Planktonic archaea reveal stronger dispersal limitation and more network connectivity than planktonic bacteria in the Jinsha River of southwestern China

Abstract Planktonic archaea and bacteria play important roles in biogeochemical cycling, but their biogeographical patterns and underlying ecological processes remain poorly understood, particularly in large‐scale rivers. We collected 43 water samples covering a 2279 km reach of the Jinsha River, one of the largest rivers in southwest China, and performed high‐throughput sequencing analysis on planktonic archaeal and bacterial communities. Partial Mantel analysis and neutral model were used to assess the factors influencing microbial distributions. The associations among different microbial species and their geographical distribution patterns were linked through co‐occurrence networks, and the putative key taxa in the archaeal and bacterial networks were analysed. The Shannon index of both archaeal and bacterial communities was highest in the midstream reach. The Pielou's evenness of archaea did not vary among the three reaches, whereas those of bacteria increased from upstream to downstream. The archaeal and bacterial community compositions were significantly different in the three reaches, but the differences among the bacterial communities were greater than among the archaeal communities. Both dispersal limitation and environmental selection affected the community compositions of the archaea and bacteria, but dispersal limitation was the most influential factor. Compared to archaea, bacteria were less affected by dispersal limitation and more by environmental selection. The co‐occurrence network analysis demonstrated that, compared with the bacterial network of all sites, the archaeal network with larger graph density had higher connectivity and complexity, but a lower proportion of negative correlations. The putative key taxa belonged to Nitrososphaeraceae and Candidatus_Nitrocosmicus from the archaeal community, and Hydrogenophaga and Sphingorhabdus from the bacterial community. Taken together, these findings demonstrated that the planktonic archaea were more dispersal‐limited and showed more network connectivity than the planktonic bacteria in the Jinsha River. This study enhances our understanding of the biogeographical distribution patterns and underlying ecological processes of planktonic microorganisms over large‐scale freshwater systems.