The cosmopolitan algae Phaeocystis globosa forms harmful algal blooms frequently in a number of tropical and subtropical coastal regions in the past two decades. During the bloom, the giant colony, which is formed by P. globosa, is the dominant morphotype. However, the microenvironment and the microbial composition in the intracolonial fluid are poorly understood. Here, we used high-throughput 16S rRNA amplicon sequencing to examine the bacterial composition and predicted functions in intracolonial fluid. Compared with the bacterial consortia in ambient seawater, intracolonial fluids possessed the lower levels of microbial richness and diversity, implying selectivity of bacteria by the unique intracolonial microenvironment enclosed within the P. globosa polysaccharide envelope. The bacterial consortia in intracolonial fluid were dominated by Balneola (48.6% of total abundance) and Labrezia (28.5%). The bacteria and microbial function enriched in intracolonial fluid were involved in aromatic benzenoid compounds degradation, DMSP and DMS production and consumption, and antibacterial compounds synthesis. We suggest that the P. globosa colonial envelope allows for the formation of a specific microenvironment; thus, the unique microbial consortia inhabiting intracolonial fluid has close interaction with P. globosa cells, which may benefit colony development.

Plankton microorganisms play central roles in the marine food web and global biogeochemical cycles, while their distribution and abundance are affected by environmental variables. The determinants of microbial community composition and diversity in estuaries and surrounding waters with multiple environmental gradients at a fine scale remain largely unclear. Here, we investigated bacterial and protistan community assembly in surface waters from 27 stations across the Changjiang Estuary to the ocean, with salinity ranging from 0 to 32.1, using 16S rRNA and 18S rRNA gene amplicon sequencing. Statistical analyses revealed that salinity is the major factor structuring both bacterial and protistan communities. Salinity also acted as a significant environmental determinant influencing alpha-diversity patterns. Alpha diversity indices for bacterial and protistan communities revealed a species minimum in higher-salinity waters (22.1–32.1). Contrary to the protistan community, the highest bacterial diversity was identified in medium-salinity waters (2.8–18.8), contrasting Remane’s Artenminimum concept. The distribution of major planktonic taxa followed the expected pattern, and the salinity boundary for Syndiniales was specifically identified. These findings revealed the significant effects of salinity on the microbial community across an estuary to ocean transect and the distinct response to salinity between bacterial and protistan communities.