Antagonistic Potential of Endophytic Bacteria against Colletotrichum truncatum Causing Fruit Rot in Chilli

Abstract

Aim: To isolate and evaluate root-associated endophytic bacteria from solanaceous plants for their antagonistic activity against Colletotrichum truncatum (syn. C. capsici), the causal agent of fruit rot in chilli, and to identify potential bacterial biocontrol agents for eco-friendly disease management. Study Design: The research utilized a Complete Randomized Design (CRD) Place and Duration of Study: SRM College of Agricultural Sciences, Baburayanpettai, Chengalpattu District, Tamil Nadu from 2024 to 2025. Methodology: Infected chilli fruits were collected, and the pathogen was isolated on Potato Dextrose Agar (PDA) medium and identified morphologically and through ITS-based molecular methods. Pathogenicity testing on chilli fruits was performed using different methods, with the pinprick method showing the highest disease severity. Root samples from ten solanaceous plants were collected, surface sterilized and plated on Nutrient Agar (NA) to isolate 80 endophytic bacterial strains. These were screened for antagonistic activity against Colletotrichum truncatum using dual culture and paper disc assays. Inhibition zones and mycelial growth reduction were recorded. Potent bacterial isolates were identified through 16S rRNA sequencing. Result: The pathogen was confirmed as Colletotrichum truncatum through ITS-based molecular identification. Among the different inoculation methods, pinprick with mycelial disc (T2) showed the highest disease incidence (80%) and lesion size (20 mm), establishing its reliability for pathogenicity testing. Among the 80 endophytic bacterial isolates screened against C. truncatum, twenty bacteria exhibited notable antagonistic activity in preliminary tests. In dual plate assays, isolate EB38 showed the highest mycelial inhibition (48.88%), followed closely by EB40, EB22, and EB01. Paper disc assays further validated the antifungal potential, with EB22 recording 81.44% inhibition and a 12.33 mm zone of inhibition, followed by EB47 and EB01. The potential bacterial endophytes were molecularly identified through 16S rRNA with amplicon size of 1800 bp.  The results clearly highlighted that identified endophytic bacteria such as Bacillus subtilis (EB22), Brevundimonas diminuta (EB47), and Brevundimonas naejangsanensis (EB01) exhibit significant potential as effective antagonist in combating Chilli fruit rot. Conclusion: The study demonstrated that root-associated endophytic bacteria from solanaceous crops effectively suppressed chilli fruit rot caused by Colletotrichum truncatum. Among the isolates tested, Bacillus subtilis (EB22), Brevundimonas diminuta (EB47), and Brevundimonas naejangsanensis (EB01) showed strong antifungal activity, highlighting their potential as biocontrol agents for sustainable chilli disease management.