Flame disinfection is a new technology that uses high temperatures to kill pathogens and control soil-borne diseases. In order to determine the feasibility of applying flame disinfection technology to flue-cured tobacco, a field experiment was conducted in Pianpo Village (test site I) and Lühuai Village (test site II), Luquan County, Yunnan Province. The effects of flame disinfection on soil-borne disease control, flue-cured tobacco growth agronomic traits, the tobacco yield and quality, and the soil microbial community in the flue-cured tobacco field were investigated. The results were as follows. (1) After flame disinfection, the control rates of the four main soil-borne diseases—black root rot, root rot, wilt, and root knot nematodes—were all over 70%. (2) Samples were taken from the experimental site of Pianpo Village at 0 and 114 days after disinfection (tobacco boom period) to study the effects of soil microbial communities by high-throughput sequencing. Compared with the control group, after 0 days of flame disinfection, the abundance of bacterial actinobacteria, Nocardia, Streptomyces, and fungal ascomycetes decreased, while the abundance of bacterial Proteobacteria, Bacteroidetes, Arthrobacter, and mycospora increased. After 114 days of disinfection, the abundance of bacterial actinobacteria, Proteobacteria, chloromyces, and fungal ascomycetes decreased. The abundance of Mortierella was recovered, the abundance of Gibberella and Fusarium increased, and the abundance of Trichospora and Basidiomycetes decreased in both periods. (3) After flame disinfection treatment, the tobacco yield in the two experimental areas was increased by 50.80% and 54.70%, respectively, and the proportion of high-quality tobacco was also increased. In conclusion, flame disinfection before tobacco planting can improve the soil conditions, effectively control soil-borne tobacco diseases, and improve the quality and yield of tobacco leaves.
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