Chlorpyrifos (Chlp), one of the major organophosphates is extensively used in agriculture to control pests. With a half-life of 7–120 d, it may persist for up to one year in soil depending on the soil conditions and affect the soil microflora. Chlp degradation by soil microbes proves to be an effective and environment friendly method to remove it from the soil. This study aims to identify and characterize Chlp degrading soil microbes. Total 173 bacteria isolated from different soil samples were screened for Chlp degradation. Characterization of 10 selected samples showed that all the strains produced excessive exo-polysaccharides (EPSs), which positively correlated with the Chlp degradation under in vitro conditions. Among these 10 bacterial strains, the most potent Chlp degrading bacteria was identified to be Alcaligenes faecalis (NBRI OSS2-5) which paired with the Chlp degrading Pseudomonas in the phylogenetic tree. The strain was shown to possess opd gene reported for Chlp degradation. From the study, it was concluded that EPS production may be a common feature of Chlp degrading microbes which may have some role in the Chlp biodegradation process and the pesticide-contaminated fields may not necessarily be the ideal source of isolating pesticide degrading microbes.

The study aimed to determine the pathogenicity of Fusarium species currently prevalent in tomato fields having history of chemical fungicide applications and determine the bio-efficacy of Bacillus subtilis NBRI-W9 as a potent biological control agent. Fusarium fungus was isolated from surface-sterilized infected tomato plants collected from fields. Pathogenicity of 30 Fusarium isolates was determined by in vitro and in vivo assays. Following Koch's postulates, F. chlamydosporum (FOL7) was identified as a virulent pathogen. The biological control of FOL 7 by B. subtilis NBRI-W9 (W9) and colonization potential of W9 was established using spontaneous rifampicin-resistant mutants. W9 showed 82% inhibition of FOL7 on dual-culture plate and colonization levels in tomato plants of ̴ 5.5, ̴ 3.3, and ̴ 2.2 log₁₀ CFU/g in root, stem, and leaf tissue respectively. Antagonistic activity was shown by SEM and cell-wall degradative enzymes. W9 reduced FOL7 infection in net-house and field experiments by 60% and 41%, respectively. Biochemical investigation, defense enzymes, defense gene expression analysis, SEM, and field studies provide evidence of hyper-parasitism and induced resistance as the mode of biological control. The study also demonstrates that potent biocontrol agent W9, isolated from Piper, can colonize tomato plants, control fungal disease by inducing ISR and SAR simultaneously, and increase crop yield by 21.58% under field conditions. This study concludes that F. chlamydosporum (NBRI-FOL7) is a potent, fungicide-resistant pathogen causing wilt in tomatoes. NBRI-W9 controlled FOL7 through mycoparasitism and simultaneously activated ISR and SAR in plants, providing an attractive tool for disease control that acts at multiple levels.

Endophytes are plant inhabitants acting as its extended genome. The present study highlights the importance of maintaining plant endophytes for sustainable disease resistance in plants.