Rapid changes in root gene expression in response to nitrogen availability: Linking molecular biology, plant physiology, and soil biogeochemical processes

Background/Question/Methods

Plant root nitrogen (N) uptake and assimilation systems are highly responsive to external N availability.  Expression patterns of genes involved in these systems may serve as a sensitive “plant’s eye view” of soil N availability, even in situations when N cycling is so rapid that plant/microbial N uptake and N mineralization are tightly coupled and inorganic N does not accumulate.  This would allow better understanding of N mineralization-immobilization dynamics, and thus factors that lead to pulses of N excess and periods of N deficiency in agroecosystems.  We explored the relationship between soil biogeochemical processes and dynamic plant nutrient uptake by using novel applications of molecular biology techniques coupled with conventional metrics of soil N availability at an organic farm in the Sacramento Valley, California.  Following N treatments (6.5 and 65 µg-NH₄⁺-N g^-1 soil) designed to simulate a nutrient patch, we measured changes in expression of tomato (Solanum lycopersicum L.) root genes involved in N uptake and assimilation as well labile soil N pools, bioassays for microbial N transformations, and root/shoot N concentration.  Since organic agriculture relies on microbial transformations of soil organic matter to render N available for strong plant demand, it is an excellent system to test these interactions.

Results/Conclusions

Tomato root genes responded rapidly to N additions and to the subsequent changes in soil inorganic N concentrations.  The high N treatment significantly increased soil ammonium (NH₄⁺) and nitrate (NO₃^-) pools after 48 hours and significantly increased expression of an NH₄⁺ transporter, LeAMT2, and glutamine synthetases, LeGS and LeGTS1.  These genes also trended toward higher expression levels under the low N treatment, in spite of the lack of a detectable increase in soil inorganic N for this treatment.  Root N concentration was significantly higher in both the low and high N treatments relative to the control after 120 hours.  Rapid depletion of soil NH₄⁺ after 48 hours indicates high N demand and likely high nitrification rates, since soil NO₃^- levels remained elevated 120 hours following N treatments.  No differences in gene expression were observed 120 hours after the treatments.  Soil microbial biomass carbon did not differ among the treatments, suggesting that N was not limiting to microbial abundance.

The high sensitivity of these N uptake and assimilation genes to soil N cycling makes them strong candidates for diagnostic indicators of plant N availability, which could facilitate adaptive nutrient management on organic farms.