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Background Peanut stem rot is a serious plant disease that causes great economic losses. At present, there are no effective measures to prevent or control the occurrence of this plant disease. Biological control is one of the most promising plant disease control measures. In this study,  Pseudomonas chlororaphis  subsp.  aurantiaca  strain zm-1, a bacterial strain with potential biocontrol properties isolated by our team from the rhizosphere soil of  Anemarrhena asphodeloides , was studied to control this plant disease. Methods We prepared extracts of  Pseudomonas chloroaphis  zm-1 extracellular antibacterial compounds (PECEs), determined their antifungal activities by confrontation assay, and identified their components by UPLC-MS/MS. The gene knockout strains were constructed by homologous recombination, and the biocontrol efficacy of  P. chlororaphis  zm-1 and its mutant strains were evaluated by pot experiments under greenhouse conditions and plot experiments, respectively. Results P. chlororaphis  zm-1 could produce extracellular antifungal substances and inhibit the growth of  Sclerotium rolfsii , the main pathogenic fungus causing peanut stem rot. The components of PECEs identified by UPLC-MS/MS showed that three kinds of phenazine compounds, i.e., 1-hydroxyphenazine, phenazine-1-carboxylic acid (PCA), and the core phenazine, were the principal components. In particular, 1-hydroxyphenazine produced by  P. chlororaphis  zm-1 showed antifungal activities against  S. rolfsii , but 2-hydroxyphenazine did not. This is quite different with the previously reported. The extracellular compounds of two mutant strains, Δ phzH  and Δ phzE , was analysed and showed that Δ phzE  did not produce any phenazine compounds, and Δ phzH  no longer produced 1-hydroxyphenazine but could still produce PCA and phenazine. Furthermore, the antagonistic ability of Δ phzH  declined, and that of Δ phzE  was almost completely abolished. According to the results of pot experiments under greenhouse conditions, the biocontrol efficacy of Δ phzH  dramatically declined to 47.21% compared with that of wild-type  P. chlororaphis  zm-1 (75.63%). Moreover, Δ phzE  almost completely lost its ability to inhibit  S. rolfsii  (its biocontrol efficacy was reduced to 6.19%). The results of the larger plot experiments were also consistent with these results. Conclusions P. chlororaphis  zm-1 has the potential to prevent and control peanut stem rot disease. Phenazines produced and secreted by  P. chlororaphis  zm-1 play a key role in the control of peanut stem rot caused by  S. rolfsii . These findings provide a new idea for the effective prevention and treatment of peanut stem rot.

Characteristics of biological control and mechanisms of Pseudomonas chlororaphis zm-1 against peanut stem rot