Community Structures and Antifungal Activity of Root-Associated Endophytic Actinobacteria in Healthy and Diseased Cucumber Plants and Streptomyces sp. HAAG3-15 as a Promising Biocontrol Agent

Microorganisms related to plant roots are vital for plant growth and health and considered to be the second genome of the plant. When the plant is attacked by plant pathogens, the diversity and community structure of plant-associated microbes might be changed. The goal of this study is to characterize differences in root-associated endophytic actinobacterial community composition and antifungal activity between Fusarium wilt diseased and healthy cucumber and screen actinobacteria for potential biological control of Fusarium wilt of cucumber. In the present research, three healthy plants (also termed “islands”) and three obviously diseased plants (naturally infected by F. oxysporum f. sp. cucumerinum) nearby the islands collected from the cucumber continuous cropping greenhouse were chosen as samples. Results of culture-independent and culture-dependent analysis demonstrated that actinomycetes in the healthy roots were significantly more abundant than those of diseased roots. Moreover, there were seven strains with antifungal activity against F. oxysporum f. sp. cucumerinum in healthy cucumber roots, but only one strain in diseased cucumber roots. Out of these eight strains, the isolate HAAG3-15 was found to be best as it had the strongest antifungal activity against F. oxysporum f. sp. cucumerinum, and also exhibited broad-spectrum antifungal activity. Thus, strain HAAG3-15 was selected for studying its biocontrol efficacy under greenhouse conditions. The results suggested that the disease incidence and disease severity indices of cucumber Fusarium wilt greatly decreased (p < 0.05) while the height and shoot fresh weight of cucumber significantly increased (p < 0.05) after inoculating strain HAAG3-15. On the basis of morphological characteristics, physiological and biochemical properties and 100% 16S ribosomal RNA (rRNA) gene sequence similarity with Streptomyces sporoclivatus NBRC 100767(T), the isolate was assigned to the genus Streptomyces. Moreover, azalomycin B was isolated and identified as the bioactive compound of strain HAAG3-15 based on analysis of spectra using a bioactivity-guided method. The stronger antifungal activity against F. oxysporum f. sp. cucumerinum, the obvious effect on disease prevention and growth promotion on cucumber seedlings in the greenhouse assay, and the excellent broad-spectrum antifungal activities suggest that strain HAAG3-15 could be developed as a potential biocontrol agent against F. oxysporum f. sp. cucumerinum used in organic agriculture. These results suggested that the healthy root nearby the infected plant is a good source for isolating biocontrol and plant growth-promoting endophytes.