Partial organic substitution increases microbial diversity but has divergent effects on functional microorganisms under various fertilization regimes in an ultisol

Manure substitution is increasingly acknowledged as a key practice for enhancing soil health in agricultural systems. However, its effects on soil microbial diversity and functional microorganisms vary across soil conditions. This study examined the effects of partial manure substitution on microbial diversity, community composition, and functional gene abundance in soils subjected to various mineral fertilization treatments using metagenomic sequencing. The results showed that partial manure substitution increased archaeal, bacterial, and fungal richness but did not influence functional gene richness. The microbial community structure was significantly altered by manure substitution, with soil pH and available phosphorus as the key variables. The abundance of Firmicutes was consistently increased, while Chloroflexi decreased due to the manure substitution. The effect of partial manure substitution on the relative abundance of genes involved in organic C degradation and N cycling varied across treatments. Specifically, partial manure substitution increased labile C degradation genes more significantly in the N treatment compared to the NP and NPK treatments. Additionally, it increased the relative abundance of dissimilatory nitrate reduction to ammonium (DNRA) associated genes in the NPK treatment, but not in the N or NP treatments. These findings suggest that manure substitution can enhance soil microbial diversity, but its impact on key functional microorganisms, such as those involved in organic carbon degradation and nitrogen cycling, depends on the mineral fertilization regime. This underscores the importance of accounting for initial soil mineral fertilization when implementing manure substitution as a management practice, particularly in the context of optimizing carbon and nitrogen cycling in agricultural ecosystems. • Manure substitution increases soil microbial diversity across all treatments. • Manure substitution alters soil microbial community structure, with pH and AP as key regulatory factors. • Manure substitution increases labile C degradation genes to a greater extent in N than in NP or NPK. • DNRA-associated genes are enriched only in the NPK treatment by Manure substitution.