Hydrochloric acid, acetyl chloride and boron trifluoride have been tested as the acid catalysts for direct esterification/transesterification and consequent gas chromatographic determination of the total fatty acid content in cyanobacteria and algae. Acetyl chloride resulted to be the most efficient and was applied for the analysis of freshwater cyanobacteria Aphanizomenon flos-aquae, Planktothrix agardhii and green algae Monoraphidium griffithii, Scenedesmus acutus. All tested species contained significant quantities of palmitic acid and α-linolenic acid. The oleic acid and linoleic acid occurred in the highest amounts in green algae M. griffithii and S. acutus.

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