Mix tank effluent samples (10 mL in a 15 mL conical tube) were collected once daily. Samples were diluted to approximately 1x10 6 particles per milliliter prior to running on a FlowCam 5000 flow imaging microscope (Yokogawa Fluid Imaging Technologies, Inc.). The resulting collection of detected particles was screened to remove background objects, then used as input data fora deep learning classification model trained on representative libraries of the dominant taxonomic groups observed in the system. Details are in SI Section S5.