AUTHOR=Cheng Yunqing , Jiang Xingtong , He Xinyi , Wu Zhaoyang , Lv Qiang , Zhao Shuang , Zhang Xinyue , Wang Shuai , He Hongli , Liu Jianfeng 

TITLE=Bacillus velezensis 20507 promotes symbiosis between Bradyrhizobium japonicum USDA110 and soybean by secreting flavonoids

JOURNAL=Frontiers in Microbiology

VOLUME=Volume 16 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1572568

DOI=10.3389/fmicb.2025.1572568

ISSN=1664-302X

ABSTRACT=IntroductionWhile co-inoculation with rhizobia and plant growth-promoting rhizobacteria (PGPR) can enhance soybean growth and nodulation, the interaction mechanisms between Bacillus velezensis 20507 and Bradyrhizobium japonicum USDA110 under varying nitrogen (N) supply levels (0–10 mmol/L) remain unclear. This study investigates how their synergistic interactions influence soybean nitrogen content per plant and molecular pathways.MethodsSoybean plants were co-inoculated with B. velezensis and B. japonicum across four N levels. Nodulation, plant growth, physiology, and N content were quantified. Transcriptome sequencing of soybean roots under N deficiency compared single and co-inoculation treatments. Flavonoids in B. velezensis fermentation broth were identified via mass spectrometry, and rutin’s regulatory effects on B. japonicum nodulation genes (NodD1/NodD2) were tested in coculture.ResultsCo-inoculation significantly increased nodulation, biomass, and N content per plant compared to single inoculations across all N levels. Under N deficiency, co-inoculation induced 5,367 differentially expressed genes (DEGs), with Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment in phenylpropanoid (ko00940) and flavonoid biosynthesis (ko00941). B. velezensis produced 29 flavonoids and 4 isoflavonoids (including rutin). Rutin (5–10 mg/L) upregulated NodD1 and suppressed NodD2 in B. japonicum.DiscussionB. velezensis enhances B. japonicum-soybean symbiosis via flavonoid secretion, particularly rutin, which modulates nodulation gene expression. This metabiotic interaction improves soybean N assimilation and growth, even under low N conditions. The findings provide a foundation for designing composite inoculants to optimize soybean yield and nitrogen-use efficiency.