Molecular bioindicators for assessing environmental impacts of emerging contaminants

Emerging contaminants (ECs) exert subtle yet persistent pressures on environmental systems, often escaping detection by traditional chemical or ecological monitoring. Molecular bioindicators, i.e., genes, enzymes, or pathways whose presence, abundance, or expression reflects contaminant exposure or biological stress, offer a mechanistic basis to trace pollutant fate and functional disruption. These include degradation and transformation genes reflecting detoxification potential, resistance and adaptation genes such as antimicrobial resistance determinants, and toxicity-response genes indicating metabolic or physiological stress across microbial and higher organisms. Although numerous functional genes and pathways associated with ECs have been identified and increasingly explored in environmental studies, their interpretation as molecular bioindicators remains fragmented, with limited standardization in bioindicator selection, sensitivity evaluation, and cross-system validation. This review synthesizes current methodologies for molecular bioindicator discovery, spanning culture-dependent functional assays, strain-level genomics, and community-scale omics integration, and highlights how combining mechanistic verification with data-driven approaches can enhance interpretability and transferability. To facilitate consistent validation and reuse, we further propose a structured, community-curated database linking contaminants, molecular bioindicator types, ecological contexts, and evidence tiers. By linking molecular responses to contaminant stress with measurable ecological outcomes, molecular bioindicators can offer a mechanistically grounded basis for interpreting EC impacts and support more integrative and evidence-based environmental risk assessment.