Assessing the long-term survival of bakanae pathogen Fusarium fujikuroi in rice-wheat cropping system in Northern - India using advanced metagenomic and qPCR techniques

Abstract

Bakanae disease, caused by Fusarium fujikuroi, is emerging as a major threat to rice crops worldwide, posing a significant challenge to basmati rice farming in India. The difficulty in managing the disease is compounded by the morphological similarities between various pathogenic species and the limited research on its soil-borne nature, especially in the context of Indian farming conditions. This study utilized quantitative PCR (qPCR) and metagenomic approaches to monitor Fusarium fujikuroi population in soil from a rice-wheat cropping system during 2021–22 in North Indian conditions. The qPCR analysis revealed changes in Fusarium fujikuroi abundance, with the highest colonization in August 2021 (1.19 × 10¹⁰) and a notable decline by June 2022 (1.84 × 10⁶). Metagenomic studies based abundance analysis at the phylum level showed the prevalence of ascomycetes in all the samples taken for the study. The key fungal genera observed in bakanae infected field following rice-wheat cropping system included Talaromyces, Mortierella, Trichoderma, Aspergillus, Penicillium, Emericellopsis, Fusarium, Chaetomium, Westerdykella and Amesia. Talaromyces was most abundant in September 2021 (34.40 %) which corresponded with the lowest Fusarium abundance (0.22 %) in soil samples tested. Other beneficial fungi such as Trichoderma, Penicillium and Westerdykella etc. were also detected during the evaluation, supporting their role in managing bakanae disease. The decrease in the Fusarium fujikuroi population over the study period, as revealed by quantitative PCR and metagenomics, indicates that the viability of Fusarium fujikuroi as a soil-borne pathogen is limited. This suggests the importance of maintaining a proper interval of 6–7 months between harvest and the next sowing. Further, the study emphasized the potential use of biocontrol agents to mitigate bakanae disease problem along with the promotion of sustainable and resilient rice farming systems.