DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes
Open accessAbstract
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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Eukaryotic genome characterization from metagenomes is still underappreciated due to multiple limitations from possible biases in DNA extraction to more challenging MAG reconstructions, and the approach employed can be a step toward standardizing these analyses.
“Eukaryotic genome characterization from metagenomes is still underappreciated due to multiple limitations from possible biases in DNA extraction 123 to more challenging MAG reconstructions, and the approach employed can be a step toward standardizing these analyses.”
From Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. (2024) · cites this paper as [123]
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Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome.
Carlino, N., Blanco-Míguez, A., Punčochář, M., Mengoni, C., Pinto, F., Tatti, A., Manghi, P., Armanini, F., Avagliano, M., Barcenilla, C., et al. (2024) · Cell · doi:10.1016/j.cell.2024.07.039 · Cited by 146 · see citing works
- Authors
- Brauer, A., & Bengtsson, M. M.
- Affiliations
- Institute of Microbiology University of Greifswald Greifswald Germany
- Universität Greifswald (DE)
- Corresponding author
- Bengtsson, Mia M.
- Venue
- MicrobiologyOpen
- Publisher
- Wiley
- Published
- 2022-09-30
- Volume
- 11
- Issue
- 5
- Pages
- e1323-e1323
- ISSN
- 2045-8827 (ISSN-L)
- PMC
- PMC9524606
- OpenAlex
- W4298132398
- Cited by
- 16
- References
- 26
- Citations by year
- 2026: 3 · 2025: 4 · 2024: 4 · 2023: 4 · 2022: 1
- FWCI
- 1.73
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- MicrobiologyOpen (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Bundesministerium für Bildung und Forschung (03F0859C)
- Deutsche Bundesstiftung Umwelt (20019/635)
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
- Keywords
- DNA extraction bias, protists, prokaryotes, eukaryotic community composition, phototrophic biofilms, seagrass, Zostera marina, nematodes, diatoms, Baltic Sea
- MeSH terms
- Archaea, Bacteria, DNA, Eukaryota, Microbiota
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