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Carbon (C) and nitrogen (N) coupling regulated by intensified microbial activity and turnover in the rhizosphere hotspots are essential for balancing C-N budgets, sustaining agroecosystem productivity and mitigating global climate changes. However, it remains unclear whether and how the (different) spatial distribution of root-derived C from rhizosphere to non-rhizosphere will regulate N transport and transformation. To address this, a rhizobox (100 × 80 × 80 cm) experiment was conducted on soils from the same site using 13C-CO2 (for 2 weeks) and 15 N-urea labelling for two cultivation systems, upland wheat and paddy rice. The paddy system showed larger proportion (43.5 versus 10.1%) of root-derived 13C retained into bulk soil, wider spatial transportation of both C and N (> 40 mm versus < 6.7 mm), higher proportion of plant-N uptake from soil pool (86.4 versus 62.3%), and higher loss of N derived from fertilizer pool (29.7 versus 13.2%), compared to the upland system. We identified that in paddy rice, larger amounts of N can be horizontally transported from bulk soil to the rhizosphere; the effects of root-derived C on N transformation mediated by soil microorganisms are more profound; higher plant uptake of soil-N as well as higher loss of fertilizer-N than those of upland wheat. Our results suggest that the transport and transformation of N are under the regulation of the spatial distribution of root-derived C and the associated microbial activities. This paves a new path towards proper management for weighing nutrient availability against fertilization reduction and balancing productivity with sustainability. [ABSTRACT FROM AUTHOR]