Abstract
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.
Highlights
Finding efficient cell disruption techniques is crucial to various scientific fields
Differential resistance during cell disruption can bias the extraction of biomolecules towards easy-to-lyse microbes, which can skew the previously estimated microbiome compositions, ranging from the human gut[7] to forest soil ecosystems[8]
These differences in resistance could derive from differences in the cell wall chemistry since muramic acid exclusively occurs in bacterial cell walls[9,10] whereas fungal cell walls are the dominant source of glucosamine[9] or from the varying degrees of cell aggregates in fungi to shield individual cells from the disruption treatment[11]
Summary
Robert Starke[1,2], Nico Jehmlich 3, Trinidad Alfaro[1], Alice Dohnalkova[1], Petr Capek 1, Sheryl L. Ultra-sonication in a bath for 10 min revealed a strong resistance of the fungal and the gram-positive bacterial enrichment culture, both remained almost intact, whereas no intact cells could be found in the gram-negative bacterial enrichment culture after identical treatment, suggesting complete cell disruption beyond recognition (Figs 2 and S2–4). This could be the reason for the underrepresentation of resistant microbes, fungi, in ecological studies[15,16,17] that might skew microbiomes of various nature towards easy-to-lyse microbes.
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