Abstract:

Coastal microbial communities respond rapidly to environmental change, making them promising taxonomic and functional indicators of ecosystem condition and anthropogenic disturbance. However, coastal waters are inherently dynamic and heterogeneous, being shaped by interacting environmental processes and pronounced differences between free-living and particle-associated microhabitats. Conventional environmental assessments often characterize whole-water or sediment samples without resolving microhabitat structures. This approach may obscure habitat-specific microbial responses and reduce their interpretability as indicators of environmental change. Here, we assessed how anthropogenic pressure shaped coastal microbial communities across three microhabitats and four seasons in two contrasting Hong Kong embayments: highly impacted Deep Bay and less impacted Ko Lau Wan. Analysis of 16S rRNA gene amplicons identified microhabitat as the strongest determinant of community variation. After accounting for hydrodynamics, season and microhabitat, a broad sets of contaminants, including trace metals, nutrients, pharmaceuticals, PFAS and chlorinated paraffins, explained only 4.6% of community variations. Inferred functional profiles showed enrichment of metal-stress-related pathways in Deep Bay, whereas other pollution-associated functions, including antibiotic resistance, showed no clear differences between two bays. The moderate concordance between taxonomic composition and inferred functional potential indicates that these measures capture complementary dimensions of ecosystem response. These findings suggest that microbial bioassessment in dynamic coastal waters should explicitly account for microhabitat variations and independently validate taxonomic and functional metrics before combining them into an integrated indicator system.