Manure substitution of mineral fertilizers increased functional stability through changing structure and physiology of microbial communities

• Long-term manure substitution and reduction of mineral fertilizers were investigated.
• Microbial stability of crop litter decomposition to Cu addition and heating were investigated.
• Manure application increased functional stability due to shifted microbial community structure.
• Mineral fertilization increased the resistance to heating only due to shifted community level physiology.
• Functional and physiological shifts in communities changed with soil organic matter and aggregation.

Soil function, such as decomposition of organic materials, is of crucial importance to sustain soil fertility and may be enhanced through soil management. We hypothesized that manure amendment would increase soil functional stability more effectively than mineral fertilization when soil nutrients were not limited. By using a 22-yr field experiment, the objectives were 1) to determine the effects of manure substitution and reduction of mineral fertilizers on soil physio-chemical properties, soil microbial community structure, and soil biological functional stability; 2) to isolate the effects of organic amendment from those of mineral fertilization on soil biologic functional stability; and 3) to elucidate the controlling mechanisms on the soil functional stability. Soils were sampled from the field treatments, no fertilization (CK), mineral N, P and K (NPK), two doses of NPK (2NPK), manure amendment (OM) and OM in combination with NPK (NPK + OM). The nutrient inputs were similar in treatments OM and 2NPK. The functional stability was quantified by measuring the decomposition rate of crop litter added to the soils following Cu addition and heating. Soil nutrients, organic carbon and pH increased due to mineral fertilization and organic amendment. The principal component analysis of phospholipid fatty acid (PLFA) profiles demonstrated that the structure of soil microbial communities shifted between the mineral-fertilized soils and manure-amended soils and the shifts were not due to nutrient limitation because the soil microbial communities were not separated between the treatments of NPK and 2NPK. The manure amendment enhanced the resistance and resilience to Cu and heating more than the mineral fertilization, to a larger extent in treatment NPK + OM than in treatment OM. The resistance and resilience to Cu addition was positively correlated with soil organic matter, soil aggregate stability, while only the resistance to heating was positively correlated to soil aggregate stability. Moreover, the resistance and resilience were correlated with the shifts of functional and physiological structure of soil microbial communities due to long-term manure amendment and mineral fertilization. In conclusion, the partial substitution of mineral fertilizers with manure (NPK + OM) increased soil functional stability to heavy metal pollution and global warming through altered structure and physiology of soil microbial communities due to improved soil aggregation with higher soil organic matter.