Green manure covering alters the supply-demand relationship between soil resources and microorganisms by improving soil structure and increasing carbon inputs. However, it remain unclear how soil microorganism respond to the imbalance between resources and demands at the aggregate scale. The present study analyzed the stoichiometric ratios of organic carbon, nitrogen, and phosphorus nutrients, microbial extracellular enzyme activities, and biomass in large macroaggregates (LMA, 2–8 mm), small macroaggregates (SMA, 0.25–2 mm), and microaggregates (MIA, < 0.25 mm) under smooth vetch covering. The relationship between microbial carbon use efficiency and nutrient restriction in soil aggregates was elucidated and the alteration was revealed in microbial metabolic pathways and carbon sequestration functions within soil aggregates under green manure covering. The results showed that: (1) Smooth vetch covering significantly increased the C: N resource imbalance (ln(MBC: MBN)/ln(SOC: TN)) in soil aggregates from 0.50 to 0.69, and thus increased the nitrogen requirement of soil aggregates. However, the N:P resource imbalance (ln(MBN: MBP)/ln(TN: TP)) decreased from 2.25 to 1.78, especially in microaggregates. (2) To mitigate the limitation imposed by nitrogen availability at the aggregate level, microorganisms have ramped up the activity of C- (46.72 %–98.64 %), N- (2.32 %–121.00 %), and P- acquiring enzymes (119.11 %–187.78 %). Nevertheless, the spatial heterogeneity inherent in soil aggregates, characterized by varying particle sizes, has led to a pivotal shift in microbial nutrient limitation. As soil aggregate size diminishes, the primary constraint on microbial activity transitions from nitrogen limitation to phosphorus limitation, reflecting the dynamic interplay between soil structure and nutrient availability. (3) In addition, smooth vetch covering increased the microbial carbon use efficiency of soil aggregates, and it increased with the increase of the particle size of soil aggregates: LMA (178.80 %) > SMA (147.23 %) > MIA (9.99 %). Microorganisms allocated more energy to generate biomass instead of obtaining limiting nutrient elements. These results indicate that smooth vetch covering could increase the organic carbon content of soil aggregates. In addition, in order to adapt to nutrient imbalance, soil aggregates microorganisms choose a “egoistic” metabolic pathway, which alleviates nutrient limitation and assimilated more energy and nutrients into their own biomass and reduces the release of organic carbon. It is evident that integrating Vicia villosa Roth var. glabresens Koch as a ‘green manure’ in orchards serves a dual purpose: it mitigates the environmental impact of chemical fertilizers while simultaneously promoting soil carbon sequestration. This approach offers a robust theoretical framework for achieving the harmonious integration of ecological sustainability and economic viability in economic forestry, such as citrus orchards.
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