Plant and Soil

, Volume 392, Issue 1–2, pp 175–189 | Cite as

Root expression of nitrogen metabolism genes reflects soil nitrogen cycling in an organic agroecosystem

  • Timothy M. Bowles
  • Philipp A. Raab
  • Louise E. Jackson
Regular Article


Background and aims

Roots in agroecosystems encounter spatially and temporally heterogeneous nitrogen (N) availability in soil. Understanding root physiological processes in concert with soil microbial N dynamics following spatially discrete N pulses under field conditions will aid in the management of agroecosystem processes for N use efficiency.


This study examined the short-term response (<5 days) of tomato (Solanum lycopersicum L.) roots and soil N cycling to a pulse of inorganic N in an undisturbed soil patch on an organic farm using a novel combination of molecular and 15N isotopic techniques.


Tomato roots rapidly responded to and exploited the N pulse via upregulation of key N metabolism genes (e.g. cytosolic glutamine synthetase GS1) that comprise the core physiological response of roots to patchy soil N availability. Strong root activity limited accumulation of soil NO3 despite high rates of gross nitrification. Roots out-competed soil microbes for the inorganic N, even on a short time scale, likely as a result of high plant N demand and microbial C limitation. The transient root gene expression response (absent by 4 days after the N pulse) underscored the sensitivity of root N uptake to local N availability.


Root expression of genes such as GS1 could complement soil inorganic N pools and measurements of soil microbial activity to serve as integrative indicators of rapid plant-soil N cycling.


Root gene expression Cytosolic glutamine synthetase Isotope pool dilution Tomato (Solanum lycopersicumNitrogen cycling 

Supplementary material

11104_2015_2412_MOESM1_ESM.xlsx (11 kb)
Suppl. Table 1(XLSX 10 kb)
11104_2015_2412_MOESM2_ESM.xlsx (11 kb)
Suppl. Table 2(XLSX 11 kb)


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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Timothy M. Bowles
    • 1
  • Philipp A. Raab
    • 1
  • Louise E. Jackson
    • 1
  1. 1.Department of Land, Air and Water ResourcesUniversity of California DavisDavisUSA

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