The Early Response to Urea, Nitrate, or Ammonium and Iron Resupply in Tomato Roots Highlights the Induction of FER, bHLHs, UMAMITs, and MATEs

Depending on the nitrogen (N) form available to roots, plants activate different transcriptional and metabolic pathways; this can consequently translate into differences in the composition and release of root exudates. To address the existing knowledge gap regarding the relationship between the availability of Iron (Fe) and different N forms applied (nitrate, ammonium, or urea), the molecular mechanisms activated by plants to promote their acquisition have been investigated using omics data integration (“exudomic” × transcriptomic analyses). The transcriptomic and metabolomic analyses reveal a strong crosstalk among nutritional pathways, showing that tomato root responses to Fe resupply depend on the nitrogen form provided. Transcriptomic profiles after 4 h indicate similar responses under urea and ammonium, a trend also observed at the exudomic level after 24 h. Distinct molecular features emerged depending on the specific N form applied. In particular, Fe resupply with urea induced the upregulation of the expression of FER and bHLH66, moderately enhancing the Fe level in roots. Overall, integrated omics data highlight a complex network of transcription factors, metabolites, and transporters that may contribute to improved plant resilience under nutrient stress, such as transcription factors (bHLH, MYB, ZAT12), transporters (UMAMITs, MATEs) and a proteolytic regulator of a phenylpropanoid enzyme (KFB-PAL). Within the framework of sustainable agriculture, this study corroborates the occurrence of a strong interplay between Fe- and N-nutritional pathways and emphasizes how different N forms can modulate root exudation in the rhizosphere, thereby enhancing the uptake of other essential nutrients such as Fe.