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DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes

DNA extraction and preservation bias is a recurring topic in DNA sequencing‐based microbial ecology. The different methodologies can lead to distinct outcomes, which has been demonstrated especially in studies investigating prokaryotic community composition. Eukaryotic microbes are ubiquitous, diver...

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Detalles Bibliográficos
Autores principales: Brauer, Anne, Bengtsson, Mia M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9524606/
https://www.ncbi.nlm.nih.gov/pubmed/36314757
http://dx.doi.org/10.1002/mbo3.1323
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author Brauer, Anne
Bengtsson, Mia M.
author_facet Brauer, Anne
Bengtsson, Mia M.
author_sort Brauer, Anne
collection PubMed
description DNA extraction and preservation bias is a recurring topic in DNA sequencing‐based microbial ecology. The different methodologies can lead to distinct outcomes, which has been demonstrated especially in studies investigating prokaryotic community composition. Eukaryotic microbes are ubiquitous, diverse, and increasingly a subject of investigation in addition to bacteria and archaea. However, little is known about how the choice of DNA preservation and extraction methodology impacts perceived eukaryotic community composition. In this study, we compared the effect of two DNA preservation methods and six DNA extraction methods on the community profiles of both eukaryotes and prokaryotes in phototrophic biofilms on seagrass (Zostera marina) leaves from the Baltic Sea. We found that, whereas both DNA preservation and extraction method caused significant bias in perceived community composition for both eukaryotes and prokaryotes, extraction bias was more pronounced for eukaryotes than for prokaryotes. In particular, soft‐bodied and hard‐shelled eukaryotes like nematodes and diatoms, respectively, were differentially abundant depending on the extraction method. We conclude that careful consideration of DNA preservation and extraction methodology is crucial to achieving representative community profiles of eukaryotes in marine biofilms and likely all other habitats containing diverse eukaryotic microbial communities.
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spelling pubmed-95246062022-10-05 DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes Brauer, Anne Bengtsson, Mia M. Microbiologyopen Commentary DNA extraction and preservation bias is a recurring topic in DNA sequencing‐based microbial ecology. The different methodologies can lead to distinct outcomes, which has been demonstrated especially in studies investigating prokaryotic community composition. Eukaryotic microbes are ubiquitous, diverse, and increasingly a subject of investigation in addition to bacteria and archaea. However, little is known about how the choice of DNA preservation and extraction methodology impacts perceived eukaryotic community composition. In this study, we compared the effect of two DNA preservation methods and six DNA extraction methods on the community profiles of both eukaryotes and prokaryotes in phototrophic biofilms on seagrass (Zostera marina) leaves from the Baltic Sea. We found that, whereas both DNA preservation and extraction method caused significant bias in perceived community composition for both eukaryotes and prokaryotes, extraction bias was more pronounced for eukaryotes than for prokaryotes. In particular, soft‐bodied and hard‐shelled eukaryotes like nematodes and diatoms, respectively, were differentially abundant depending on the extraction method. We conclude that careful consideration of DNA preservation and extraction methodology is crucial to achieving representative community profiles of eukaryotes in marine biofilms and likely all other habitats containing diverse eukaryotic microbial communities. John Wiley and Sons Inc. 2022-09-30 /pmc/articles/PMC9524606/ /pubmed/36314757 http://dx.doi.org/10.1002/mbo3.1323 Text en © 2022 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Commentary
Brauer, Anne
Bengtsson, Mia M.
DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes
title DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes
title_full DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes
title_fullStr DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes
title_full_unstemmed DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes
title_short DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes
title_sort dna extraction bias is more pronounced for microbial eukaryotes than for prokaryotes
topic Commentary
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9524606/
https://www.ncbi.nlm.nih.gov/pubmed/36314757
http://dx.doi.org/10.1002/mbo3.1323
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