Pseudomonas chlororaphis ZH2: Evaluation of the Biocontrol Potential of Continuous Cropping Obstacles on the Basis of Genome Analysis, Autotoxic Substance Degradation and In Vitro Antifungal Activity

Abstract

The accumulation of autotoxic substances and fungal pathogens in soil are the two leading causes of continuous cropping obstacles. In this context, the use of beneficial strains for the biological control of continuous cropping obstacles is a promising research direction. In this work, the functions of Pseudomonas chlororaphis ZH2 in antagonizing pathogenic fungi and degrading autotoxic substances during continuous cropping were studied via genome-wide sequence analysis, antifungal activity in vitro, and autotoxic substances degrading tests. The results revealed that the genome of ZH2 contains 7,249,755 base pairs, has a GC content of 62.61%, and is predicted to contain 6551 genes. The phylogenetic results of 16S rRNA, atpD, recA, and carA gene analysis and the average nucleotide identity analysis revealed that ZH2 belongs to P. chlororaphis subsp. aurantiaca. KEGG analysis revealed that some genes of ZH2 were annotated to the biodegradation pathway of benzoate, p-hydroxybenzoic acid, and other autotoxic substances. Nineteen types of secondary metabolite biosynthesis-related gene clusters were predicted to exist in ZH2 via antiSMASH software, and it is predicted that ZH2 can produce a variety of secondary metabolites with antifungal and siderophore functions. The autotoxic substance degradation tests confirmed that ZH2 can degrade benzoate, p-hydroxybenzoic acid, vanillin, and vanillic acid, and the antagonism tests confirmed that ZH2 can inhibit the growth of pathogenic fungi such as Fusarium solani, Rhizopus oryzea, Pestalotiopsis mangiferae, Fusarium oxysporum f.sp. cucumerinum and Botryosphaeria dothidea. These results show that ZH2 degrades autotoxic substances and antagonizes pathogens. Therefore, it is a promising strain that can be used for the biological control of continuous cropping obstacles.