Scale-Dependent Structuring of Sediment Bacterial Communities on Coral Reefs

Sediment-associated microbiomes play key roles in coral reef biogeochemistry, yet the drivers of their spatial variability in tropical reef systems remain poorly understood. We characterised sediment bacterial communities from lagoonal habitats surrounding coral patch reefs at One Tree Island using 16S rRNA gene metabarcoding. We assessed lagoon-scale variation across 21 sites and examined microhabitat differences at 13 sites to evaluate the influence of spatial and environmental drivers, including distance from the island, sediment granulometry and nutrient composition. Sediment bacterial communities were strongly structured by spatial context, with site-level variation exceeding microhabitat effects. Environmental gradients, particularly nutrient availability and distance-related spatial structure, contributed to sediment bacterial communities, while microhabitat differences were present but comparatively weak and inconsistent. Although overall alpha diversity remained stable across reef zones, compositional differences were driven by shifts in the relative abundance of specific taxa. Sediment communities were also more diverse than adjacent seawater and contained a substantially higher proportion of habitat-exclusive taxa, highlighting strong environmental filtering between benthic and pelagic systems. These findings demonstrate that coral reef sediment microbiomes are highly structured across lagoonal scales, and highlight the importance of spatial replication in reef microbiome studies. The results provide a valuable baseline for understanding bacterial community responses to future environmental change.