。这证明根面是根系中最为活跃的生境，也是植物-土壤-环境互作的热点区域。此外，相较于根际与非根际土壤，橡胶树根面的细菌与真菌群落组装过程更具随机性。

讨论
本研究拓展了我们对根系相关微生物群落结构与功能的认知，可为通过生物过程管理实现可持续农业提供科学依据。