Phytophthora root rot induces compositional and functional changes in avocado rhizosphere bacterial communities

Abstract

Understanding how plant pathogens modulate the rhizosphere microbiota is essential to integrated disease management. Here, we assessed the compositional and functional shifts in the avocado rhizosphere bacteriome induced by Phytophthora cinnamomi to elucidate the microbial functions modulated by the infection and identify taxa potentially recruited by the plant as a defense response. Through metabarcoding with metatranscriptomics, we showed that Phytophthora root rot (PRR) induced compositional shifts in bacterial communities, leading to the enrichment of members of MND1, RB41 and Nitrospira. Functional analysis showed that this enrichment may be due to the release of nutrients following root rot, as carbohydrate metabolism was stimulated in rhizobacterial communities of infected trees. We detected evidence of a cry-for-help strategy by the infected plant, as the most active genera in the rhizosphere of PRR-symptomatic trees up-regulated genes associated with stress response and cell signaling, suggesting that they were recruited to mitigate the adverse effects of infection. Our findings highlight the need to combine compositional and functional microbiome data to differentiate between taxa attracted by nutrient release and those actively recruited by the plant. The interactions of the latter with the pathogen should be further studied, as they may constitute promising biocontrol agents.