Exploring the communities of bacteria, fungi and ammonia oxidizers in rhizosphere of Fusarium-diseased greenhouse cucumber

Long-term greenhouse vegetable cultivation commonly incurs soil-borne diseases, which seriously threaten the sustainability of greenhouse production system. Rhizomicrobiome plays an important role in ensuring plant health and driving soil nutrient cycling. However, how rhizomicrobiome respond to the occurrence of soil-borne disease is still not completely clear. Increasing knowledge involved would benefit to the prevention of soil-borne disease in intensive greenhouse production by providing the insight into soil microbial ecology. Herein, with the help of a continuously cultivated greenhouse cucumber field, soil physicochemical and biochemical properties and the abundances (quantitative real-time PCR) and communities (high-throughput amplicon sequencing) of bacteria, fungi, ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the rhizosphere of healthy and Fusarium-diseased cucumbers were investigated. Diseased cucumber rhizosphere had significantly higher available nutrient contents and acidity compared to healthy cucumber rhizosphere, but significantly lower microbial activity and nitrification capacity. Although there was no significant difference in the abundances of bacteria, fungi, AOA and AOB, diseased cucumber rhizosphere had more abundant Fusarium oxysporum. For bacteria, only community richness in diseased cucumber rhizosphere was significantly lower than that in healthy cucumber rhizosphere, whereas for fungi both community richness and Shannon diversity were significantly lower. Community structures of bacteria, fungi, AOA and AOB all significantly differed between healthy and diseased cucumber rhizosphere. Particularly, healthy cucumber rhizosphere had more abundant beneficial microbes (Bacillus and Penicillium) and putative biocontrol microbes (Mycothermus) as well as Nitrosospira briensis Clade-related AOB. These results revealed significantly different rhizomicrobiome between Fusarium wilt diseased and healthy cucumbers under long-term intensive greenhouse cultivation, and suggested that rhizomicrobiome may play an important role in the occurrence of Fusarium wilt disease of cucumber. The findings obtained here also provided potential directions towards the prevention of soil-borne diseases and the improvement of N turnover in diseased soil by manipulating rhizosphere microbiome.