Institute of Microbiology, University of Greifswald, Greifswald, Germany.
Institute of Marine Biotechnology, Greifswald, Germany.
Microbiologyopen. 2022 Oct;11(5):e1323. doi: 10.1002/mbo3.1323.
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.
DNA 提取和保存偏倚是基于 DNA 测序的微生物生态学中一个反复出现的主题。不同的方法可能会导致不同的结果，这在研究原核群落组成的研究中尤其明显。真核微生物无处不在，种类繁多，除了细菌和古菌之外，它们也越来越成为研究的对象。然而，人们对 DNA 保存和提取方法的选择如何影响所感知的真核群落组成知之甚少。在这项研究中，我们比较了两种 DNA 保存方法和六种 DNA 提取方法对波罗的海海草草叶上光养生物膜中真核生物和原核生物群落图谱的影响。我们发现，尽管 DNA 保存和提取方法都对真核生物和原核生物的群落组成产生了显著的偏差，但提取偏差对真核生物的影响比原核生物更为明显。特别是，分别像线虫和硅藻这样的软躯体和硬壳真核生物，根据提取方法的不同，其丰度也不同。我们的结论是，在海洋生物膜中以及可能所有其他含有多样真核微生物群落的生境中，对 DNA 保存和提取方法的仔细考虑对于获得真核生物群落的代表性图谱至关重要。
