Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples [Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay subsoil]
Abstract
Here we show that a commercial blocking reagent (G2) based on modified eukaryotic DNA significantly improved DNA extraction efficiency. We subjected G2 to an inter-laboratory testing, where DNA was extracted from the same clay subsoil using the same batch of kits. The inter-laboratory extraction campaign revealed large variation among the participating laboratories, but the reagent increased the number of PCR-amplified16S rRNA genes recovered from biomass naturally present in the soils by one log unit. Furthermore, an extensive sequencing approach demonstrated that the blocking reagent was free of contaminating DNA, and may therefore also be used in metagenomics studies that require direct sequencing.
- Authors:
-
[4];
[6];
more »
- Univ. of Aaruhus, Roskilde (Denmark); Geological Survey of Denmark and Greenland, Copenhagen (Denmark)
- Univ. of Copenhagen, Frederiksberg (Denmark); NovoZymes A/S, Copenhagen (Denmark)
- Univ. of Copenhagen, Frederiksberg (Denmark)
- Aalborg Univ., Aalborg (Denmark)
- Academy of Sciences of the Czech Republic, Bron (Czech Republic); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Univ. of Aaruhus, Roskilde (Denmark)
- Academy of Sciences of the Czech Republic, Bron (Czech Republic)
- Norwegian Univ. of Life Sciences, As (Norway)
- Univ. of Aarhus, Aarhus (Denmark); NIRAS A/S, Aarhus (Denmark)
- The Arctic Univ. of Norway, Tromso (Norway)
- Thunen-Institut fur Biodiversitat, Braunschweig (Germany)
- Univ. of Bergen, Bergen (Norway)
- Geological Survey of Denmark and Greenland, Copenhagen (Denmark)
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Uppsala Univ., Uppsala (Sweden)
- Univ. of Waikato, Hamilton (New Zealand)
- Univ. of Montana, Missoula, MT (United States)
- Univ. of Copenhagen, Copenhagen (Denmark)
- Geological Survey of Denmark and Greenland, Copenhagen (Denmark); Chr Hansen A/S, Horsholm (Denmark)
- Publication Date:
- Research Org.:
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Sponsoring Org.:
- USDOE National Nuclear Security Administration (NNSA)
- OSTI Identifier:
- 1474353
- Report Number(s):
- LLNL-JRNL-738627
Journal ID: ISSN 2045-2322; 891928
- Grant/Contract Number:
- AC52-07NA27344
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Scientific Reports
- Additional Journal Information:
- Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 2045-2322
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Jacobsen, Carsten Suhr, Nielsen, Tue Kjærgaard, Vester, Jan Kjølhede, Stougaard, Peter, Nielsen, Jeppe Lund, Voriskova, Jana, Winding, Anne, Baldrian, Petr, Liu, Binbin, Frostegård, Åsa, Pedersen, Dorthe, Tveit, Alexander Tøsdal, Svenning, Mette Marianne, Tebbe, Christoph C., Øvreås, Lise, Jakobsen, Pia Bach, Blazewicz, Steven J., Hubablek, Valerie, Bertilsson, Stefan, Hansen, Lars Hestbjerg, Cary, S. Craig, Holben, William E., Ekelund, Flemming, and Bælum, Jacob. Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples [Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay subsoil]. United States: N. p., 2018.
Web. doi:10.1038/s41598-018-24082-y.
Jacobsen, Carsten Suhr, Nielsen, Tue Kjærgaard, Vester, Jan Kjølhede, Stougaard, Peter, Nielsen, Jeppe Lund, Voriskova, Jana, Winding, Anne, Baldrian, Petr, Liu, Binbin, Frostegård, Åsa, Pedersen, Dorthe, Tveit, Alexander Tøsdal, Svenning, Mette Marianne, Tebbe, Christoph C., Øvreås, Lise, Jakobsen, Pia Bach, Blazewicz, Steven J., Hubablek, Valerie, Bertilsson, Stefan, Hansen, Lars Hestbjerg, Cary, S. Craig, Holben, William E., Ekelund, Flemming, & Bælum, Jacob. Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples [Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay subsoil]. United States. doi:https://doi.org/10.1038/s41598-018-24082-y
Jacobsen, Carsten Suhr, Nielsen, Tue Kjærgaard, Vester, Jan Kjølhede, Stougaard, Peter, Nielsen, Jeppe Lund, Voriskova, Jana, Winding, Anne, Baldrian, Petr, Liu, Binbin, Frostegård, Åsa, Pedersen, Dorthe, Tveit, Alexander Tøsdal, Svenning, Mette Marianne, Tebbe, Christoph C., Øvreås, Lise, Jakobsen, Pia Bach, Blazewicz, Steven J., Hubablek, Valerie, Bertilsson, Stefan, Hansen, Lars Hestbjerg, Cary, S. Craig, Holben, William E., Ekelund, Flemming, and Bælum, Jacob. Mon .
"Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples [Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay subsoil]". United States. doi:https://doi.org/10.1038/s41598-018-24082-y. https://www.osti.gov/servlets/purl/1474353.
@article{osti_1474353,
title = {Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples [Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay subsoil]},
author = {Jacobsen, Carsten Suhr and Nielsen, Tue Kjærgaard and Vester, Jan Kjølhede and Stougaard, Peter and Nielsen, Jeppe Lund and Voriskova, Jana and Winding, Anne and Baldrian, Petr and Liu, Binbin and Frostegård, Åsa and Pedersen, Dorthe and Tveit, Alexander Tøsdal and Svenning, Mette Marianne and Tebbe, Christoph C. and Øvreås, Lise and Jakobsen, Pia Bach and Blazewicz, Steven J. and Hubablek, Valerie and Bertilsson, Stefan and Hansen, Lars Hestbjerg and Cary, S. Craig and Holben, William E. and Ekelund, Flemming and Bælum, Jacob},
abstractNote = {Here we show that a commercial blocking reagent (G2) based on modified eukaryotic DNA significantly improved DNA extraction efficiency. We subjected G2 to an inter-laboratory testing, where DNA was extracted from the same clay subsoil using the same batch of kits. The inter-laboratory extraction campaign revealed large variation among the participating laboratories, but the reagent increased the number of PCR-amplified16S rRNA genes recovered from biomass naturally present in the soils by one log unit. Furthermore, an extensive sequencing approach demonstrated that the blocking reagent was free of contaminating DNA, and may therefore also be used in metagenomics studies that require direct sequencing.},
doi = {10.1038/s41598-018-24082-y},
journal = {Scientific Reports},
number = 1,
volume = 8,
place = {United States},
year = {2018},
month = {4}
}
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Works referencing / citing this record:
Validating DNA Extraction Protocols for Bentonite Clay
journal, October 2019
- Engel, Katja; Coyotzi, Sara; Vachon, Melody A.
- mSphere, Vol. 4, Issue 5
Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR
journal, April 2019
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