نبذة مختصرة : Summary Roots of healthy plants are inhabited by soil-derived bacteria, fungi, and oomycetes that have evolved independently in distinct kingdoms of life. How these microorganisms interact and to what extent those interactions affect plant health are poorly understood. We examined root-associated microbial communities from three Arabidopsis thaliana populations and detected mostly negative correlations between bacteria and filamentous microbial eukaryotes. We established microbial culture collections for reconstitution experiments using germ-free A. thaliana. In plants inoculated with mono- or multi-kingdom synthetic microbial consortia, we observed a profound impact of the bacterial root microbiota on fungal and oomycetal community structure and diversity. We demonstrate that the bacterial microbiota is essential for plant survival and protection against root-derived filamentous eukaryotes. Deconvolution of 2,862 binary bacterial-fungal interactions ex situ, combined with community perturbation experiments in planta, indicate that biocontrol activity of bacterial root commensals is a redundant trait that maintains microbial interkingdom balance for plant health.
Graphical Abstract
Highlights • Roots of healthy plants are colonized by multi-kingdom microbial consortia • Bacterial Root Commensals (BRCs) shape fungal and oomycetal community structure • BRCs protect plants against fungi and oomycetes • Biocontrol activity of BRCs is a redundant trait and essential for plant survival
An interkingdom analysis of the microbes associated with Arabidopsis roots explains their functional contributions to plant survival.
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