Survival of a potential bacterial biocontrol agent in the soil and its impact on microbial communities

Sclerotinia sclerotiorum is a major crop pathogen commonly managed using fungicides. Efficient biological alternatives are needed but it is essential to determine whether a biocontrol agent persists in soil and affects non-target microbiota. Here, we assessed the environmental fate and the impact of a novel Bacillus sp. strain (SCL1) on soil microbial communities from three contrasted agricultural soils. The fate and effects of SCL1 applied at an agronomical (LD) or elevated (HD) dose were compared with a commercial biocontrol product, tebuconazole, and an untreated control.

SCL1 persistence was monitored by selective plate counts and strain-specific quantitative polymerase chain reaction (qPCR) analysis. After inoculation, SCL1 declined rapidly but remained detectable up to day 168; at late time points the SCL1 population stabilized at low levels [~10³ colony-forming units (CFU) g^-1 in the high-dose treatment], supporting its long-term persistence. Treatment effects on microbial community composition were limited: differentially abundant operational taxonomic units (OTUs) represented up to 9.9% of bacterial and 3.8% of fungal communities. Fungal taxa associated with soil functioning increased under SCL1 treatment in some soils; e.g., Mortierellomycetes in Trugny soil (5.7% in control versus 10.7% under low-dose SCL1 at day 56).

SCL1 persisted for at least 6 months in soil microcosms and induced small shifts in bacterial and fungal communities, comparable with reference products. These findings support further field studies to evaluate the efficacy of SCL1 against S. sclerotiorum in rapeseed crops, as well as its persistence and potential non-target effects on soil microbiota. © 2026 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.