Evaluating microbe-plant interactions and varietal differences for enhancing biocontrol efficacy in root rot disease challenged cotton crop

The performance of cyanobacteria and Trichoderma based biocontrol formulations was evaluated in two cotton varieties (Gossypium hirsutum F1861 and Gossypium arboreum CISA 310). Evaluation of mortality after 4 weeks revealed a significant reduction, particularly in G. hirsutum F1861, with values of 13 % (lower by 2 % over the Trichoderma commercial biocontrol agent). The percent mortality after drenching with the compost tea prepared using respective formulations, ranged from 28 to 75 % in G. arboreum CISA 310, with significantly lower values of 6–37.3 % in G. hirsutum. The Anabaena laxa RPAN8 formulation showed the lowest mortality. The activity of hydrolytic enzymes—β-1, 3 glucanase (EGase EC 3.2.1.39), β-1, 4 glucanase (EGase EC, 3.2.1.4) and chitosanase (EC 3.2.1.99) showed a significant enhancement in the inoculated treatments (T1–T6), with Calothrix sp. being among the top ranked treatments in both varieties. Comparison of DNA fingerprints (HIP-TG profiles) of rhizospheric soil DNA with those of corresponding pure cultures revealed a high degree of similarity, confirming the colonization of inoculated organisms. An amplicon of 1000 bp was observed in the soil metagenomic PCR-DNA profiles from both varieties, which confirmed the presence of an endoglucanase gene. Comparative analyses of responses of the two varieties revealed that Gossypium hirsutum F1861 showed higher values of hydrolytic enzymes and available N in soil. On the other hand, microbial inoculation elicited higher levels of chitosanase and defense enzyme activity in Gossypium arboreum CISA 310. This represents a first report illustrating the significance of varietal responses in cotton in relation to the efficacy of microbial biocontrol formulations and their establishment in the rhizosphere.