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Title: Incomplete cell disruption of resistant microbes

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.

Authors:
 [1]; ORCiD logo [2];  [3];  [3];  [3]; ORCiD logo [3]; ORCiD logo [4]
  1. Institute of Microbiology of the CAS, Praha (Czech Republic). Lab. of Environmental Microbiology; Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
  2. Helmholtz-Center for Environmental Research, UFZ, Leipzig (Germany)
  3. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
  4. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL); Iowa State Univ., Ames, IA (United States)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1558408
Report Number(s):
PNNL-SA-141081
Journal ID: ISSN 2045-2322
Grant/Contract Number:  
AC05-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English

Citation Formats

Starke, Robert, Jehmlich, Nico, Alfaro, Trinidad D., Dohnalkova, Alice, Capek, Petr, Bell, Sheryl L., and Hofmockel, Kirsten S. Incomplete cell disruption of resistant microbes. United States: N. p., 2019. Web. doi:10.1038/s41598-019-42188-9.
Starke, Robert, Jehmlich, Nico, Alfaro, Trinidad D., Dohnalkova, Alice, Capek, Petr, Bell, Sheryl L., & Hofmockel, Kirsten S. Incomplete cell disruption of resistant microbes. United States. doi:10.1038/s41598-019-42188-9.
Starke, Robert, Jehmlich, Nico, Alfaro, Trinidad D., Dohnalkova, Alice, Capek, Petr, Bell, Sheryl L., and Hofmockel, Kirsten S. Thu . "Incomplete cell disruption of resistant microbes". United States. doi:10.1038/s41598-019-42188-9. https://www.osti.gov/servlets/purl/1558408.
@article{osti_1558408,
title = {Incomplete cell disruption of resistant microbes},
author = {Starke, Robert and Jehmlich, Nico and Alfaro, Trinidad D. and Dohnalkova, Alice and Capek, Petr and Bell, Sheryl L. and Hofmockel, Kirsten S.},
abstractNote = {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.},
doi = {10.1038/s41598-019-42188-9},
journal = {Scientific Reports},
number = 1,
volume = 9,
place = {United States},
year = {2019},
month = {4}
}

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