Plant specialised metabolites modulate the molecular signatures of host-bacteria and bacteria-bacteria interactions

Plants participate in intricate interactions with a multitude of microorganisms, many of which also influence each other. This holobiont is situated in a chemical soil environment that is defined, in parts, by the specialised metabolite legacy of proximal and preceding organisms, including other plants. Here, we investigated the influence of external plant-derived specialised metabolites on the interactions among root-associated bacterial strains, and between these strains and a plant host. Using benzoxazinoids and their derivatives as a model in both simplified pairwise experiments and more complex multi-organism analyses, we show that these chemicals can modulate bacteria-bacteria, as well as bacteria-plant interactions. While the chemical environment alone had little effect on the plant at the molecular level, it differentially affected plant chemical defences, immunity, and sugar transport when combined with single-isolate or micro-community inoculums. Our study underlines the importance of the chemical environment in modulating organismic interactions and illustrates the value of combining reduced-complexity, bottom-up reconstruction approaches with top-down holobiont profiling. SIGNIFICANCEMany plant species secrete specialized metabolites into the soil, where they can have a long-lasting effect on subsequent plant generations and their associated microbiomes. Understanding the effect of this chemical environment on soil- and plant-associated microbiomes is crucial to determine the impact of soil legacy on host plants, for example in the context of crop rotations. Here, we report that the interactions among root-associated microbes are modulated by specialized metabolites of the benzoxazinoid family, which are prominent metabolites in many grasses. We further show that the chemical environment can inhibit the defence capacity of the plant towards colonizing bacteria, and that more complex bacterial communities are able to mitigate these effects. Our work highlights the importance of deconstructing bacterial communities and the chemical environment to gain insights into the fine-tuned molecular mechanisms that determine the outcome of complex organismic interactions.