Urbanisation reshapes community assembly differently across coastal beach and dune habitats

Coastal beach and dune ecosystems face increasing urban pressures, but the links between urbanisation, community composition, and the processes structuring species distributions often remain unclear. We analysed fauna from 660 sediment cores across four habitat zones (established dunes, incipient dunes, upper intertidal, lower intertidal) along the Dutch North Sea coast using environmental DNA metabarcoding and joint species distribution models (JSDMs) to characterise communities and infer assembly patterns. Across all habitats, beta diversity was dominated by species turnover rather than nestedness, indicating reassembly of communities through species replacement rather than species loss. Turnover was significantly associated with urbanisation and environmental gradients, with the strongest effects in incipient dune habitats, but assembly responses differed by habitat. In dune zones, local anthropogenic disturbance was associated with weaker environmental filtering and stronger species co-distribution, while greater distance from the city centre (more remote sites) generally corresponded to stronger environmental filtering. In contrast, environmental filtering remained the dominant factor in the intertidal, where hydrodynamic influences are more important than local urban impacts and increased at more remote sites. Analysis of OTU-level responses identified candidate taxa for tolerance and sensitivity to urban stressors, highlighting the potential of combining eDNA with JSDMs for bioindicator development. Overall, our results demonstrate that urbanisation changes not only which species occur where, but also the environmental, spatial, and biotic processes structuring beach and dune communities. These findings show the need for habitat-specific management that protects both biodiversity and the ecological patterns that sustain it in urban coastal systems.