Microbe-derived bioactive metabolites
Microbe-derived compounds that trigger enhanced plant growth and defense are therefore attractive and promising alternatives to agricultural chemicals. In particular, rhizosphere bacteria produce a portfolio of bioactive secondary metabolites (BSMs) and inhibitory allelochemicals that are responsible for Induced Systemic Resistance (IR), biocontrol, and ecological fitness (Fig. 2A). For example, the typical plant-associated species,Bacillus velezensis has considerable biocontrol potential, based on its ability to trigger IR leading to rapid and robust defense responses, as well as direct antagonistic actions on pathogens (Ongena et al., 2007). Over 12% of the genome in bacteria such as B. velezensis is devoted to the synthesis of compounds that contribute to ecological competence and biocontrol activity. They produce a wide range of non-ribosomally synthesized compounds such as oligopeptides, cyclic lipopeptides (CLPs), and polyketides (PKs), in addition to post-translationally-modified lanthipeptides and bacteriocins. These molecules play a key role in multitrophic interactions because they can be antagonistic with other microbes and/or beneficial to the host via the stimulation of innate immune responses leading to IR. BSMs are not only produced in vitro conditions but also in planta by bacterial cells evolving as biofilm-structured microcolonies on root tissues (Andrić et al., 2021; Cawoy et al., 2015; Zihalirwa Kulimushi, Argüelles Arias, Franzil, Steels, & Ongena, 2017).
Plant-associated bacteria have evolved a polymer-sensing system to perceive the host. They increase BSM synthesis in response to the perception of root exudates. For example, the production of the cyclic lipopeptide surfactin by B. velezensis  is stimulated by pectin, which is recognized as a cell surface molecular pattern in root exudates. Surfactin, which is synthesized non-ribosomally by a complex enzyme system, is formed as a mix of naturally coproduced homologs with fatty acid chains of various lengths (Hoff et al., 2021). It optimizes biofilm formation, motility, and early root colonization by the bacterium. It also reinforces the defensive capacity of the host. The IR phenotypes triggered by surfactin and other PBBs are an attractive addition to the crop protection toolbox, as bio-sourced alternatives to chemicals. However, the underlying biochemical and molecular basis for PBB action remains poorly understood.