Organic fertilization increases the abundance of bacteria, fungi, and protists and their co-occurrence complexity in acidic soils

Abstract Background and aims Organic fertilization highly influences microbial populations and diversity in the soil. This study aimed to understand how organic fertilizer application affects bacterial, fungal, and protist communities in acidic soils and thus reshapes their interactions. Methods Soil samples were collected from a long-term field experiment consisting of four fertilization treatments: no fertilization (control), inorganic fertilization (NPK), organic fertilization (OM), and their combination (NPKOM). The abundance and composition of bacterial, fungal, and protist communities were analyzed. Results The total abundance of bacteria, fungi, and protists increased by at least 2.95, 3.47, and 0.66 times after organic fertilizer application. The composition of the bacterial, fungal, and protist communities was significantly different between the inorganic and organic fertilization treatments. Organic fertilization increased the complexity of co-occurrence among bacteria, fungi, and protists by increasing the number of keystone taxa and inter-kingdom associations. The abundance, community structure, and keystone taxa of bacteria, fungi, and protists significantly correlated with soil organic matter, total phosphorus, and available phosphorus content. Conclusions Soil pH, organic matter, and phosphorus levels were important factors in determining bacterial, fungal, and protist community structures and the complexity of microbial co-occurrence in acidic soils. This study provided insights into the relationship between agricultural management practices and soil bacterial, fungal, and protist communities.