Emerging contaminants shift the rare biosphere, decoupling microbial co-occurrence network complexity from stability...

Urban wastewater treatment plants are critical nodes for both removal and discharge of emerging contaminants (ECs). However, how evolving chemical fingerprints during biological treatment influence microbial community assembly and ecological networks remains poorly understood. Here, high-resolution mass spectrometry-based non-target screening (NTS) and high-throughput sequencing were integrated to investigate coupling mechanisms between EC migration/transformation and microbial community dynamics in a typical anaerobic/anoxic/aerobic (A²/O) system. NTS identified 2609 chemical features exhibiting marked stage-specific removal and transformation patterns along the treatment train. Microbial selection pressure primarily arose from degradation of specific compound classes, including lipids and organic acids, together with accumulation of transformation intermediates. EC chemical diversity significantly altered community assembly, exerting asynchronous effects on distinct sub-communities. Abundant biospheres were mainly governed by stochastic drift (76.45%-100%), whereas rare biospheres were dominated by strong homogeneous selection driven by ECs (36.60%-63.77%), highlighting the critical role of rare taxa in responding to chemical stress. Partial least squares path modelling further showed that efficient EC removal increased microbial co-occurrence network complexity, fostering inter-species interactions associated with synergistic metabolism. However, this increased complexity did not enhance system stability and may increase system vulnerability through over-specialisation. Overall, this study establishes an integrated assessment framework combining chemical fingerprinting with community assembly theory, highlights the central role of the rare biosphere in contaminant biotransformation, and emphasises the need to synchronously evaluate transformation products and microbial ecosystem robustness in wastewater-treatment risk assessment.