show Abstracthide AbstractFungi as an efficient technique to flocculate C .vulgaris can effectively form fungi-microalgal aggregates and facilitate the resource utilization of microalgae. In this study, the efficiency, characteristics and the optimal parameters of flocculation of flocculating fungi that isolated from a municipal wastewater treatment plant (MWWTP) were evaluated. The flocculants were analyzed by metabolomics and flocculation process and mechanisms were analyzed through transcriptomics. The results showed that Alternaria alternata J-28 was a strain of flocculating fungi with flocculation efficiency up to 97% within 30 min. The optimal flocculation parameters were the mycelium pellets dosage of 2.5 g/L and the F-supernatant volume of 150 mL/L at 140 rpm. It was observed that the network structure of mycelium facilitated C. vulgaris flocculation, while the natural flocculants such as N-Acetyl-D-Phenylalanine, N-Acetyl-L-Tyrosine, and N-Acetyl-D-Tryptophan, etc. were secreted by Alternaria alternata J-28. The synthesis of these natural flocculants that had no effects on the growth of C. vulgaris was regulated by multiple pathways such as signal transduction, amino acid metabolism, carbohydrate metabolism, cofactors and vitamins metabolism, membrane transport, etc. Alternaria alternata J-28 flocculated C. vulgaris with high efficiency, offered reference for developing new symbiotic bacteria-algae wastewater treatment technologies.