Keeping it cool: Soil sample cold pack storage and DNA shipment up to 1 month does not impact metabarcoding results
Abstract With the advances of sequencing tools, the fields of environmental microbiology and soil ecology have been transformed. Today, the unculturable majority of soil microbes can be sequenced. Although these tools give us tremendous power and open many doors to answer important questions, we mus...
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doaj-c733d199675847259c58c8ac247e09682021-03-02T07:22:36ZengWileyEcology and Evolution2045-77582020-06-0110114652466410.1002/ece3.6219Keeping it cool: Soil sample cold pack storage and DNA shipment up to 1 month does not impact metabarcoding resultsCamille S. Delavaux0James D. Bever1Erin M. Karppinen2Luke D. Bainard3Department of Ecology and Evolutionary Biology The University of Kansas Lawrence KS USADepartment of Ecology and Evolutionary Biology The University of Kansas Lawrence KS USASwift Current Research and Development Centre Agriculture and Agri‐Food Canada Swift Current SK CanadaSwift Current Research and Development Centre Agriculture and Agri‐Food Canada Swift Current SK CanadaAbstract With the advances of sequencing tools, the fields of environmental microbiology and soil ecology have been transformed. Today, the unculturable majority of soil microbes can be sequenced. Although these tools give us tremendous power and open many doors to answer important questions, we must understand how sample processing may impact our results and interpretations. Here, we test the impacts of four soil storage methods on downstream amplicon metabarcoding and qPCR analyses for fungi and bacteria. We further investigate the impact of thaw time on extracted DNA to determine a safe length of time during which this can occur with minimal impact on study results. Overall, we find that storage using standard cold packs with subsequent storage at −20°C is little different than immediate storage in liquid nitrogen, suggesting that the historical and current method is adequate. We further find evidence that storage at room temperature or with aid of RNAlater can lead to changes in community composition and in the case of RNAlater, lower gene copies. We therefore advise against these storage methods for metabarcoding analyses. Finally, we show that over 1 month, DNA extract thaw time does not impact diversity or qPCR metrics. We hope that this work will help researchers working with soil bacteria and fungi make informed decisions about soil storage and transport to ensure repeatability and accuracy of results and interpretations.https://doi.org/10.1002/ece3.6219bacteriafungimetabarcodingmicrobial biology |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Camille S. Delavaux James D. Bever Erin M. Karppinen Luke D. Bainard |
spellingShingle |
Camille S. Delavaux James D. Bever Erin M. Karppinen Luke D. Bainard Keeping it cool: Soil sample cold pack storage and DNA shipment up to 1 month does not impact metabarcoding results Ecology and Evolution bacteria fungi metabarcoding microbial biology |
author_facet |
Camille S. Delavaux James D. Bever Erin M. Karppinen Luke D. Bainard |
author_sort |
Camille S. Delavaux |
title |
Keeping it cool: Soil sample cold pack storage and DNA shipment up to 1 month does not impact metabarcoding results |
title_short |
Keeping it cool: Soil sample cold pack storage and DNA shipment up to 1 month does not impact metabarcoding results |
title_full |
Keeping it cool: Soil sample cold pack storage and DNA shipment up to 1 month does not impact metabarcoding results |
title_fullStr |
Keeping it cool: Soil sample cold pack storage and DNA shipment up to 1 month does not impact metabarcoding results |
title_full_unstemmed |
Keeping it cool: Soil sample cold pack storage and DNA shipment up to 1 month does not impact metabarcoding results |
title_sort |
keeping it cool: soil sample cold pack storage and dna shipment up to 1 month does not impact metabarcoding results |
publisher |
Wiley |
series |
Ecology and Evolution |
issn |
2045-7758 |
publishDate |
2020-06-01 |
description |
Abstract With the advances of sequencing tools, the fields of environmental microbiology and soil ecology have been transformed. Today, the unculturable majority of soil microbes can be sequenced. Although these tools give us tremendous power and open many doors to answer important questions, we must understand how sample processing may impact our results and interpretations. Here, we test the impacts of four soil storage methods on downstream amplicon metabarcoding and qPCR analyses for fungi and bacteria. We further investigate the impact of thaw time on extracted DNA to determine a safe length of time during which this can occur with minimal impact on study results. Overall, we find that storage using standard cold packs with subsequent storage at −20°C is little different than immediate storage in liquid nitrogen, suggesting that the historical and current method is adequate. We further find evidence that storage at room temperature or with aid of RNAlater can lead to changes in community composition and in the case of RNAlater, lower gene copies. We therefore advise against these storage methods for metabarcoding analyses. Finally, we show that over 1 month, DNA extract thaw time does not impact diversity or qPCR metrics. We hope that this work will help researchers working with soil bacteria and fungi make informed decisions about soil storage and transport to ensure repeatability and accuracy of results and interpretations. |
topic |
bacteria fungi metabarcoding microbial biology |
url |
https://doi.org/10.1002/ece3.6219 |
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