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Repeated applications of mineral and/or organic fertilizer will probably affect gross nitrogen (N) dynamics in soils in the long term but only a limited number of observations are available. Here we present results of a 15N tracing study with soil from the various fertilizer treatments of the Huang-Huai-Hai Plain experiment that has been in operation for more than 17 years. Mineral fertilizer in various combinations of N, phosphorus (P) and potassium (K), organic manure (OM) or a mixture of mineral fertilizer and manure had been repeatedly applied for 17 years. The gross N transformation rates were quantified with a 15N tracing model, which uses a parameter optimization routine based on Bayesian principles. Mineralization of soil organic matter was at least 2.7 times greater in all fertilizer treatments compared with the untreated control (0.67 µg N g−1 day−1). While application of mineral N enhanced mineralization from recalcitrant organic N, the application of organic fertilizers stimulated the mineralization of labile organic N. Gross nitrate (NO3) production solely resulted from ammonium (NH4+) oxidation. Compared with the gross NO3 production in the control treatment (2.22 µg N g−1 day−1), long-term N applications stimulated gross nitrification by more than 5.3 times. The largest gaseous N emissions were associated with the organic manure treatments. The ratio of gross NO3 production to total mineral N consumption, a ratio proposed previously to determine potential NO3 loss, was a good indicator except for the treatment without N application. This ratio increased from 0.8 in the control to 2.7 in the mixture of mineral fertilizer and manure treatment. The largest gaseous N emissions (N2O + NO) (P < 0.05) were generally found at greater ratios. Results clearly showed that various fertilizers have a differential effect on N dynamics and potential gaseous N losses in the long term.