Small changes in soil aggregates-associated organic carbon and soil nitrogen (N) can induce huge fluctuations in greenhouse gas emissions and soil fertility. However, there is a knowledge gap regarding the responses to long-term continuous rotation systems, especially in N-fixing and non-N-fixing crop wheat in terms of the distribution of soil aggregates and the storage of soil carbon (C) and N in aggregates in the semiarid calcareous soil of Central China. This information is critical for advancing knowledge on C and N sequestration of soil aggregates in rainfed crop rotation systems. Our aim was to determine which legume (soybean (Glycine max)– or mung bean (Vigna radiata)–wheat (Triticum aestivum) rotation practice is more conducive to the formation of good soil structure and C and N fixation. A 10-year field experiment, including a soybean (Glycine max)–winter wheat (Triticum aestivum) rotation (SWR) with yield increments of 2020 compared to 2010 achieving 18.28% (soybean) and 26.73% (wheat), respectively, and a mung bean (Vigna radiata)–winter wheat rotation (MWR) achieving 32.66% (mung bean) and 27.38% (wheat), as well as farmland fallow, was conducted in Henan Province, China. The soil organic carbon (SOC), N content in the soil, and the soil aggregates were investigated. Legume–wheat rotation cropping enhanced the proportion of the >2 mm soil fractions and reduced the 2 mm aggregate fractions than the MWR. Two legume–winter wheat rotations enhanced the C and N sequestration that varied with soil depths and size fractions of the aggregate. In contrast, the MWR had greater SOC stocks in all fractions of all sizes in the 0–40 cm soil layers. In addition, the greater storage of N in the macro-, micro-, and silt + clay fractions was observed in the 0–30 cm layers; the MWR enhanced the C/N ratios in most of the size aggregates compared with the SWR. The MWR cropping system is more beneficial to the formation of good soil structure and the increasement of C and N reserves in soil. Thus, these findings show that mung bean, in contrast with soybean in the legume–wheat rotation system of a semiarid temperate zone, may offer soil quality improvement.

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