Investigating of efficacy of endophytic bacteria isolated from cucumber in biocontrol of Fusarium crown and root rot disease of cucumber

Background and objectives Cucumber crown and root rot, caused by Fusarium oxysporum f. sp. radicis cucumerinum, is one of its major destructive agents in the glasshouse planting in Iran. This disease is also known as the Fusarium damping-off. Several methods, such as chemical control and agronomic methods have been recommended so far to control this disease, but none of them has established effective control over this disease. One of the newly established strategies for the management of this disease is the biological control using endophytic bacteria, which live inside plants and can enhance plant growth by improving nutrient uptake and producing phytohormones. These bacteria can compete and control the population of other bacteria and plant pathogens within plants. This study evaluated the biocontrol capability of some selected cucumber endophytic bacteria over Fusarium crown and root disease. Materials and methods Endophytic bacteria were isolated from roots, stems, leaves, flowers, fruits, and seeds of different healthy cucumber cultivars including, Negin, Danje 98, Danje 195, Nagin and, Native Basmang. Bacterial strains were isolated from plant tissues using different culture media. In-vitro biological control assays, such as cross-culture and agar permeable metabolite assays, were performed to determine the biocontrol efficiency of endophytic bacteria against F. oxysporum f.sp. radicis cucumerinum. The bacterial strains with better results were chosen for glasshouse assay. Two isolates with significant biocontrol efficiency were selected for molecular indentification. The 16srDNA barcoding was performed using universal primers for bacterial identification. Then, the sequencing results were analyzed using MEGA-X software, and phylogenic trees were drawn using the neighbor-joining method. The selected biochemical tests confirmed the molecular results. Results and discussion A total of 140 endophytic bacterial isolates were isolated and purified from roots, stems, leaves, flowers, fruits, and seeds of some common healthy cucumber cultivars. Based on initial cross-culture, 14 isolates out of 140 isolates showed significant antagonism properties in the cross-culture and agar permeable metabolite assays, which were selected for further studies. After evaluation of the effective mechanisms, their antagonistic properties, such as the production capability of antibiotics, volatile compounds, siderophore, auxins, hydrogen cyanide, and protease enzyme, eight isolates were selected as the most potential bacterial isolates for biocontrol activity in the greenhouse. Finally, two bacterial isolates were selected for molecular identification using 16srDNA barcoding. The sequencing results indicated that the two selected isolates with 98% similarity could belong to Lysinibacillus mangiferihumi and Lyisinibaillus fusiformis species. The biochemical results confirmed the molecular results.