Differences in temporal patterns of bacterial community assembly between soybean rhizosphere and endosphere

The two-step selection model is a widely accepted explanation of the mechanism of root-associated microbial communities. However, few studies have explained it from a time-series succession perspective. We analyzed the time-series succession patterns of bacterial communities in the rhizosphere and endosphere of soybeans using 16S ribosomal RNA (16S rRNA) sequencing. Rhizosphere selection showed temporal variation, with intensity increasing over time and leading to a decrease in the similarity between the rhizosphere and bulk soil communities from 0.42 to 0.17 during the first nine weeks. In contrast, endosphere selection was strong in the early stage but gradually weakening — with similarities between endosphere and bulk soil communities increasing from 0.10 to 0.12, and between endosphere and rhizosphere communities from 0.31 to 0.69. Predicted community functions also showed a gradient shift from bulk soil to rhizosphere and endosphere, further supporting the selection effect. The most representative functional taxa were those exhibiting chemoheterotrophy and aerobic chemoheterotrophy. Operational Taxonomic Units (OTUs) strongly associated with the growth stages, primarily from Proteobacteria, Acidobacteria, and Actinobacteria, showed decreasing abundance in the rhizosphere but increasing abundance in the endosphere. These results indicate that both rhizosphere selection and endosphere selection vary with plant growth. Rhizosphere selection is a gradually strengthening process dominated by inhibition, while endosphere selection is a gradually weakening process dominated by enrichment. The observed differences in temporal succession highlight distinct mechanisms of rhizosphere and endosphere selection, providing important insights into the two-step selection model.