Biomolecules for OMIC analysis of microbial communities are commonly extracted by bead-beating or ultra-sonication, but both showed varying yields. In addition to that, different disruption pressures are necessary to lyse bacteria and fungi. However, the disruption efficiency and yields comparing bead-beating and ultra-sonication of different biological material have not yet been demonstrated. Here, we show that ultra-sonication in a bath transfers three times more energy than bead-beating over 10 min. TEM imaging revealed intact gram-positive bacterial and fungal cells whereas the gram-negative bacterial cells were destroyed beyond recognition after 10 min of ultra-sonication. DNA extraction using 10 min of bead-beating revealed higher yields for fungi but the extraction efficiency was at least three-fold lower considering its larger genome. By our critical viewpoint, we encourage the review of the commonly used extraction techniques as we provide evidence for a potential underrepresentation of resistant microbes, particularly fungi, in ecological studies.

• MeSH
• Bacteria genetika   MeSH
• bakteriální léková rezistence genetika   MeSH
• bakteriální proteiny chemie   izolace a purifikace   MeSH
• DNA bakterií genetika   MeSH
• DNA chemie   izolace a purifikace   MeSH
• fungální léková rezistence genetika   MeSH
• fungální proteiny chemie   izolace a purifikace   MeSH
• houby genetika   MeSH
• mikrosféry MeSH
• vibrace ultrazvukové metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• bakteriální proteiny MeSH
• DNA bakterií MeSH
• DNA MeSH
• fungální proteiny MeSH