Influence of nitrogen fertilization on rhizosphere microbial regulation of soil organic carbon mineralization in greenhouse-grown tomato

Excessive nitrogen (N) input has become a defining feature of high-intensity agricultural systems, particularly in greenhouse vegetable production (GVP). Over decades of application, nitrogen fertilizers not only modify soil nutrient pools but also reshape the intricate interactions within the rhizosphere, where plant roots, microbial communities, and soil organic matter (SOM) dynamics converge to regulate soil organic carbon (SOC) turnover. Despite significant progress in understanding impacts of nitrogen fertilization on soil biogeochemistry, the mechanisms by which N fertilization influences SOC cycling through rhizosphere-mediated biological pathways remains insufficiently understood. This thesis integrates findings from two complementary studies conducted in a 15-year GVP system to clarify how nitrogen regulates plant–soil–microbe interactions and alters key processes underpinning soil carbon dynamics. In this study, paired rhizosphere and bulk soil samples were collected from a 15-year greenhouse tomato production system under four chemical N fertilizer treatments: 0 (N0), 102 (N1), 327 (N2), and 552 (N3) kg N ha–1 yr–1, in addition to uniform manure and straw amendment at 123 kg N ha−1 yr−1.
1. Root exudation regulates microbial resource limitation and carbon use efficiency
The first study focused on the role of root exudation rates in modulating microbial nutrient acquisition under different N fertilization regimes. Long-term nitrogen fertilization significantly reduced both root C and N exudation rates across all N treatments. Compared with the unfertilized control (N0 treatment), root C exudation rates decreased by 34–57%, and root N exudation rates by 24–43% under fertilizer application (N1–N3 treatments), with the most pronounced suppression under medium N input (N2 treatment). These reductions had cascading effects on microbial nutrient limitations: as root exudate inputs declined, microbial C, N, and P limitations intensified, reflecting stronger competition for resources in the rhizosphere. Importantly, microbial carbon use efficiency (CUE)—a measure of how effectively microbes convert organic C into biomass—was negatively correlated with microbial resource limitation. In other words, limited availability of root-derived labile C led microbes to invest more in nutrient acquisition (e.g., enzyme production), thereby reducing their metabolic efficiency. Random Forest (RF) analysis identified root C and N exudation rates as key predictors of microbial resource limitation and CUE. Structural equation model (SEM) analysis further revealed that soil NH₄⁺ content directly influenced root exudation rates under long-term N fertilization, which in turn shaped microbial resource dynamics. Notably, increased root exudation rates were associated with intensified microbial nutrient limitations, ultimately reducing CUE and soil C sequestration. Overall, these findings highlight root exudation not merely as a carbon source but as a central mediator of microbial strategies and soil carbon retention capacity in plant–soil systems
2. Root-mediated priming effect counteracts nitrogen-suppressed soc decomposition
The second study examined the priming effect (PE)—a phenomenon where fresh carbon inputs stimulate or suppress the decomposition of native soil organic matter (SOM)—under long-term N fertilizer application. By using 13C-labeled glucose and analyzing PLFA biomarkers, we traced carbon incorporation and microbial community responses in paired rhizosphere and bulk soil samples. The results revealed that nitrogen fertilizer application consistently suppressed the PE, with values declining from +2% in unfertilized control (N0 treatment) to −10% under fertilizer application (N1–N3 treatments) in both rhizosphere and bulk soils. This suppression was closely associated with increases in dissolved organic nitrogen (DON), glucose-derived microbial biomass carbon (13MBC), and microbial CUE, which together reduced microbial reliance on native SOC as an energy source. Notably, rhizosphere soils showed weaker negative PE values than bulk soils, reflecting lower DON concentrations and higher microbial abundance and activity, suggesting that root-mediated processes partially counteracted the suppressive effect of N fertilization. These findings underscore that while elevated N fertilization input enhances microbial C assimilation and reduce the need for SOC decomposition; rhizosphere processes sustain SOC turnover by stimulating microbial biomass and activity.
Synthesis and Implications
This research provides an integrated perspective on how long-term nitrogen (N) fertilization reshapes plant–soil–microbe interactions and regulates soil carbon (C) cycling in intensive greenhouse vegetable systems. Nitrogen fertilization influences SOC dynamics not only through nutrient availability and chemical stabilization, but also via biologically mediated processes that alter root exudation, microbial resource limitations, priming effects, and community functioning. Root exudation emerges as a central regulator in this network, acting both as a source of labile C for microbial nutrient acquisition and as a modulator of rhizosphere processes. While increased N input enhances microbial C assimilation and constrains SOC decomposition, rhizosphere processes sustain microbial activity and C turnover, thereby balancing soil C stabilization and loss. These findings underscore the dual role of nitrogen in simultaneously constraining and sustaining SOC dynamics, and highlight the rhizosphere as a key regulatory interface where root traits, microbial metabolism, and biogeochemical processes converge.