The soil microbiota interacts with plants closely and exerts strong influences on plant health and productivity. However, the relationship between the microbiota and the bacterial canker of tomato that is caused by Clavibacter michiganensis subsp. michiganensis (Cmm) is still unclear. In order to establish causal relationship between the microbiota and plant phenotypes, the microbial communities of 49 tomato samples (including 15 cultivars) with different canker symptoms collected from the greenhouse in Gansu province, China were investigated via 16S ribosomal RNA sequencing. Roots exhibited a strong filter effect in the process of root colonization by microorganisms according to the α-diversity and the separation patterns of the microbiota in bulk soil, rhizosphere and endosphere. In addition, the gradually decreased cluster extent from bulk soil to endosphere indicating the selective effect of tomato on microbiota. Although the composition of the microbiota is similar, the potential beneficial bacteria and functions (e.g. antibiotics production, pollution degradation, nutrition acquisition) enriched in the rhizosphere and endosphere of healthy samples compared to those in the diseased ones. Furthermore, more robust networks occurred in the rhizosphere and endosphere of healthy samples compared to the diseased ones. Our research provided substantial evidence that although the plant genotype is the dominant factor of phenotype, the rhizosphere and endosphere microbiota, as part of phytobiomes or holobiont, could contribute to the host's phenotype. This causal relationship between microbiota and host phenotypes could guide us in rationally designing novel synthetic communities (SynComs) for tomato canker biocontrol in the near future.

土壤微生物群与植物紧密相互作用，并对植物健康和生产力产生强烈影响。然而，由密歇根氏杆菌引起的番茄微生物群和细菌性溃疡病之间的关系。密歇根州（Cmm）仍不清楚。为了建立微生物群与植物表型之间的因果关系，通过16S核糖体RNA测序技术对甘肃省温室大棚采集的49个番茄样品（包括15个栽培品种）的微生物群落进行了调查。根据散装土壤，根际和内层土壤中微生物群落的α-多样性和分离模式，根在微生物的根定殖过程中表现出强大的过滤作用。此外，从散装土壤到内层土壤的簇集程度逐渐降低，表明番茄对微生物群具有选择性。尽管微生物区系的组成相似，但潜在的有益细菌和功能（例如，抗生素的产生，污染的降解，营养获取）与患病样本相比，富含健康样本的根际和内层。此外，与患病样品相比，健康样品的根际和内层中存在更强大的网络。我们的研究提供了充分的证据，尽管植物基因型是表型的主导因素，但根际和内层微生物区系（作为植物生物群系或全生命周期的一部分）仍可能有助于宿主的表型。微生物群与宿主表型之间的因果关系可以指导我们在不久的将来合理设计新的合成群落（SynComs）以进行番茄溃疡病的生物防治。与患病样品相比，在健康样品的根际和内层中存在更强大的网络。我们的研究提供了充分的证据，尽管植物基因型是表型的主导因素，但根际和内层微生物区系（作为植物生物群系或全生命周期的一部分）却可能有助于宿主的表型。微生物群与宿主表型之间的这种因果关系可以指导我们在不久的将来合理设计新的合成群落（SynComs）以进行番茄溃疡病的生物防治。与患病样品相比，在健康样品的根际和内层中存在更强大的网络。我们的研究提供了充分的证据，尽管植物基因型是表型的主导因素，但根际和内层微生物区系（作为植物生物群系或全生命周期的一部分）仍可能有助于宿主的表型。微生物群与宿主表型之间的因果关系可以指导我们在不久的将来合理设计新的合成群落（SynComs）以进行番茄溃疡病的生物防治。