The selective effect of plant secondary metabolites on the beneficial microbiome

Abstract

Plant roots release a diverse array of metabolites into their surrounding soil, creating a chemically complex interface known as the plant rhizosphere. These exuded compounds play an important role in shaping the structure and function of soil microbial communities and in fostering mutually beneficial plant–microbe interactions. By selectively stimulating or recruiting groups or species of microorganisms, plants can influence the composition of their associated microbiota and thereby enhance their ability to adapt to pathogens and other stressors. Root-derived metabolites serve not only as nutrient sources but also as highly specific chemical signals that guide microbial behaviour, colonization patterns, and interspecific communication. Through the production and secretion of these signalling molecules, plants effectively communicate their physiological status and ecological needs to the surrounding microbial community. Certain metabolites promote the attraction and establishment of plant growth–promoting rhizobacteria, mycorrhizal fungi, and other beneficial microorganisms. These interactions can improve nutrient acquisition, modulate hormone signalling pathways, enhance stress tolerance, and strengthen plant immune responses. In doing so, exuded metabolites contribute to the fine-tuning of plant niche adaptation by coordinating direct effects, such as stimulation of microbial growth, and indirect effects, such as the suppression of pathogens through competitive exclusion or induced systemic resistance. The expression levels and composition of these metabolites are highly dynamic and influenced by developmental stage, plant species, soil characteristics, and the presence of biotic stressors such as pathogens or herbivores. Under conditions of biotic stress, food crop plants often alter their exudation profiles to favour the recruitment of protective or antagonistic microbes. These shifts can reshape microbial community dynamics, enhance resilience against disease, and support sustained growth and productivity. This review synthesizes current knowledge on the interactions of secondary metabolites and rhizosphere microbiota by examining, defence regulation, multifaceted modes of action and functional roles of key signalling metabolites involved across literature. It specifically aims to highlight the promising candidates of plant-microbe interactions and the net outcomes for plant growth and development, particularly under biotic stress conditions. Plant secondary metabolites that have the ability to recruit beneficials that elucidate in plant health through various ways, are hypothesized to be the most promising for future crop protection strategies. By examining how these metabolites mediate communication between crops and their microbiota, the review provides insight into strategies for harnessing rhizosphere chemistry to improve agricultural sustainability and crop resilience.