Microbial efficiency drives depth-dependent soil carbon storage under organic fertilization

The activity of microorganisms and their turnover strongly influence soil organic carbon (SOC) accumulation. However, microbial life-death cycles mediate the influence of fertilization on SOC storage across soil depths escapes mechanistic clarity. We analyzed 0-15 cm (surface) and 30-50 cm (deep) soils from a 45-year long-term fertilization field experiment, which included no fertilization (Control), mineral fertilization (NPK), pig manure (M), and a combination of mineral and pig manure (NPKM). Microbial carbon use efficiency (CUE) was measured using a H₂¹⁸O labelling approach and microbial necromass was indicated by amino sugars. Over 45 years, both M and NPKM increased microbial growth by 1.8- to 5.9-fold, CUE by 65-100% compare with NPK in surface soils by alleviating microbial nutrient stoichiometric imbalances (reduced C:N imbalance) and improving soil physical structure (lower bulk density). This consequently caused greater microbial necromass yield by 38-61% as compared to NPK. While microbial biomass, necromass, and CUE declined with soil depths, manure enriched Fe oxides and Ca² that stabilized microbial necromass, and subsequently induced a higher contribution of total microbial necromass to SOC in deep (74-76%) compared to surface soils (34-43%). Consequently, subsoils under manure shifted from C-limited zones to dominant SOC sinks. Thus, improving microbial CUE, especially via organic manure, promotes SOC sequestration by efficiently converting fresh inputs into persistent, microbially-derived organic matter across the soil profile.