This paper presents novel data illustrating how soil aggregates control nitrogen (N) dynamics within conventional and alternative Mediterranean cropping systems. An experiment with 15 N-labeled cover crop residue and synthetic fertilizer was conducted in long-term (11 years) maize–tomato rotations: conventional (synthetic N only), low-input (reduced synthetic and cover crop-N), and organic (composted manure- and cover crop-N). Soil and nitrous oxide (N 2 O) samples were collected throughout the maize growing season. Soil samples were separated into three aggregate size classes. We observed a trend of shorter mean residence times in the silt-and-clay fraction than macro- (>250 μm) and microaggregate fractions (53–250 μm). The majority of synthetic fertilizer-derived 15 N in the conventional system was associated with the silt-and-clay fraction (<53 μm), which showed shorter mean residence times (2.6 months) than cover crop-derived 15 N in the silt-and-clay fractions in the low-input (14.5 months) and organic systems (18.3 months). This, combined with greater N 2 O fluxes and low fertilizer-N recoveries in both the soil and the crop, suggest that rapid aggregate-N turnover induced greater N losses and reduced the retention of synthetic fertilizer-N in the conventional system. The organic system, which received 11 years of organic amendments, sequestered soil organic carbon (SOC) and soil N, whereas the conventional and low-input systems merely maintained SOC and soil N levels. Nevertheless, the low-input system showed the highest yield per unit of N applied. Our data suggests that the alternating application of cover crop-N and synthetic fertilizer-N in the low-input system accelerates aggregate-N turnover in comparison to the organic system, thereby, leading to tradeoffs among N loss, benefits of organic amendments to SOC and soil N sequestration, and N availability for plant uptake.
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