Tomato root transcriptome response to a nitrogen-enriched soil patch. Solanum lycopersicum

Nitrogen (N), the primary limiting factor for plant growth and yield in agriculture, has a patchy distribution in soils due to fertilizer application or decomposing organic matter. Studies in solution culture over-simplify the complex soil environment where microbial competition and spatial and temporal heterogeneity challenge roots’ ability to acquire adequate amounts of nutrients required for plant growth. In this study, various ammonium treatments (as 15N) were applied to a discrete volume of soil containing tomato (Solanum lycopersicum) roots to simulate encounters with a localized enriched patch of soil. Transcriptome analysis was used to identify genes differentially expressed in roots 53 hrs after treatment. Results: The ammonium treatments resulted in significantly higher concentrations of both ammonium and nitrate in the patch soil. The plant roots and shoots exhibited increased levels of 15N over time, indicating a sustained response to the enriched environment. Root transcriptome analysis identified 585 genes differentially regulated 53 hrs after the treatments. Nitrogen metabolism and cell growth genes were induced by the high ammonium (65 ug NH4+-N g-1 soil), while stress response genes were repressed. The complex regulation of specific transporters following the ammonium pulse reflects a simultaneous and synergistic response to rapidly changing concentrations of both forms of inorganic N in the soil patch. Transcriptional analysis of the phosphate transporters demonstrates cross-talk between N and phosphate uptake pathways and suggests that roots increase phosphate uptake via the arbuscular mycorrhizal symbiosis in response to N. Conclusion: This work enhances our understanding of root function by providing a snapshot of the response of the tomato root transcriptome to a pulse of ammonium in a complex soil environment. This response includes an important role for the mycorrhizal symbiosis in the utilization of an N patch. Overall design: 9 Total samples were analyzed across 3 treatment groups (3 biological replicates per group). We generated the following pairwise comparisons using JMP Genomics software: Control vs. Low N, Control vs. high N, and low N vs. high N. One way ANOVA was used to determine significantly different expression. Genes with an FDR≤10% were presented.

氮（Nitrogen, N）是农业中限制植物生长与产量的核心因子，施肥或有机质分解会导致土壤中氮素呈现斑块状分布。溶液培养相关研究过于简化了复杂的土壤环境——在真实土壤中，微生物竞争以及时空异质性都会对根系获取植物生长所需足量养分的能力造成挑战。本研究中，我们向含有番茄（Solanum lycopersicum）根系的离散土壤区域施加不同铵态氮处理（标记为15N），以模拟根系遭遇局部富营养斑块的场景。通过转录组分析，我们鉴定了处理53小时后根系中差异表达的基因。

**结果**：铵态氮处理使斑块土壤中的铵态氮与硝态氮浓度均显著升高。随着时间推移，植株根系与地上部分的15N水平均有所提升，表明植株对富营养环境产生了持续性响应。根系转录组分析共鉴定出585个在处理后53小时内差异调控的基因。高浓度铵态氮（65 μg NH4+-N·g⁻¹ 土壤）诱导了氮代谢与细胞生长相关基因的表达，同时抑制了胁迫响应基因的表达。铵态氮脉冲处理后特定转运蛋白的复杂调控模式，反映了植株对土壤斑块中两种无机氮形态浓度快速变化的协同同步响应。对磷酸盐转运蛋白的转录分析显示，氮与磷酸盐吸收通路之间存在交叉对话，且根系会通过丛枝菌根共生体提升磷酸盐吸收以响应氮素变化。

**结论**：本研究通过解析复杂土壤环境中番茄根系转录组对铵态氮脉冲处理的响应图谱，加深了我们对根系功能的认知。该响应过程中，菌根共生体在氮斑块利用环节发挥了重要作用。

**实验设计**：本研究共设置3个处理组（每组3个生物学重复），总计分析9个样本。我们使用JMP Genomics软件进行了以下两两比较：对照组与低氮组、对照组与高氮组，以及低氮组与高氮组。采用单因素方差分析（One-way ANOVA）鉴定差异表达基因，最终筛选出错误发现率（False Discovery Rate, FDR）≤10%的基因。