Trophic interactions play a central role in driving microbial community assembly and function. In gut or soil ecosystems, successful inoculants are always facilitated by efficient colonization; however, the metabolite exchanges between inoculants and resident bacteria are rarely studied, particularly in the rhizosphere. Here, we used bioinformatic, genetic, transcriptomic, and metabonomic analyses to uncover syntrophic cooperation between inoculant (Bacillus velezensis SQR9) and plant-beneficial indigenous Pseudomonas stutzeri in the cucumber rhizosphere. We found that the synergistic interaction of these two species is highly environmental dependent, the emergence of syntrophic cooperation was only evident in a static nutrient-rich niche, such as pellicle biofilm in addition to the rhizosphere. Our results identified branched-chain amino acids (BCAAs) biosynthesis pathways are involved in syntrophic cooperation. Genome-scale metabolic modeling and metabolic profiling also demonstrated metabolic facilitation among the bacterial strains. In addition, biofilm matrix components from Bacillus were essential for the interaction. Importantly, the two-species consortium promoted plant growth and helped plants alleviate salt stress. In summary, we propose a mechanism in which synergic interactions between a biocontrol bacterium and a partner species promote plant health.

营养相互作用在推动微生物群落组装和功能方面发挥着核心作用。在肠道或土壤生态系统中，成功的接种剂总是通过有效的定殖得到促进；然而，很少研究接种剂和常驻细菌之间的代谢物交换，尤其是在根际。在这里，我们使用生物信息学、遗传学、转录组学和代谢组学分析来揭示接种剂 ( Bacillus velezensis SQR9) 和对植物有益的本地假单胞菌施氏杆菌之间的互生合作在黄瓜根际。我们发现这两个物种的协同相互作用高度依赖于环境，互生合作的出现仅在静态的营养丰富的生态位中很明显，例如除了根际之外的薄膜生物膜。我们的结果确定了支链氨基酸 (BCAAs) 生物合成途径参与了互养合作。基因组规模的代谢建模和代谢谱分析也证明了细菌菌株之间的代谢促进作用。此外，来自芽孢杆菌的生物膜基质成分对于互动来说是必不可少的。重要的是，这两个物种的联合促进了植物生长并帮助植物缓解了盐胁迫。总之，我们提出了一种机制，其中生物防治细菌和伙伴物种之间的协同相互作用促进植物健康。