Divergent assembly patterns of core and non-core microbial taxa under low environmental heterogeneity in the surface waters of the Xisha Islands

Microbial communities play essential roles in marine biogeochemical cycling, yet the respective roles of environmental and spatial drivers of community assembly remain incompletely understood, particularly under low environmental heterogeneity and across distinct microbial subcommunities. We investigated microbial communities from 39 surface-water samples collected across the Xisha Islands (South China Sea) by distinguishing core and non-core taxa to assess associations of environmental gradients and geographic distance with community composition, assembly, and predicted functional potential. Physicochemical conditions varied narrowly (temperature 29.5°C-31.5°C; salinity 30.47%-30.93%, pH 7.85-8.22), reflecting low environmental heterogeneity. Core taxa comprised 1.15% of richness and contributed >50% of total abundance, whereas non-core taxa accounted for 98.85% of richness and disproportionately structured the co-occurrence network. Environmental variables (particularly temperature and pH) together with geographic distance were significantly associated with community composition, with variation partitioning revealing a relatively greater spatial component in non-core communities, consistent with their stronger spatial structuring (distance-decay slopes: -0.118 vs -0.061 for core taxa). Assembly analyses revealed contrasting patterns: core-community comparisons were classified as dispersal limitation, whereas non-core comparisons were primarily associated with homogeneous selection (46.96%) and dispersal limitation (45.21%). Predicted community functional structure was primarily associated with temperature, pH, and redox conditions. These findings suggest that environmental gradients and geographic distance are associated with microbial community composition, assembly, and predicted functional potential in marine environments with low environmental heterogeneity, and core and non-core taxa exhibit contrasting assembly patterns. This study highlights the importance of considering microbial subcommunities when investigating community assembly in marine ecosystems.IMPORTANCEMicrobial communities play fundamental roles in marine biogeochemical cycling. However, most understanding of microbial community assembly derives from systems with strong environmental gradients or large spatial scales, where pronounced heterogeneity may obscure subtle ecological processes. This bias limits our understanding of microbial community assembly and functional potential in relatively stable marine environments, where subtle environmental and spatial gradients may still exert important influences. In addition, whether microbial groups with contrasting occurrence patterns respond differently to these processes remains insufficiently evaluated. This study shows that, despite the relatively low environmental heterogeneity of tropical marine surface waters in the Xisha Islands, environmental gradients (particularly temperature and pH) and geographic distance remain associated with microbial community composition, assembly, and predicted functional potential. In addition, core and non-core taxa exhibited contrasting assembly patterns. Our findings provide a framework for understanding microbial community assembly by considering core and non-core subcommunities separately.