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Article|01 Oct 2020|OPEN
Enrichment of beneficial cucumber rhizosphere microbes mediated by organic acid secretion
Tao Wen1, Jun Yuan1,, Xiaoming He2, Yue Lin2, Qiwei Huang1 & Qirong Shen1
1Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, 210095 Nanjing, China
2Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong, China

Horticulture Research 7,
Article number: 20154 (2020)
doi: 10.1038/hortres.2020.154
Views: 82

Received: 02 Mar 2020
Revised: 05 Jul 2020
Accepted: 10 Jul 2020
Published online: 01 Oct 2020


Resistant cultivars have played important roles in controlling Fusarium wilt disease, but the roles of rhizosphere interactions among different levels of resistant cultivars are still unknown. Here, two phenotypes of cucumber, one resistant and one with increased susceptibility to Fusarium oxysporum f.sp. cucumerinum (Foc), were grown in the soil and hydroponically, and then 16S rRNA gene sequencing and nontargeted metabolomics techniques were used to investigate rhizosphere microflora and root exudate profiles. Relatively high microbial community evenness for the Foc-susceptible cultivar was detected, and the relative abundances of Comamonadaceae and Xanthomonadaceae were higher for the Foc-susceptible cultivar than for the other cultivar. FishTaco analysis revealed that specific functional traits, such as protein synthesis and secretion, bacterial chemotaxis, and small organic acid metabolism pathways, were significantly upregulated in the rhizobacterial community of the Foc-susceptible cultivar. A machine-learning approach in conjunction with FishTaco plus metabolic pathway analysis revealed that four organic acids (citric acid, pyruvate acid, succinic acid, and fumarate) were released at higher abundance by the Foc-susceptible cultivar compared with the resistant cultivar, which may be responsible for the recruitment of Comamonadaceae, a potential beneficial microbial group. Further validation demonstrated that Comamonadaceae can be “cultured” by these organic acids. Together, compared with the resistant cultivar, the susceptible cucumber tends to assemble beneficial microbes by secreting more organic acids.