Microbial community assembly elucidates differential biotic homogenization in soils caused by agricultural expansion in the Yangtze River estuary

Agricultural expansion induces the homogenization of soil bacterial communities on a global scale; however, the extent to which this phenomenon affects different microbial taxa and the consistency of the underlying mechanisms remain largely unexplored. Here, we conducted a comprehensive survey at the Yangtze River estuary, comparing coastal wetlands with adjacent croplands converted from these wetlands. By integrating 16S rRNA gene amplicon sequencing with null model approaches, we characterized soil bacterial and archaeal communities and identified key ecological drivers. Our results reveal that land conversion leads to biotic homogenization across both bacterial and archaeal domains, particularly in archaea. While microbial communities in wetlands are primarily influenced by hydrological factors (e.g., soil moisture and electrical conductivity), total carbon and nitrogen content emerge as the dominant determinants in croplands. Network analysis indicated a significant reduction in the complexity and stability of microbial networks in croplands compared to wetlands. Null model analysis further suggested that homogenizing dispersal, rather than selection, predominantly shapes community structure for both bacteria and archaea. Interestingly, heterogeneous filtering mitigated this homogenization in soil bacteria, accounting for the differences in community similarity observed following agricultural expansion. Specifically, agricultural management induced the dominance of ammonia-oxidizing Thaumarchaeota in archaea, with a significant 86.65 % increase in Nitrososphaerales in croplands, driven by homogenization, while sulfate-reducing bacteria Desulfocapsa showed the strongest response to homogeneous dispersal in bacteria. Overall, our study elucidates the widespread impact of microbial homogenization due to agricultural expansion and clarifies the mechanisms responsible for the observed disparities among microbial taxa.