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Total DNA extraction is the key stage allowing the implementation of various downstream applications in molecular ecology. The widespread application of downstream technologies has led to an increasing demand for highly pure biomolecules. Manual methods and proprietary extraction kits used for the purification of nucleic acids can be laborious and time‐consuming. The breadth of sample types encountered and the increasing number of samples processed result in seeking new ways to enhance sample preparation efficiency and reliability. Representativeness, sensitivity and reproducibility are essential requirements for such an extraction technique that should be applied in a high throughput mode.