Modulation of the rhizosphere microbiome by soil‐borne pathogens: Digging into the pathobiome concept

Abstract Soil‐borne diseases are responsible for huge crop losses worldwide. A deeper understanding of plant–soil–microbe interactions in the presence of soil‐borne pathogens is needed for the integrated management of soil‐borne diseases and tailored use of rhizosphere microbiomes for plant and soil health. In this review, we examine how soil‐borne pathogens influence rhizosphere microbiomes at the compositional and functional levels, and how the study of pathobiomes allows the identification of key microbial taxa that prevent or contribute to disease development. Although soil‐borne pathogens induce contrasting effects on rhizosphere microbial diversity, shifts in rhizosphere microbiome structure and function have been consistently reported in a wide range of pathosystems. These shifts are induced by changes in root exudate patterns upon infection and subsequent defence response activation, and by the recruitment of beneficial microbial taxa by the infected plants. A better understanding of these alterations could help detect functional shifts linked with the plant defence response and identify resistance markers, thus opening new avenues for plant breeding or microbiome manipulation. Moreover, incorporating the pathobiome concept into the design of disease management strategies would assist in pinpointing possible biocontrol agents and identifying biomarkers for early disease detection. We advocate for future pathobiome studies to gain mechanistic insights on the interactions between pathogens and plant microbiomes in non‐model pathosystems and perform validation experiments to unravel how cross‐talk within the pathobiome may lead to disease development or suppression.