Synergistic Effects of Amino Acids and Bacillus velezensis N35 on Suppressing Phelipanche aegyptiaca Parasitism and Modulating Tomato Growth: Insights from Transcriptomic Profiling

Phelipanche aegyptiaca is a root parasitic weed that causes severe yield losses in tomato production. Current control methods are constrained by limited efficacy and environmental concerns. Although biocontrol microbes and amino acids have each been reported to suppress broomrape parasitism individually, their synergistic effects and underlying molecular mechanisms remain largely unexplored. This study evaluated the biocontrol performance of Bacillus velezensis strain N35, applied alone or in combination with five amino acids (methionine, isoleucine, valine, histidine, and proline), against P. aegyptiaca parasitism in tomato using pot experiments coupled with transcriptomic profiling of host roots. Both individual and combined treatments significantly reduced the number and fresh weight of P. aegyptiaca parasitic tubercles. Notably, the combinations of methionine + N35 and isoleucine + N35 achieved near-complete suppression of parasitism. Transcriptomic analysis revealed extensive reprogramming of gene expression in tomato roots, with significant enrichment in pathways associated with plant hormone signal transduction, MAPK signaling, phenylpropanoid biosynthesis, and carotenoid biosynthesis. The synergistic treatments coordinately activated ethylene, jasmonic acid, and salicylic acid-mediated signaling, while suppressing auxin and abscisic acid signaling. Moreover, key strigolactone biosynthesis genes (CCD7 and CCD8) were strongly downregulated, and specific genes involved in the biosynthesis of defense-related secondary metabolites were selectively upregulated. Collectively, these findings demonstrate a pronounced synergy between B. velezensis N35 and specific amino acids in suppressing P. aegyptiaca parasitism. This enhanced host resistance is achieved through the coordinated reprogramming of hormonal and metabolic networks, particularly via interference with strigolactone-mediated germination signal secretion. This study provides a theoretical basis for the development of microbe–metabolite synergistic strategies as sustainable and environmentally benign alternatives for broomrape management.