Plant root-associated bacteria can confer protection against pathogen infection. By contrast, the beneficial effects of root endophytic fungi and their synergistic interactions with bacteria remain poorly defined. We demonstrate that the combined action of a fungal root endophyte from a widespread taxon with core bacterial microbiota members provides synergistic protection against an aggressive soil-borne pathogen in Arabidopsis thaliana and barley. We additionally reveal early inter-kingdom growth promotion benefits which are host and microbiota composition dependent. Using RNA-sequencing, we show that these beneficial activities are not associated with extensive host transcriptional reprogramming but rather with the modulation of expression of microbial effectors and carbohydrate-active enzymes.

植物根部相关细菌可以提供针对病原体感染的保护。相比之下，根内生真菌的有益作用及其与细菌的协同相互作用仍不清楚。我们证明，来自广泛分类单元的真菌根内生菌与核心细菌微生物群成员的联合作用为拟南芥和大麦中的侵袭性土传病原体提供了协同保护。我们还揭示了依赖于宿主和微生物群组成的早期王国间生长促进益处。使用 RNA 测序，我们表明这些有益活动与广泛的宿主转录重编程无关，而是与微生物效应子和碳水化合物活性酶的表达调节有关。