Rice Root Exudate Modulates Functional Traits of Plant-Growth-Promoting Bacteria: A Step Towards Rhizosphere Engineering

Abstract

Rhizosphere engineering offers a promising strategy to improve crop productivity and soil health by optimizing plant-microbe interactions through targeted modulation of rhizosphere functioning. A key step in this approach is effective recruitment and functional activation of inoculated plant growth-promoting rhizobacteria (PGPR), mainly driven by root exudate-mediated signaling. This study investigates the response of five phylogenetically diversified PGPR strains, Azotobacter chroococcum (Ac1), Azospirillum lipoferum (Az204), Pseudomonas chlororaphis (ZSB15), Bacillus altitudinis (FD48), and Pristia endophytica (NE14) to root exudates derived from three different rice cultivars (BPT5204, Co51, and Co55) at active tillering and panicle initiation stages. Functional traits including growth, chemotaxis, biofilm formation, and cell wall-degrading enzyme activity of rhizobacteria were assessed. The results revealed strain- and cultivar-specific modulation of these traits, with NE14 and FD48 showing significant upregulation of assessed traits in response to exudates from BPT5204 and Co51. Gas chromatography-mass spectrometry profiling of root exudates confirmed compositional differences between cultivars and developmental stages, highlighting key metabolites such as hexadecanoic acid, propionic acid, octadecenoic acid methyl ester, and trans-3-hydroxycinnamic acid as potential regulators of PGPR chemotaxis, colonization, and biofilm formation. Principal component and correlation analyses identified cell wall-degrading enzymes and chemotaxis as contributors to strain variability, underscoring their role in establishing rhizosphere competence. These findings strengthen the importance of functional trait-based screening for identifying PGPR strains with high adaptability to the rhizosphere environment. By demonstrating that root exudate-mediated modulation of PGPR traits can enhance bacterial colonization and functionality, this study offers a conceptual foundation and experimental framework for PGPR-mediated rhizosphere engineering.