Identification of functional microorganisms and genes mediating ciprofloxacin degradation in dynamic habitats of algal bloom decomposition.

Decay of algal blooms in eutrophic lakes generates detritus-rich, redox-dynamic microhabitats that modulate the degradation of emerging pollutants as antibiotics. The degradation pathways of antibiotics within algal-detritus accumulation zones and the associated microbial assimilators remain insufficiently understood. In this study, localized algal bloom decay zones were simulated using static lake microcosms, and DNA-stable isotope probing (DNA-SIP) combined with metagenomic analysis were employed to elucidate ciprofloxacin (CIP) degradation pathways and to identify microorganisms potentially involved in CIP assimilation under elevated CIP exposure. Results demonstrate that ecological succession linked to algal decomposition was closely synchronized with CIP degradation, which primarily proceeded via defluorination, decarboxylation, and piperazine ring modification. The bottom detritus layer showed enrichment of aromatic compound-degrading bacteria, including Hydrogenophaga, Reyranella, and Rhodoblastus, in heavy DNA fractions, indicating their potential role in CIP assimilation. This layer also contained functional genes associated with benzoate, halogenated aromatic compounds, and polycyclic aromatic hydrocarbon degradation pathways. In addition, enrichment of the AAC(6')-Ib-cr gene family in the bottom layer coincided with detection of N-acetylated CIP products, suggesting a possible acetylation-mediated inactivation mechanism. Collectively, the study identified candidate microorganisms and genes linked to CIP-derived assimilation and degradation in algal-detritus-rich microhabitats, providing mechanistic insights into antibiotic degradation in polluted algal decay hotspots.