Biological treatments have been widely applied to remove wastewater nutrients, while single biological treatment is insufficient to achieve desired efficiency. Moving beyond removal of nutrient, equivalent focus on ecological consequences and biotic pollutants (e.g., pathogens) along the decontamination procedures is lacking. Herein, we established an efficient biological treatment system by integrating biofilm, shellfish and Spartina, which efficiently reduced the levels of wastewater nutrients (> 62.7 %) and sediment antibiotics (> 84.6 %) before discharge, with unsatisfied removal of total phosphorus and diversified potential pathogens. Our biological treatments potentiated C storage and ammoxidation process, and mitigated CH4 emission, of which are conjointly governed by the direct effect of nutrient pollutions and the indirect effect of antibiotics. In contrast, denitrification potential in wastewater and sediment was divergent, resulting in an uncertainty on net N2O emission. We identified diverse ammonia-oxidizing bacteria assistors that were candidates for improving ammoxidation. Intriguingly, bacterial biomakers could quantitatively and accurately diagnose wastewater entropy water quality index and sediment multi-nutrient cycling index, with overall 81.9 % and 91.1 % accuracy, respectively. The combined biological treatments can be a double-edged sword between water quality improvement and mitigating pathogenicity. These findings greatly deepen our understanding of the biological and ecological consequences of a biofilm-shellfish-phytoremediation system, and accordingly some strategies are informed for improving decontamination efficiency.
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