Spatial heterogeneity dominates bacterial biogeography in the surface waters from the South China Sea by structuring environmental gradients

Studies in environmental bacterial communities are updating our view of the powerful small-scale environmental pressures governing the bacterial community assembly. However, it remains unclear about the processes acting at broader scales, such as the thousand-kilometer scale and highly connected marine habitats. We employed a high-coverage sampling strategy combined with 16S rRNA gene sequencing to investigate the biogeography, assembly mechanisms, and co-occurrence relationships of bacterial communities in the surface waters from the intensively human-affected coasts to the open ocean of the South China Sea. Results revealed a clear geographical clustering of both environmental factors and bacterial communities from a semi-enclosed bay of the Beibu Gulf (BG), a coastal sea area of the Guangdong coast (GD), and an open region of the western South China Sea (WS). Determinant environmental drivers of bacterial communities in the three regions were also distinct: dissolved nutrients in GD, SiO₃^2--Si and Chl <i>a</i> in BG, and temperature and Chl <i>a</i> in WS. The spatial and shared variations of environmental and spatial factors explained the bacterial beta-diversity dominantly. The assembly of bacterial communities was dominated by deterministic processes, particularly homogeneous selection in all regions, but showed significant regional variations in stochastic processes. Key discriminant subcommunities Pseudomonadota and Bacteroidota were assembled by notably high stochastic processes, possibly contributing to the varied bacterial assembly process. Network analysis demonstrated distinctly different co-occurrence patterns among the three regions. Our results highlight the role of spatial features associated with human activity in structuring environmental factors and then driving bacterial distribution patterns in the South China Sea.IMPORTANCECurrent research on the assembly processes of environmental bacterial communities at broader scales, such as the thousand-kilometer scale and highly connected marine habitats, remains limited. The South China Sea is the largest marginal sea in the western Pacific Ocean, exhibiting significant spatial heterogeneity across broader scales from densely human-activity coastal areas to the open ocean. Our findings reveal that the assembly mechanisms of bacterial communities along the thousand-kilometer scale from the coastal areas of the South China Sea to its western regions are dominated by homogeneous selection. Additionally, we discovered that spatial heterogeneity, by structuring local environmental gradients, plays a leading role in shaping the community structure, distribution patterns, and co-occurrence networks of surface water bacteria in the South China Sea. This study enhances the understanding of assembly mechanisms at broader scales and deepens the comprehension of the impact of spatial heterogeneity on bacterial communities.