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When running a nitrogen crop response model with 100kgN/ha fertilizer input I found that the quantity of nitrogen in the top 90 cm of the soil reduced compared to when zero nitrogen was added (66kgN/ha versus 93kgN/ha). No other variables in the model were changed (that is, organic matter content, rainfall and so on). The other results given by the model were:

For 100kgN/ha added - crop yield 3.9t/ha with %N content 3.52, N leaching below 90cm 94 kgN/ha
For 0kgN/ha added - crop yield 1.99 t/ha with %N content 2.17, N leaching below 90cm 94 kgN/ha

I understand why the crop yield and % N content went up in response to the added nitrogen however why did the amount of stored nitrogen in the soil go down - what am I missing regarding the nitrogen cycle that would describe this?

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