Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples
This study aims to act as a methodological guide for contamination monitoring, decontamination, and DNA extraction for peaty and silty permafrost samples with low biomass or difficult to extract DNA. We applied a biological tracer, either only in the field or both in the field and in the lab, via ei...
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ftpubmed:oai:pubmedcentral.nih.gov:7459103 2023-05-15T17:55:35+02:00 Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples Saidi-Mehrabad, Alireza Neuberger, Patrick Cavaco, Maria Froese, Duane Lanoil, Brian 2020-08-31 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7459103/ http://www.ncbi.nlm.nih.gov/pubmed/32868827 https://doi.org/10.1038/s41598-020-71234-0 en eng Nature Publishing Group UK http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7459103/ http://www.ncbi.nlm.nih.gov/pubmed/32868827 http://dx.doi.org/10.1038/s41598-020-71234-0 © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. CC-BY Sci Rep Article Text 2020 ftpubmed https://doi.org/10.1038/s41598-020-71234-0 2020-09-06T00:52:25Z This study aims to act as a methodological guide for contamination monitoring, decontamination, and DNA extraction for peaty and silty permafrost samples with low biomass or difficult to extract DNA. We applied a biological tracer, either only in the field or both in the field and in the lab, via either spraying or painting. Spraying in the field followed by painting in the lab resulted in a uniform layer of the tracer on the core sections. A combination of bleaching, washing, and scraping resulted in complete removal of the tracer leaving sufficient material for DNA extraction, while other widely used decontamination methods did not remove all detectable tracer. In addition, of four widely used commercially available DNA extraction kits, only a modified ZymoBIOMICS DNA Microprep kit was able to acquire PCR amplifiable DNA. Permafrost chemical parameters, age, and soil texture did not have an effect on decontamination efficacy; however, the permafrost type did influence DNA extraction. Based on these findings, we developed recommendations for permafrost researchers to acquire contaminant-free DNA from permafrost with low biomass. Text permafrost PubMed Central (PMC) Scientific Reports 10 1 |
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Article Saidi-Mehrabad, Alireza Neuberger, Patrick Cavaco, Maria Froese, Duane Lanoil, Brian Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples |
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This study aims to act as a methodological guide for contamination monitoring, decontamination, and DNA extraction for peaty and silty permafrost samples with low biomass or difficult to extract DNA. We applied a biological tracer, either only in the field or both in the field and in the lab, via either spraying or painting. Spraying in the field followed by painting in the lab resulted in a uniform layer of the tracer on the core sections. A combination of bleaching, washing, and scraping resulted in complete removal of the tracer leaving sufficient material for DNA extraction, while other widely used decontamination methods did not remove all detectable tracer. In addition, of four widely used commercially available DNA extraction kits, only a modified ZymoBIOMICS DNA Microprep kit was able to acquire PCR amplifiable DNA. Permafrost chemical parameters, age, and soil texture did not have an effect on decontamination efficacy; however, the permafrost type did influence DNA extraction. Based on these findings, we developed recommendations for permafrost researchers to acquire contaminant-free DNA from permafrost with low biomass. |
format |
Text |
author |
Saidi-Mehrabad, Alireza Neuberger, Patrick Cavaco, Maria Froese, Duane Lanoil, Brian |
author_facet |
Saidi-Mehrabad, Alireza Neuberger, Patrick Cavaco, Maria Froese, Duane Lanoil, Brian |
author_sort |
Saidi-Mehrabad, Alireza |
title |
Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples |
title_short |
Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples |
title_full |
Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples |
title_fullStr |
Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples |
title_full_unstemmed |
Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples |
title_sort |
optimization of subsampling, decontamination, and dna extraction of difficult peat and silt permafrost samples |
publisher |
Nature Publishing Group UK |
publishDate |
2020 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7459103/ http://www.ncbi.nlm.nih.gov/pubmed/32868827 https://doi.org/10.1038/s41598-020-71234-0 |
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permafrost |
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permafrost |
op_source |
Sci Rep |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7459103/ http://www.ncbi.nlm.nih.gov/pubmed/32868827 http://dx.doi.org/10.1038/s41598-020-71234-0 |
op_rights |
© The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
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CC-BY |
op_doi |
https://doi.org/10.1038/s41598-020-71234-0 |
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