Rhizosphere microbiota has received much attention due to their associations with plant growth and their fundamental importance in terrestrial ecosystems. However, relatively few studies have focused on rhizosphere microbial communities associated with aquatic macrophytes in freshwater lakes. We hypothesized that the rhizosphere microbiome would reflect the presence of macrophyte roots and the concomitant microhabitat conditions the roots create. Here, high‐throughput sequencing and network analysis were employed to compare the composition and structure of bacterial communities in the rhizosphere of two common emergent macrophytes, Zizania latifolia and Phragmites australis, with the surrounding sediments in Lake Taihu (China). Results indicated that bacterial diversity, community composition, and co‐occurrence networks differed between the communities of bulk sediments and the communities of rhizosphere and surface sediments. Richness and phylogenetic diversity were higher and more taxa were enriched in the rhizosphere and surface sediment communities compared with bulk sediment communities. No differences were detected between bacterial communities in rhizosphere and surface sediments, nor between rhizospheres sediment communities of the two macrophyte species. Anaerobic taxa were more abundant in bulk sediment communities. Among the co‐occurrence networks, more nodes (operational taxonomic units) and edges (connections) with higher average degree as well as more topologically important nodes were found in rhizosphere and surface sediment communities relative to bulk communities. These findings suggest that rhizosphere microbiome communities are influenced by the presence of macrophyte roots, with oxygenated rhizosphere and surface sediment communities being more diverse, and organized into more interconnected co‐occurrence networks.

To investigate the differences in the interactions of microbial communities in two regions in Taihu Lake with different nutrient loadings [Meiliang Bay (MLB) and Xukou Bay (XKB)], water samples were collected and both intra- and inter-kingdom microbial community interactions were examined with network analysis. It is demonstrated that all of the bacterioplankton, microeukaryotes and inter-kingdom communities networks in Taihu Lake were non-random. For the networks of bacterioplankton and inter-kingdom community in XKB, higher clustering coefficient and average degree but lower average path length indexes were observed, indicating the nodes in XKB were more clustered and closely connected with plenty edges than those of MLB. The bacterioplankton and inter-kingdom networks were considerably larger and more complex with more module hubs and connectors in XKB compared with those of MLB, whereas the microeukaryotes networks were comparable and had no module hubs or connectors in the two lake zones. The phyla of Acidobacteria, Cyanobacteria and Planctomycetes maintained greater cooperation with other phyla in XKB, rather than competition. The relationships between microbial communities and environmental factors in MLB were weaker. Compared with the microbial community networks of XKB, less modules in networks of MLB were significantly correlated with total phosphorous and total nitrogen.

Understanding the composition and assembly mechanisms of root-associated microbial communities of plants is crucial for understanding the interactions between plants and soil. Most previous studies of the plant root-associated microbiome focused on model and economic plants, with fewer temporal or seasonal investigations. The assembly mechanisms of root-associated bacterial communities in different seasons remain poorly known, especially for the aquatic macrophytes. In this study, we compared the diversity, composition, and relative importance of two different assembly processes (stochastic and deterministic processes) of bacterial communities associated with bulk sediment and the rhizosphere and endosphere of Phragmites australis in summer and winter. While we found apparent differences in composition, diversity, and assembly processes of bacterial communities among different compartments, season played important roles in determining BCCs and their diversity patterns and assemblages. We also found that endosphere bacteria mainly originated from the rhizosphere. The results add new knowledge regarding the plant-microbe interactions in aquatic ecosystems.