Function-driven analytical strategies for identifying contaminants of emerging concern-degrading bacteria: From enrichment cultures to single-cell technologies.

Ecosystems worldwide are subjected to the widespread of occurrence and contamination of contaminants of emerging concern (CECs). In response, microbial degradation has emerged as a potent and sustainable countermeasure. While specific CEC-degrading bacteria have been documented, a comprehensive overview of advanced, function-driven discovery strategies remains fragmented. Unlike existing reviews that emphasize either omics-based inference or enrichment-based isolation, this review synthesizes the latest progress in the isolation of CEC-degrading bacteria analytical pipelines, emphasizing the shift from traditional enrichment-based approaches to integrated, multi-technological, single-cell level frameworks. Moreover, a novel approach that connects culture-dependent and culture-independent techniques is elucidated. We critically discuss the synergistic potential of molecular and analytical tools, including fluorescence in situ hybridization (FISH), stable isotope probing (SIP), and Raman spectroscopy activated cell sorting (RACS). Particular attention is given to the necessity of linking microbial genotypic identity to specific spectroscopic signatures and metabolic indicators to confirm biodegradation activity. Furthermore, the future prospects of the rapid identification of CEC-degrading bacteria and their application in CEC bioremediation are outlined. By consolidating contemporary analytical frameworks, this review offers a strategic benchmark based on spectral features and microbial metabolic characteristics for accelerating the discovery and isolation of CEC-degrading microbes in complex environmental matrices.