Microbial Diversity in Compost is Critical in Suppressing Plant Fungal Pathogen Survival and Enhancing Cucumber Seedling Growth

ABSTRACT Compost is commonly used in agriculture to improve soil quality and enhance plant growth, which is considered to be related to microbial communities in compost. However, effects of microbial communities in compost on infecting microorganisms have remained underexplored. In this study, cucumber seedlings were grown in sterilized potting mix amended with sterilized straw composts inoculated with suspensions (4 dilution levels including 100, 10−3, 10−6, and 10−9) of the same compost that was not sterilized. Cucumber seedlings were challenged by a pathogenic F. oxysporum f. sp. radicis-cucumerinum. The microbial communities were evaluated by using a 16 S rRNA multiplex 454 pyrosequencing approach. In general, in the presence of F. oxysporum sp. radicis-cucumerinum, increasing dilution level increased disease severity index and decreased plant productivity. The logarithmic numbers of F. oxysporum sp. radicis-cucumerinum were significantly negatively correlated with the bacterial phylum and OTU (Operational taxonomic unit) richness in compost. The promotion of F. oxysporum sp. radicis-cucumerinum survival in compost with low microbial diversity, might be related to loss of antagonistic activity (as reflected by the copy numbers of the genes rhlB and hcnBC), which was caused by loss of microbial diversity in compost. In summary, microbial diversity in compost is critical in suppressing plant pathogen survival and then enhancing cucumber seedling growth.