Short-Term Fertilization with the Nitrogen-Fixing Bacterium (NFB) Kosakonia radicincitans GXGL-4A Agent Can Modify the Transcriptome Expression Profiling of Cucumber (Cucumis sativus L.) Root

The application of nitrogen-fixing bacteria (NFB) as a biofertilizer can greatly reduce or even avoid environmental pollution caused by the excessive use of chemical nitrogen fertilizers. To explore the effect of short-term fertilization of GXGL-4A on the expression of functional genes in the roots of the cucumber (Cucumis sativus L.) cultivar “Xintaimici”, this study used transcriptome sequencing technology combined with fluorescent quantitative RT-PCR (qRT-PCR) verification to compare the gene transcription profiles of GXGL-4A-treated and control (sterile-water-treated) groups. A total of 418 differentially expressed genes (DEGs) were detected. The transcription levels of genes Csa5G161290 and Csa3G027720, which encode nitrate transporters, showed significant up-regulation (3.04- and 2.27-fold, respectively) in roots inoculated with GXGL-4A. The genes CsaV3_5G006200, encoding cytokinin dehydrogenase involved in the biosynthesis of zeatin, CsaV3_1G011730, encoding a wound-responsive protein, and CsaV3_6G015610, encoding a heat stress transcription factor, were significantly up-regulated at the transcriptional level (p < 0.05). However, the transcription of nitrogen cycling functional genes CsaV3_3G036500, CsaV3_1g008910, and CsaV3_3G018610, which encode nitrate reductase, high-affinity nitrate transporter (NRT), and ferredoxin-nitrite reductase, respectively, showed significant down-regulation (p < 0.05). Only the KEGG pathway of phenylpropanoid biosynthesis reached a significant level (p < 0.05). This study contributes to a deeper understanding of the interaction between NFB and plants and provides theoretical guidance for the development of GXGL-4A as a mature biological agent for sustainable agricultural production under drought stress.