Agronomy and Horticulture Department


Date of this Version



BMC Plant Biology 2010, 10:75 ; doi: 10.1186/1471-2229-10-75


© 2010 Ruzicka et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License.


Background: 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 oversimplify 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 μg 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.

Additional files attached below.

Schachtman BMCPB 2010 SUPPL 1.xls (285 kB)
Microarray analysis of differentially expressed genes across all treatments including the Affymetrix probeset ID, Genbank public ID, linear fold changes, FDR P-values, gene annotation information, and probeset redundancy information.

Schachtman BMCPB 2010 SUPPL2.xls (55 kB)
Genes similarly regulated by high NH4+ and low NH4+ treatments compared to the water control.

Schachtman BMCPB 2010 SUPPL3.xls (33 kB)
Primer sequences for genes assayed with qRT-PCR.