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.

Department of Ecology Evolution and Organismal Biology Iowa State University Iowa USA

Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Richland Washington USA

Helmholtz Center for Environmental Research UFZ Leipzig Germany

Laboratory of Environmental Microbiology Institute of Microbiology of the CAS Praha Czech Republic

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Brown, M. R., Jeffrey, S. W., Volkman, J. K. & Dunstan, G. A. Nutritional properties of microalgae for mariculture. In Aquaculture10.1016/S0044-8486(96)01501-3 (1997).

Halim, R., Danquah, M. K. & Webley, P. A. Extraction of oil from microalgae for biodiesel production: A review. Biotechnology Advances10.1016/j.biotechadv.2012.01.001 (2012). PubMed

Halim, R., Rupasinghe, T. W. T., Tull, D. L. & Webley, P. A. Mechanical cell disruption for lipid extraction from microalgal biomass. Bioresour. Technol. 10.1016/j.biortech.2013.04.067 (2013). PubMed

Lee, I. & Han, J. I. Simultaneous treatment (cell disruption and lipid extraction) of wet microalgae using hydrodynamic cavitation for enhancing the lipid yield. Bioresour. Technol. 10.1016/j.biortech.2015.03.045 (2015). PubMed

Balasundaram, B. & Pandit, A. B. Selective release of invertase by hydrodynamic cavitation. Biochem. Eng. J. 10.1016/S1369-703X(01)00114-0 (2001).

Kelemen, M. V. & Sharpe, J. E. Controlled cell disruption: a comparison of the forces required to disrupt different micro-organisms. J. Cell Sci. (1979). PubMed

Sommer, F. & Bäckhed, F. The gut microbiota-masters of host development and physiology. Nature Reviews Microbiology, 10.1038/nrmicro2974 (2013). PubMed

Hartmann, M. et al. Resistance and resilience of the forest soil microbiome to logging-associated compaction. ISME J. 10.1038/ismej.2013.141 (2014). PubMed PMC

Appuhn, A., Joergensen, R. G., Raubuch, M., Scheller, E. & Wilke, B. The automated determination of glucosamine, galactosamine, muramic acid, and mannosamine in soil and root hydrolysates by HPLC. J. Plant Nutr. Soil Sci. 10.1002/jpln.200321302 (2004).

Millar, W. N. & Casida, L. E. Jr. Evidence for muramic acid in soil. Can. J. Microbiol. 10.1139/m70-054 (1970). PubMed

Beck, A., Hunt, K. & Carlson, R. Measuring Cellular Biomass Composition for Computational Biology Applications. Processes10.3390/pr6050038 (2018).

Wendt, J. F. et al. Computational fluid dynamics: An introduction. Computational Fluid Dynamics10.1007/978-3-540-85056-4 (2009).

Suslick, K. S. Sonochemistry. Science, 10.1126/science.247.4949.1439 (1990). PubMed

Suslick, K. S. The Chemical Effects of Ultrasound. Sci. Am. 10.1038/scientificamerican0289-80 (1989).

Bastida, F. et al. Differential sensitivity of total and active soil microbial communities to drought and forest management. Glob. Chang. Biol. 23, (2017). PubMed

Bastida, F. et al. The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon availability in Mediterranean semi-arid soils. Mol. Ecol. 25 (2016). PubMed

Starke, R. et al. Ecological and functional adaptations to water management in a semiarid agroecosystem: A soil metaproteomics approach. Sci. Rep. 7 (2017). PubMed PMC

Kunst, F. et al. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature, 10.1038/36786 (1997). PubMed

Kaneko, T. et al. Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res. 10.1093/dnares/9.6.189 (2002). PubMed

Galagan, J. E. et al. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature, 10.1038/nature04341 (2005). PubMed

Koonin, E. V. The Logic of Chance: The Nature and Origin of Biological Evolution. Biometrika, 10.2307/2334241 (2011).

Duiker, S. W., Rhoton, F. E., Torrent, J., Smeck, N. E. & Lal, R. Iron (Hydr)Oxide Crystallinity Effects on Soil Aggregation. Soil Sci. Soc. Am. J, 10.2136/sssaj2003.6060 (2003).

Rillig, M. C. & Mummey, D. L. Mycorrhizas and soil structure. New Phytologist, 10.1111/j.1469-8137.2006.01750.x (2006). PubMed

Baldock, J. A. & Skjemstad, J. O. Role of the soil matrix and minerals in protecting natural organic materials against biological attack. in Organic Geochemistry, 10.1016/S0146-6380(00)00049-8 (2000).

Subba Rao, N. S. Soil microorganisms and plant growth. (Oxford and IBH Pub. Co. 1977).

Gray, M. L., Stafseth, H. J. & Thorp, F. The use of potassium tellurite, sodium azide, and acetic acid in a selective medium for the isolation of Listeria monocytogenes. J. Bacteriol. (1950). PubMed PMC

Warcup, J. H. & Baker, K. F. Occurrence of dormant ascospores in soil. Nature, 10.1038/1971317a0 (1963).

Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning: A Labortaroy Manual. Society. 1989 doi: 10.1128/AEM.68.3.1232. DOI

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