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

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 N-15 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.