title: Tomato root transcriptome response to a nitrogen-enriched soil patch.
abstract: 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 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 mug 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Donald Danforth Plant Science Center, 975 N Warson Rd., St. Louis. MO 63132, USA.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Ruzicka
authors.forename: Felipe H
authors.initials: FH
authors.lastname: Barrios-Masias
authors.forename: Natasha T
authors.initials: NT
authors.lastname: Hausmann
authors.forename: Louise E
authors.initials: LE
authors.lastname: Jackson
authors.forename: Daniel P
authors.initials: DP
authors.lastname: Schachtman
mesh_terms: D002455:Cell Division / Q000187:drug effects / Q000235:genetics; D002473:Cell Wall / Q000187:drug effects / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D017343:Genes, Plant / Q000235:genetics; D018551:Solanum lycopersicum / Q000166:cytology / Q000187:drug effects* / Q000235:genetics*; D009584:Nitrogen / Q000378:metabolism / Q000494:pharmacology*; D020411:Oligonucleotide Array Sequence Analysis; D028061:Phosphate Transport Proteins / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000166:cytology / Q000187:drug effects* / Q000235:genetics*; D000644:Quaternary Ammonium Compounds / Q000494:pharmacology; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012987:Soil / Q000032:analysis*; D013312:Stress, Physiological / Q000187:drug effects / Q000235:genetics; D014158:Transcription, Genetic / Q000187:drug effects
chemical_list: D028061:Phosphate Transport Proteins; D000644:Quaternary Ammonium Compounds; D012987:Soil; D009584:Nitrogen