Substituting Chemical by Organic Fertilizer Improves Soil Quality, Regulates the Soil Microbiota and Increases Yields in Camellia oleifera

The partial substitution of chemical fertilizer with organic fertilizer has been regarded as an effective strategy for enhancing crop yield and soil quality. Nevertheless, its effects on soil properties and microbes remain contentious. In this study, we examined the effects of four different fertilization strategies (including without fertilizer (CK), 100% chemical fertilizer (NPK), 30% organic fertilizer + 70% chemical fertilizer (LOM) and 60% organic fertilizer + 40% chemical fertilizer (HOM)) on soil nutrients and microbial communities through metagenomic sequencing in a <i>Camellia oleifera</i> field experiment. Compared to CK and NPK, HOM significantly increased SOC, TN, TP, AK and AN contents. The substitution of organic fertilizer notably increased <i>Camellia oleifera</i> yield, with the highest increase of 93.35% observed in HOM relative to NPK. Soil bacterial and fungal communities responded inconsistently to fertilization patterns. Bacteria predominated as the main soil microorganisms, and higher rates of organic fertilizer substitution facilitated a shift from bacterial to fungal communities. Organic fertilizer substitution significantly increased soil bacteria diversity and fungal richness, particularly in the HOM. Soil bacterial community structure was more sensitive to fertilization regimes than soil fungi. High rates of organic fertilizer substitution substantially suppressed oligotrophic and increased copiotrophic bacterial communities. <i>Mucoromycota</i> emerged as the dominant fungal group, with a considerable increment in HOM soils. SOC and TN were the main factors affecting <i>Camellia oleifera</i> yield and shaping soil bacteria and fungal diversity and composition. This study provided crucial insights into the ecological implications of organic fertilizer application and the potential of managing soil microorganisms for sustainable <i>Camellia oleifera</i> productivity.