Extracellular polymeric substances (EPS) were quantified in flocculent and aerobic granular sludge developed in two sequencing batch reactors with the same shear force but different settling times. Several EPS extraction methods were compared to investigate how different methods affect EPS chemical characterization, and fluorescent stains were used to visualize EPS in intact samples and 20-m cryosections. Reactor 1 (operated with a 10-min settle) enriched predominantly flocculent sludge with a sludge volume index (SVI) of 120 ؎ 12 ml g ؊1 , and reactor 2 (2-min settle time) formed compact aerobic granules with an SVI of 50 ؎ 2 ml g ؊1 . EPS extraction by using a cation-exchange resin showed that proteins were more dominant than polysaccharides in all samples, and the protein content was 50% more in granular EPS than flocculent EPS. NaOH and heat extraction produced a higher protein and polysaccharide content from cell lysis. In situ EPS staining of granules showed that cells and polysaccharides were localized to the outer edge of granules, whereas the center was comprised mostly of proteins. These observations confirm the chemical extraction data and indicate that granule formation and stability are dependent on a noncellular, protein core. The comparison of EPS methods explains how significant cell lysis and contamination by dead biomass leads to different and opposing conclusions.The efficiency of biological wastewater treatment depends, first, upon the selection and growth of metabolically capable microorganisms and, second, upon the efficient separation of those organisms from the treated effluent. Bacteria usually aggregate to form suspended flocs, which can cause bulking and foaming problems if filamentous bacteria are present. Activated sludge flocs also settle relatively slowly, requiring large primary and secondary settling tanks before clear effluent can be released. Alternatively, aerobic granular sludge aggregates have been formed in sequencing batch reactors (SBRs) with short fill periods and various substrates (1a, 13, 15). As opposed to flocs, granules are dense and have high settling velocities. They can be described as a collection of self-immobilized cells into a somewhat spherical form and are considered to be a special case of biofilm growth (10).Microbial aggregates form biofilms by creating a network of cells and extracellular polymeric substances (EPS), which include any substances of biological origin (9). The abbreviation "EPS" has often been expanded to extracellular polysaccharides or exopolysaccharides. However, EPS have been shown to be a rich matrix of polymers, including polysaccharides, proteins, glycoproteins, nucleic acids, phospholipids, and humic acids. EPS are typically reported to aid in the formation of a gel-like network that keeps bacteria together in biofilms, cause the adherence of biofilms to surfaces, and protect bacteria against noxious environmental conditions (24).Because EPS are a major component of cell flocs and biofilms, they are hypothesized to play a central ...