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]

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

doi:10.1038/s41598-018-24082-y

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]

Journal Article · Mon Apr 09 00:00:00 EDT 2018 · Scientific Reports

DOI:https://doi.org/10.1038/s41598-018-24082-y· OSTI ID:1474353

Jacobsen, Carsten Suhr ^[1]; Nielsen, Tue Kjærgaard ^[1]; Vester, Jan Kjølhede ^[2]; Stougaard, Peter ^[3]; ^[4]; Voriskova, Jana ^[5]; ^[6]; Baldrian, Petr ^[7]; Liu, Binbin ^[8]; Frostegård, Åsa ^[8]; Pedersen, Dorthe ^[9]; Tveit, Alexander Tøsdal ^[10]; Svenning, Mette Marianne ^[10]; Tebbe, Christoph C. ^[11]; Øvreås, Lise ^[12]; Jakobsen, Pia Bach ^[13]; Blazewicz, Steven J. ^[14]; Hubablek, Valerie ^[15]; Bertilsson, Stefan ^[15]; Hansen, Lars Hestbjerg ^[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)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA)

Grant/Contract Number:: AC52-07NA27344

OSTI ID:: 1474353

Report Number(s):: LLNL-JRNL--738627; 891928

Journal Information:: Scientific Reports, Journal Name: Scientific Reports Journal Issue: 1 Vol. 8; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Validating DNA Extraction Protocols for Bentonite Clay Engel, Katja; Coyotzi, Sara; Vachon, Melody A. mSphere, Vol. 4, Issue 5 https://doi.org/10.1128/msphere.00334-19	journal	October 2019
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 Gobbi, Alex; Santini, Rui G.; Filippi, Elisa PLOS ONE, Vol. 14, Issue 4 https://doi.org/10.1371/journal.pone.0200979	journal	April 2019

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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]

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