A collaborative research from the Innovation Team of Agricultural Microbial Resources of the Institute of Agricultural Resources and Regional Planning and the Vegetable Functional Genomics Team of the Institute of Vegetables and Flowers has uncovered a new mechanism by which specific cucumber genotypes recruit beneficial endophytic microbes in the xylem to promote plant growth.

Their findings were recently published in Microbiome under the title "Host Genetic Regulation of Xylem-Resident Pseudomonas Enhances Cucumber Growth." The study systematically analyzed the genetic basis of the cucumber xylem microbiome and revealed that the host gene CsXPR1 promotes cucumber growth by selectively recruiting beneficial Pseudomonas bacteria, with the growth-promoting effect strongly dependent on host genotype.

Endophytic microbes play an important role in plant growth and stress resistance. However, the genetic mechanisms by which plants precisely select and recruit beneficial microbes—especially within the xylem, the vascular tissue responsible for long-distance transport of water and nutrients—have remained largely unclear.

In this study, researchers conducted a genome-wide association analysis (GWAS) of the xylem microbiome across 109 cucumber core germplasm accessions with broad genetic diversity. The results revealed that cucumber xylem hosts a highly conserved core microbial community dominated by Pseudomonas species.

Further analysis identified a key host genetic locus, CsXPR1, which encodes a tetratricopeptide repeat (TPR) protein and precisely regulates the abundance of a core beneficial bacterium, Pseudomonas fulva strain 220, within the xylem. Importantly, the study demonstrated that the growth-promoting effect of this microbe is highly genotype-dependent.

Mechanistic experiments showed that once colonized in the xylem, P. fulva strain 220 synthesizes a key metabolite—4-methyleneglutamine—which significantly increases nitrogen levels in xylem sap and thereby promotes plant growth. Inoculation experiments further confirmed that the strain significantly enhances plant height, stem diameter, leaf area, and biomass only in cucumber haplotypes with high CsXPR1 expression (Hap2). In contrast, in haplotypes with low CsXPR1 expression (Hap1), the plant's weaker ability to recruit the bacterium results in little observable growth promotion.

These findings reveal a "precision recruitment and co-evolution" mechanism between plants and their core microbiome, offering new insights into how host genetics shapes beneficial plant–microbe interactions.

Associate Professor Qin Yuxuan, Zhu Xueying, Zheng Yingying, and Wang Kun from the Institute of Vegetables and Flowers served as co-first authors. Researcher Yang Xueyong and Associate Professor Qin Yuxuan from the same institute, together with Researcher Wei Hai-Lei from the Institute of Agricultural Resources and Regional Planning, served as corresponding authors. Professor Yang Jinliang of the University of Nebraska–Lincoln also participated in the study.

The research was supported by the National Key Research and Development Program of China, the National Natural Science Foundation of China, the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences, and the State Key Laboratory of Efficient Utilization of Arable Land in Northern Arid and Semi-Arid Regions.

Original article link：https://link.springer.com/article/10.1186/s40168-025-02308-2