An Indigenous Pseudomonas chlororaphis-like Isolate M6 Is Associated with Reduced Cotton Damping-Off and Partial Redox–Phenylpropanoid Molecular Profiles

Cotton damping-off caused by Rhizoctonia solani restricts seedling establishment, and locally adapted biocontrol isolates are potential components of sustainable disease management. This study evaluated Pseudomonas chlororaphis-like isolate M6 and tested whether molecular profiles in M6-protected plants differed from those in Pathogen-infected plants in directions that moved toward Healthy Control levels. Culturable bacteria from root-associated soils were screened against R. solani by dual-culture assays, and M6 was evaluated in a greenhouse cotton damping-off assay. RNA sequencing (RNA-seq) and untargeted liquid chromatography–mass spectrometry (LC–MS) data from Healthy Control, Pathogen-infected, and M6-protected plants at 0 and 7 d were analyzed using the Pathogen-infected versus Healthy Control and M6-protected versus Pathogen-infected contrasts. M6 produced the highest inhibition among the candidate isolates (81.9%). Under greenhouse conditions, the M6-protected treatment had lower disease incidence (22.2% versus 88.9%) and disease index (16.4 versus 76.8) than the Pathogen-infected treatment. At 7 d, the primary false-discovery-rate-controlled analysis identified 4457 transcripts and 1620 LC–MS features for which the change between M6-protected and Pathogen-infected plants was opposite to the pathogen-associated change and the M6-protected group mean was closer to the Healthy Control mean. Additional nominal-p-value-only results were retained as exploratory. The two contrasts involved redox regulation, phenylpropanoid/benzenoid-related metabolism, hormone/defense signaling, protein synthesis and central metabolism. Antioxidant enzyme and quantitative reverse transcription PCR (qRT-PCR) data provided independent support for selected redox- and defense-associated differences. Because pathogen biomass, bacterial colonization and antagonism-deficient mutants were not assessed, the molecular profiles are interpreted as association-based features of the protected state rather than evidence that host recovery caused disease reduction. Most LC–MS annotations are putative and were not confirmed with authentic standards.