Impact of extended fertilization on soil microbial diversity: a comparative full-length 16S rRNA amplicon analysis

Background Soil bacterial communities are essential for regulating soil fertility, nutrient cycling, and agricultural sustainability. However, their responses to different fertilization regimes, especially in intensively managed agroecosystems, remain inadequately characterized in Chattogram. Methods This study assessed the effects of prolong applications of chemical and organic fertilizers on soil bacterial community structure using culture-independent techniques (Oxford Nanopore long-read 16S rRNA gene sequencing). Result In subsequent taxonomic composition analyses, beta diversity revealed significant differences in bacterial community composition among the fertilization regimes ( p < 0.05), suggesting that long-term differences in fertilization practices may be associated with variation in bacterial community structure. The R 2 value (0.84) indicates that the fertilization regime was associated with a substantial proportion of the observed variation in bacterial community composition. However, organic amendment was associated with significantly higher abundances of several bacterial taxa linked to plant growth promotion and nutrient cycling than chemical fertilization. Among the predominant taxa, Bacillus was represented by 8.44 ± 1.255% under chemical fertilization and 14.77 ± 0.790% under organic amendment, while Gemmataceae accounted for 7.65 ± 0.689% and 11.60 ± 0.441%, respectively. A similar upward trend was observed among the less abundant taxa, with Xanthobacteraceae comprising 2.88 ± 0.197% and 4.15 ± 0.204%, and Tumebacillus 1.35 ± 0.171% and 2.73 ± 0.183%, under chemical fertilization and organic amendment, respectively (FDR < 0.001). Bradyrhizobium and Paenibacillus showed relatively similar abundances between the two fertilization treatments. Bradyrhizobium accounted for 3.33 ± 0.240% under chemical fertilization and 2.90 ± 0.216% under organic amendment (FDR = 0.055), whereas Paenibacillus represented 2.02 ± 0.173% and 2.50 ± 0.155%, respectively (FDR < 0.001). METAGENassist predictions and multivariate functional profiling suggest that organic amendments may enhance microbial capacity for the decomposition of organic matter and nutrient turnover. Conclusion These current findings suggest that the effects of fertilization on soil bacterial communities may extend beyond overall richness and may involve changes in community structure and relative abundance. However, the effects of fertilization on soil fertility and long-term agricultural sustainability should be assessed in the context of broader soil attributes and microbial community features.