Defining Site-Specific Water Quality Guidelines for Marine Microbiomes under Contaminant Stress

Marine ecosystem resilience is closely linked to microbiome health, yet prokaryotes are typically overlooked in conservation management due to challenges in quantitatively defining microbial sensitivity thresholds. This study introduces a novel approach that combines 16S rRNA gene amplicon sequencing with ecotoxicological concentration–response modeling to assess marine microbial responses to contamination stress at both community and taxon levels. By applying propidium monoazide to differentiate intact from membrane-compromised cells combined with normalization of relative to absolute abundances via flow cytometry, no-significant-effect concentration values can be derived from individual taxon-specific stress–response curves. These thresholds inform prokaryotic sensitivity distributions, enabling the derivation of microbiome hazard concentrations that estimate the contaminant concentrations affecting x% of the microbial communitya metric fully compatible with existing eukaryotic datasets and regulatory frameworks. Applied to seawater microbiomes exposed to copper along a disturbance gradient, higher copper sensitivities were observed in microbiomes from ecologically valuable sites, such as coral reefs, compared to disturbed areas. The site-specific microbiome hazard concentrations for copper affecting 5% of community taxa ranged from 0.10 to 0.94 μg L–1, highlighting the need for stricter environmental protection of ecologically valuable sites. This quantitative approach provides a robust pathway for direct integration of site-specific microbiome sensitivity data into environmental risk assessments.