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, the compositional and functional shifts in the avocado rhizosphere bacteriome induced by Phytophthora cinnamomi were assessed to identify bacterial taxa enriched in the symptomatic condition and elucidate the microbial functions modulated by the infection. Metabarcoding and metatranscriptomics analyses revealed 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 might be due to the release of nutrients following root rot, as carbohydrate metabolism was stimulated in rhizobacterial communities of infected trees. Moreover, the relative abundance of transcripts from genes associated with stress response and cell signaling increased in some of the most active genera in the rhizosphere of PRR-symptomatic trees, suggesting their potential to mitigate the adverse effects of infection. These findings highlight the need to combine compositional and functional microbiome data to differentiate between taxa attracted by nutrient release and those contributing to the plant defense. The interactions of beneficial bacterial taxa with the pathogen should be further studied, as they may constitute promising biocontrol agents.