Bacterial and eukaryotic community interactions might contribute to shrimp culture pond soil ecosystem at different culture stages

• Positive microbial interaction dominating in sedimentary bacterial and eukaryotic communities. • Homogeneous selection process governed the assemblage of both bacterial and eukaryotic communities. • Bacterial and eukaryotic diversities were in the reverse correlations with microbial positive interaction. Sedimentary bacterial and eukaryotic communities are major components of the aquatic ecosystem. Revealing the linkages between their community structure and interactions is crucial to understand the diversity and functions of aquatic and soil ecosystems. However, how their diversity and assembly contribute to their interactions on time scale is unclear. This study examined sedimentary bacterial and eukaryotic communities in shrimp culture ponds at different culture stages. The most abundant bacteria were Proteobacteria (38.27%), whereas the most abundant eukaryotes were Chytridiomycota (27.48%). Bacterial and eukaryotic diversities were correlated (P<0.05), implying the strong interactions between bacteria and eukaryotes. Results showed that the bacterial and eukaryotic communities became increasingly similar on a local scale along with the shrimp culture. Only the eukaryotic community significantly increased in similarity along with the shrimp culture (P<0.05), suggesting that the sedimentary eukaryotic community structure is sensitive under shrimp culture. Co-occurrence network modeling indicated that positive microbial interactions were dominant. The homogeneous selection was the major driver of community assembly. Bacterial diversity negatively correlated with operational taxonomic units and positive links in networks (P<0.05), whereas eukaryotic diversities positively correlated with positive links in networks (P<0.05). This study broadens our knowledge about sedimentary microbial diversity, community assembly, and interaction patterns on time scale, providing a reference for the sustainable management in aquaculture production.