Abstract
Free‐living and particle‐associated microbial communities play critical roles in nutrient cycles in aquatic systems. However, little is known about their assembly process, function, and interactions. Here, by using 16S rRNA gene amplicon sequencing of size‐fractionated samples collected during the wet and dry seasons, we investigated the assembly processes and co‐occurrence patterns of bacterial and archaeal communities in the Shenzhen River‐Bay system, South China. The bacterial and archaeal communities showed specific distribution patterns according to the size fraction (free‐living vs. particle‐associated), habitat (river vs. estuary), and seasonality (wet vs. dry season). Neutral modeling revealed that the stochastic pattern was more pronounced for bacteria than archaea, although both deterministic and stochastic processes significantly influenced the assembly of bacterial and archaeal communities. Homogeneous selection had a relatively higher importance in structuring bacterioplankton in free‐living fractions, while this process was more important in structuring archaeaplankton in particle‐associated fractions. Aquatic microbial community composition and assembly processes were most strongly associated with salinity and water temperature. Network analysis for each size fraction of the plankton revealed higher connectivity in the particle‐associated communities than the free‐living communities for intra‐bacteria, inter‐bacteria/archaea, and intra‐archaea associations, accordingly, when nonlinear associations were considered. These findings expand the current understanding of the ecological mechanisms and Archaea‐Bacteria interactions, underlying the size‐fractionated plankton dynamics in the river‐bay system.