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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]

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:
 [1];  [1];  [2];  [3]; ORCiD logo [4];  [5]; ORCiD logo [6];  [7];  [8];  [8];  [9];  [10];  [10];  [11];  [12];  [13];  [14];  [15];  [15];  [6] more »;  [16];  [17];  [18];  [19] « less
  1. Univ. of Aaruhus, Roskilde (Denmark); Geological Survey of Denmark and Greenland, Copenhagen (Denmark)
  2. Univ. of Copenhagen, Frederiksberg (Denmark); NovoZymes A/S, Copenhagen (Denmark)
  3. Univ. of Copenhagen, Frederiksberg (Denmark)
  4. Aalborg Univ., Aalborg (Denmark)
  5. Academy of Sciences of the Czech Republic, Bron (Czech Republic); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  6. Univ. of Aaruhus, Roskilde (Denmark)
  7. Academy of Sciences of the Czech Republic, Bron (Czech Republic)
  8. Norwegian Univ. of Life Sciences, As (Norway)
  9. Univ. of Aarhus, Aarhus (Denmark); NIRAS A/S, Aarhus (Denmark)
  10. The Arctic Univ. of Norway, Tromso (Norway)
  11. Thunen-Institut fur Biodiversitat, Braunschweig (Germany)
  12. Univ. of Bergen, Bergen (Norway)
  13. Geological Survey of Denmark and Greenland, Copenhagen (Denmark)
  14. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  15. Uppsala Univ., Uppsala (Sweden)
  16. Univ. of Waikato, Hamilton (New Zealand)
  17. Univ. of Montana, Missoula, MT (United States)
  18. Univ. of Copenhagen, Copenhagen (Denmark)
  19. 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: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: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 referenced in this record:

Inter-laboratory evaluation of the ISO standard 11063 “Soil quality — Method to directly extract DNA from soil samples”
journal, March 2011


Effect of molecular characteristics of DNA on its adsorption and binding on homoionic montmorillonite and kaolinite
journal, May 2001

  • G., Pietramellara; M., Franchi; E., Gallori
  • Biology and Fertility of Soils, Vol. 33, Issue 5
  • DOI: 10.1007/s003740100341

Soil biodiversity and DNA barcodes: opportunities and challenges
journal, January 2015


Improving Griffith's protocol for co-extraction of microbial DNA and RNA in adsorptive soils
journal, August 2013


Rapid Method for Coextraction of DNA and RNA from Natural Environments for Analysis of Ribosomal DNA- and rRNA-Based Microbial Community Composition
journal, December 2000


Microcalorimetric studies on the adsorption of DNA by soil colloidal particles
journal, April 2006


Transcription dynamics of the functional tfdA gene during MCPA herbicide degradation by Cupriavidus necator AEO106 (pRO101) in agricultural soil
journal, March 2008


Effects of low-molecular-weight organic ligands and phosphate on DNA adsorption by soil colloids and minerals
journal, January 2007


An Improved DNA Extraction Method Using Skim Milk from Soils That Strongly Adsorb DNA
journal, January 2004

  • Takada-Hoshino, Yuko; Matsumoto, Naoyuki
  • Microbes and Environments, Vol. 19, Issue 1
  • DOI: 10.1264/jsme2.19.13

Evaluation of the Effects of Different Additives in Improving the DNA Extraction Yield and Quality from Andosol
journal, January 2008

  • Ikeda, Seishi; Tsurumaru, Hirohito; Wakai, Satoshi
  • Microbes and Environments, Vol. 23, Issue 2
  • DOI: 10.1264/jsme2.23.159