Impacts of long-term fertilizer reduction and organic substitution on microbe-mediated multi-nutrient in agricultural ecosystems

Organic amendment addition represents one of the most effective soil organic matter (SOM) sequestration strategies, faced with the dilemma of deepening organic carbon losses due to increased agricultural intensification. However, little is known regarding the impacts of long-term fertilizer reduction and organic substitution on microbe-mediated multi-nutrient (C, N, P, S) in agricultural ecosystems, especially with the alternation of green manure and manure application. Here, the responses of soil physicochemical properties, microbial community structure, and nutrient cycling processes to the application of fertilizer reduction and organic substitution were investigated with metagenome analysis. The results indicated that the content of SOM, pH, available phosphorus, total nitrogen and cation exchange capacity in soils with organic and chemical fertilizer combinations exhibited a significant increase (p < 0.05) compared to soil with chemical fertilizer alone. These drove significant differences in microbial community structure and enrichment in specific archaeal and bacterial groups. Additionally, chemical fertilizer reduction and organic substitution can alter soil nutrient cycling. Specifically, carbon fixation through the Wood-Ljungdahl Pathway was significantly stimulated (p < 0.05) while methanogenesis was significantly inhibited (p < 0.05). The abundance of functional genes responsible for the oxidative generation of sulfate was significantly suppressed (p < 0.05). Notably, organic fertilizers significantly enhance the potential of microorganisms to inorganic phosphorus solubilization and organic phosphorus mineralization while significantly inhibiting their potential for nitrogen fixation and nitrification. The findings underpin a scientific comprehension of agroecosystem health and eco-agriculture. • Organic substitution enhanced the content of SOM, pH, AP, TN and CEC. • Organic substitution drove enrichment of specific archaeal and bacterial groups. • Organic substitution stimulated carbon fixation through the Wood-Ljungdahl Pathway. • Organic substitution curbed the potential for nitrogen fixation and nitrification.