Host-associated microbiomes harbour hundreds of bacterial species that co-occur, creating the opportunity for manifold bacteria–bacteria interactions, which in turn contribute to the overall community structure. The mechanisms that underlie this self-organization among bacteria remain largely elusive. Here, we studied bacterial interactions in the phyllosphere microbiota. We screened for microbial interactions in planta by adding 200 endogenous strains individually to a 15-member synthetic community and tracking changes in community composition upon colonization of the model plant Arabidopsis. Ninety percent of the identified interactions in planta were negative, and phylogenetically closely related strains elicited consistent effects on the synthetic community, providing support for trait conservation. Community changes could be largely explained by binary interactions; however, we also identified a higher-order interaction of more than two interacting strains. We further focused on a prominent interaction between two members of the Actinobacteria. In the presence of Aeromicrobium Leaf245, the population of Nocardioides Leaf374 was reduced by almost two orders of magnitude. We identified a potent antimicrobial peptidase in Aeromicrobium Leaf245, which resulted in Nocardioides Leaf374 lysis. A respective Leaf245 mutant strain was necessary and sufficient to restore Nocardioides colonization in planta, demonstrating that direct bacteria–bacteria interactions were responsible for the population shift originally observed. Our study highlights the power of synthetic community screening and uncovers a strong microbial interaction that occurs despite a spatially heterogeneous environment.

宿主相关微生物群包含数百种同时存在的细菌物种，为多种细菌 - 细菌相互作用创造了机会，这反过来又有助于整体群落结构。细菌之间这种自组织的基础机制在很大程度上仍然难以捉摸。在这里，我们研究了叶际微生物群中的细菌相互作用。我们通过将 200 种内源性菌株分别添加到一个由 15 名成员组成的合成群落中，并跟踪模式植物拟南芥定植后群落组成的变化，来筛选植物群落中的微生物相互作用. 植物中 90% 的确定相互作用是负面的，系统发育密切相关的菌株对合成群落产生一致的影响，为性状保护提供支持。社区变化在很大程度上可以用二元相互作用来解释；但是，我们还确定了两个以上相互作用菌株的高阶相互作用。我们进一步关注放线菌的两个成员之间的显着相互作用。在有气微生物 Leaf245 存在的情况下，Nocardioides Leaf374的数量减少了近两个数量级。我们在Aeromicrobium Leaf245 中发现了一种有效的抗菌肽酶，它产生了NocardioidesLeaf374 裂解。相应的 Leaf245 突变菌株对于恢复诺卡氏菌在植物中的定植是必要且充分的，表明直接的细菌-细菌相互作用是最初观察到的种群转移的原因。我们的研究强调了合成群落筛选的力量，并揭示了尽管空间异质环境也会发生强烈的微生物相互作用。