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Extracellular polymeric substances (EPS) play an important role in bacterial mat formation and sediment stabilisation of coastal zones. The analysis of these secretion products on a molecular level is a prerequisite to understand their formation mechanisms and ecological function in microbial consortia. The present study focuses on the optimisation of EPS isolation and characterisation from cohesive cyanobacterial mats. Extracted EPS were analysed for quantity, content of total organic carbon and nitrogen, and bulk contents of neutral sugars, uronic acids, and proteins. These criteria are strongly influenced by the extraction conditions applied and therefore, the effects of different extraction media (NaCl or artificial seawater), addition of EDTA, centrifugal force, and purification via repeated ethanol precipitation on extraction success were determined. From this an optimised extraction procedure for EPS resulted. When using fresh mat samples, the yield of EPS amounted to 3.3 ± 0.8 mg g−1 mat (dw). The isolated EPS were composed of nearly equal amounts of proteins and uronic acids (12.7 ± 1.5 and 11.8 ± 1.1%, respectively) and the bulk content of neutral sugars was 30.5 ± 2.6%. High contents of TOC and TN indicated relatively pure EPS and only a low contribution of inorganic compounds. Furthermore, low contents of 2-keto-3-deoxyoctonate and the small protein/polysaccharide-ratio in the EPS extracted by our method, signified low contaminations by intracellular polymers and hence a low rupture of cells. Our method provides an useful tool to evaluate further investigations of the composition, characteristics and properties of EPS on a sound basis. [ABSTRACT FROM AUTHOR]