Even in homogeneous conditions, plants facing a soilborne pathogen tend to show a binary outcome with individuals either remaining fully healthy or developing severe to lethal disease symptoms. As the rhizosphere microbiome is a major determinant of plant health, we postulated that such a binary outcome may result from an early divergence in the rhizosphere microbiome assembly that may further cascade into varying disease suppression abilities. We tested this hypothesis by setting up a longitudinal study of tomato plants growing in a natural but homogenized soil infested with the soilborne bacterial pathogen Ralstonia solanacearum. Starting from an originally identical species pool, individual rhizosphere microbiome compositions rapidly diverged into multiple configurations during the plant vegetative growth. This variation in community composition was strongly associated with later disease development during the later fruiting state. Most interestingly, these patterns also significantly predicted disease outcomes 2 weeks before any difference in pathogen density became apparent between the healthy and diseased groups. In this system, a total of 135 bacterial OTUs were associated with persistent healthy plants. Five of these enriched OTUs (Lysinibacillus, Pseudarthrobacter, Bordetella, Bacillus, and Chryseobacterium) were isolated and shown to reduce disease severity by 30.4–100% when co-introduced with the pathogen. Overall, our results demonstrated that an initially homogenized soil can rapidly diverge into rhizosphere microbiomes varying in their ability to promote plant protection. This suggests that early life interventions may have significant effects on later microbiome states, and highlights an exciting opportunity for microbiome diagnostics and plant disease prevention.

即使在同质条件下，面对土传病原体的植物也往往会表现出二元结果，个体要么保持完全健康，要么出现严重甚至致命的疾病症状。由于根际微生物组是植物健康的主要决定因素，我们假设这种二元结果可能是由于根际微生物组组装的早期分歧造成的，该分歧可能进一步级联成不同的疾病抑制能力。我们通过对生长在受土传细菌病原体青枯菌感染的天然但均质土壤中的番茄植物进行纵向研究来检验这一假设。从最初相同的物种库开始，各个根际微生物组的组成在植物营养生长过程中迅速分化为多种配置。群落组成的这种变化与后期结果阶段的疾病发展密切相关。最有趣的是，这些模式还在健康组和患病组之间病原体密度差异变得明显之前两周显着预测了疾病结果。在该系统中，共有 135 个细菌 OTU 与持久健康的植物相关。其中 5 种富集的 OTU（赖氨酸芽孢杆菌、假关节杆菌、博德特氏菌、芽孢杆菌和金黄杆菌）被分离出来，并显示当与病原体共同引入时，可将疾病严重程度降低 30.4-100%。总体而言，我们的结果表明，最初均质化的土壤可以迅速分化为根际微生物组，其促进植物保护的能力各不相同。 这表明早期生命干预可能对以后的微生物组状态产生重大影响，并凸显了微生物组诊断和植物病害预防的令人兴奋的机会。