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Soil Sample Preservation Strategy Affects the Microbial Community Structure

Sample preservation is a critical procedure in any research that relies on molecular tools and is conducted in remote areas. Sample preservation options include low and room temperature storage, which require freezing equipment and specific buffering solutions, respectively. The aim of the present s...

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Autores principales: Pavlovska, Mariia, Prekrasna, Ievgeniia, Parnikoza, Ivan, Dykyi, Evgen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7966943/
https://www.ncbi.nlm.nih.gov/pubmed/33563868
http://dx.doi.org/10.1264/jsme2.ME20134
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author Pavlovska, Mariia
Prekrasna, Ievgeniia
Parnikoza, Ivan
Dykyi, Evgen
author_facet Pavlovska, Mariia
Prekrasna, Ievgeniia
Parnikoza, Ivan
Dykyi, Evgen
author_sort Pavlovska, Mariia
collection PubMed
description Sample preservation is a critical procedure in any research that relies on molecular tools and is conducted in remote areas. Sample preservation options include low and room temperature storage, which require freezing equipment and specific buffering solutions, respectively. The aim of the present study was to investigate whether DNA/RNA Shield 1x from Zymo Research and DESS (Dimethyl sulfoxide, Ethylenediamine tetraacetic acid, Saturated Salt) solution performed similarly to snap freezing in liquid nitrogen. Soil samples were stored for 1 month in each of the buffers and without any solution at a range of temperatures: –20, +4, and +23°C. All treatments were compared to the “optimal treatment”, namely, snap freezing in liquid nitrogen. The quality and quantity of DNA were analyzed, and the microbial community structure was investigated in all samples. The results obtained indicated that the quantity and integrity of DNA was preserved well in all samples; however, the taxonomic distribution was skewed in samples stored without any solution at ambient temperatures, particularly when analyses were performed at lower taxonomic levels. Although both solutions performed equally well, sequencing output and OTU numbers in DESS-treated samples were closer to those snap frozen with liquid nitrogen. Furthermore, DNA/RNA Shield-stored samples performed better for the preservation of rare taxa.
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spelling pubmed-79669432021-03-26 Soil Sample Preservation Strategy Affects the Microbial Community Structure Pavlovska, Mariia Prekrasna, Ievgeniia Parnikoza, Ivan Dykyi, Evgen Microbes Environ Regular Paper Sample preservation is a critical procedure in any research that relies on molecular tools and is conducted in remote areas. Sample preservation options include low and room temperature storage, which require freezing equipment and specific buffering solutions, respectively. The aim of the present study was to investigate whether DNA/RNA Shield 1x from Zymo Research and DESS (Dimethyl sulfoxide, Ethylenediamine tetraacetic acid, Saturated Salt) solution performed similarly to snap freezing in liquid nitrogen. Soil samples were stored for 1 month in each of the buffers and without any solution at a range of temperatures: –20, +4, and +23°C. All treatments were compared to the “optimal treatment”, namely, snap freezing in liquid nitrogen. The quality and quantity of DNA were analyzed, and the microbial community structure was investigated in all samples. The results obtained indicated that the quantity and integrity of DNA was preserved well in all samples; however, the taxonomic distribution was skewed in samples stored without any solution at ambient temperatures, particularly when analyses were performed at lower taxonomic levels. Although both solutions performed equally well, sequencing output and OTU numbers in DESS-treated samples were closer to those snap frozen with liquid nitrogen. Furthermore, DNA/RNA Shield-stored samples performed better for the preservation of rare taxa. Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles 2021 2021-02-10 /pmc/articles/PMC7966943/ /pubmed/33563868 http://dx.doi.org/10.1264/jsme2.ME20134 Text en 2021 by Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles. http://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Regular Paper
Pavlovska, Mariia
Prekrasna, Ievgeniia
Parnikoza, Ivan
Dykyi, Evgen
Soil Sample Preservation Strategy Affects the Microbial Community Structure
title Soil Sample Preservation Strategy Affects the Microbial Community Structure
title_full Soil Sample Preservation Strategy Affects the Microbial Community Structure
title_fullStr Soil Sample Preservation Strategy Affects the Microbial Community Structure
title_full_unstemmed Soil Sample Preservation Strategy Affects the Microbial Community Structure
title_short Soil Sample Preservation Strategy Affects the Microbial Community Structure
title_sort soil sample preservation strategy affects the microbial community structure
topic Regular Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7966943/
https://www.ncbi.nlm.nih.gov/pubmed/33563868
http://dx.doi.org/10.1264/jsme2.ME20134
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