Successive organic fertilizer substitution alleviated net ecosystem carbon loss in new vegetable field converted from rice paddy

Soil disturbance caused by land-use change from rice paddies to vegetable fields can lead to substantial soil carbon (C) storage losses. Partial substitution of chemical fertilizers with organic forms is an effective strategy for sustainable agriculture and may compensate for this C loss. However, how different organic fertilizers and substitution ratios maintain the soil C balance (net ecosystem C budget, NECB) in newly converted vegetable fields remains unclear. Here, the effects of substituting 25 % and 50 % chemical nitrogen (N) fertilizers with pig manure and municipal sludge, respectively, on NECB were investigated by considering soil C inputs (net primary production (NPP) and organic fertilizers) and outputs (ecosystem respiration and harvesting) in a two-year field experiment with eight consecutive vegetable cultivation. Zero N fertilizer (ZeroN) and conventional chemical N fertilizer (ConN) were used as controls. Both control treatments exhibited negative NECB values, averaging −2072 and − 2137 kg C ha⁻¹ yr⁻¹ respectively, confirming substantial C losses in converted systems. Successive organic fertilizer substitutions significantly increased NECB by 73 %–208 % and reduced net global warming potential by 35 %–138 % relative to ConN, despite 21 %–32 % higher C outputs. Of these, 50 % substitutions achieved positive NECB through enhanced NPP and direct C inputs from organic fertilizers. Moreover, repeated organic fertilizer substitution induced dynamic microbial community restructuring, favoring the dominance of bacterial high-yield strategists (Y-strategists). Such shifts in life-history strategies enhanced NECB by directly mediating the C input-output balances, and closely linked to the increase of several of these enriched microbial taxa such as Proteobacteria, Bacteroidetes and Gemmatimonadetes. These findings elucidate the dual regulation of organic substitution on C cycling in converted vegetable systems through coupled biogeochemical-microbial mechanisms, emphasizing the critical role of microbial metabolic strategies in achieving sustainable agriculture and NetZero emissions.