Partial substitution of chemical fertilizer with manure enhances soil multifunctionality and plant biomass through shifts in nitrogen forms and key nitrogen-associated microbial taxa

Long-term excessive application of chemical fertilizers has led to multiple soil degradation phenomena. Although it has been proven that organic fertilizers can optimize the efficiency of nitrogen cycling, the intrinsic mechanism of how it specifically regulates key functional microbial communities, thereby driving the transformation of soil nitrogen (N) forms and ultimately enhancing soil multifunctionality in a coordinated manner, still lacks systematic analysis. Therefore, this study established four N-equivalent treatments: chemical fertilizer only (FM), matured pig manure only (P), 70% FM + 30% P (70FP), and 50% FM + 50% P (50FP), to investigate how fertilizer type affects microbial communities, nitrogen cycling, and soil multifunctionality. The results showed that the 70% chemical fertilizer + 30% decomposed pig manure (70FP) treatment doesn't just enhance the total N pool, but it critically re-shuffles the N forms, reducing a recalcitrant form (iron-manganese oxide form N, IMOF-N) and increasing bioavailable forms (ion-exchangeable N, IEF-N). The abundance of ammonia-oxidizing bacteria (AOB) was positively correlated with nitrification, while the community structure of ammonia-oxidizing archaea (AOA) exhibited greater sensitivity to manure addition. Additionally, the 70FP treatment significantly enhanced denitrification and increased the abundance of nosZ -harboring bacteria responsible for the complete conversion of nitrate to N gas. Additionally, within the AOB community, Nitrosospira sp. III7 likely played a key role in nitrification, whereas Oligotropha was primarily involved in denitrification. Moreover, the identity and abundance of these keystone species may be more important for ecosystem functioning than overall community diversity in managed artificial systems. • Partial manure substitution improved soil N pool and multifunctionality • 70FP reduced IMOF-N and enhanced IEF-N, boosting lemon yield • 70FP increased nosZ -harboring bacteria and denitrification potential • The functional core microbiome is more important than overall community diversity