Characteristics of Bacterial Community Structure in Yellow Paddy Soil After Long-Term Chemical Fertilisation, Organic Fertilisation, and Fertilisation Mode Conversion

This study aimed to compare bacterial community structure differences in yellow paddy soil under long-term chemical/organic fertilisation and fertiliser conversion to guide farmland fertilisation strategies in yellow loam areas. Treatments included (1) continuous application of chemical fertilisers for 27 years (CF-CF); (2) application of chemical fertiliser continuously for 24 years and then application of organic fertiliser for 3 years (CF-OF); (3) continuous application of organic fertiliser for 27 years (OF-OF); and (4) application of organic fertiliser continuously for 24 years and then application of chemical fertiliser for 3 years (OF-CF). The results show that long-term fertilisation alters genus-level bacterial taxa, while fertilisation mode changes significantly increase taxa quantities at both phylum and genus levels. Different fertilisation treatments affect the relative abundance of bacteria; the relative abundance of Firmicutes in OF-OF is significantly greater than that in CF-CF, while Gemmatimonadota and Patescibacteria show the opposite trend. Compared to CF-CF, CF-OF increases the relative abundance of Firmicutes and decreases that of Cyanobacteria, whereas OF-CF increases the relative abundance of Firmicutes compared to OF-OF. Notably, Patescibacteria is significantly enriched in CF-CF, while Cyanobacteria and Bacteroidota are significantly enriched in CF-OF, and Firmicutes and Myxomycophyta are significantly enriched in the OF-OF treatment. The bacterial community composition of CF-CF and CF-OF is similar, while the bacterial community composition of OF-OF and OF-CF is similar. In bacterial assembly processes, OF-CF improves the heterogeneous selection process and reduces the homogeneous dispersal process compared to OF-OF. The bacterial assembly process of OF-CF gradually becomes similar to that of CF-CF and CF-OF. Further analyses indicate that fertilisation influences the soil bacterial community composition by affecting total nitrogen, organic matter, available phosphorus, and pH. Overall, long-term different fertilisation predominates bacterial community distribution, while short-term changes in fertilisation mode have a smaller but significant effect on bacterial community distribution, influencing the quantity and relative abundance of bacterial taxa; the application of organic fertilisers is more beneficial for the even distribution of bacteria.