Organic fertilisation enhances network complexity among bacteria, fungi, and protists by improving organic matter and phosphorus in acidic agricultural soils

Research has explored the impact of organic fertilisation on improving agroecosystem productivity and resilience, highlighting the significant contributions of protists in addition to bacteria and fungi. However, the interactions among bacteria, fungi and protists in organically fertilised soils remain largely unknown. In this study, soil samples were collected from four long-term fertilisation treatments: no fertilisation (Control), inorganic fertilisation (NPK), organic fertilisation (OM), and combined inorganic and organic fertilisation (NPKOM). The abundance and composition of bacteria, fungi, and protist communities, as well as co-occurrence networks, were analysed under different fertilisation treatments. Our results showed that the total abundance of bacteria, fungi, and protists increased by a minimum of 2.95, 3.47, and 0.66 times, respectively, after organic fertiliser application. Moreover, the application of organic fertilisers significantly altered the structures of soil microbial communities by enriching bacterial Proteobacteria and Actinobacteria, fungal Ascomycota, and protist Conosa. Changes in the total abundance of bacteria, fungi, and protists, and their community structures in soils with organic fertilisers were associated with increases in soil organic carbon and phosphorous. Additionally, microbial networks exhibited greater complexity in organically fertilised soils than in non-organically fertilised soils by possessing higher linkage density. The increased complexity may be attributed to potential interkingdom associations among bacteria, fungi, and protists in high soil organic carbon and phosphorus. These results highlight that the application of organic fertilisers has the potential to enhance the complexity of microbial coexistence in acidic agricultural soils.