Abstract: Three single cell microorganisms with extracellular polymeric substances (Rhizobium sp., G-01; Enterobacter sp., San8; and Rhodotorula mucilaginosa, R1) were studied, and the maximum periods of extracellular polymeric substances (EPS) production were determined by measuring their growth curves. The contents of polysaccharide and protein in EPS were determined by phenol-sulfuric acid method and BCA (bicinchoninic acid) protein concentration detection kit. The group composition of EPS was analyzed through infrared spectroscopy. The effects of single cell and filamentous microorganisms on the formation of aggregates were studied in a soil culture experiment, and a pot experiment was carried out to verify the effect of plant roots on soil aggregate composition in the pot experiment where different type microbes were inoculated from soil culture experiment. The results showed that the EPS contents secreted by three strains of single cell microorganisms (strain G-01, San8 and R1) were 2.12 mg (10¹⁰ cells)⁻¹, 0.56 mg (10¹⁰ cells)⁻¹ and 172.71 mg (10¹⁰ cells)⁻¹, respectively. The EPS components were mainly made of polysaccharide and protein, and the content of polysaccharide was higher than that of protein. Infrared spectra analysis showed that EPS of three strains contained many characteristic functional groups of polysaccharide and protein such as hydroxyl, carboxyl, carbonyl and polysaccharides, etc. Soil culture experiments showed that the percentages of soil macroaggregates (> 0.25 mm) in the treatment of EPS secreted by single cell microorganism were increased by 71.31% compared with those of filamentous microorganism. Compared with soil culture experiment, the proportion of macroaggregates (> 0.25 mm) in each treatment was significantly increased in the pot experiment, and the root extrusion and root exudates also promoted the formation and stability of soil macroaggregates.