DNA 提取试剂盒对淡水真菌 DNA 宏条形码分析的影响。

Influence of DNA extraction kits on freshwater fungal DNA metabarcoding.

机构信息

Field Science Education and Research Center, Kyoto University, Kyoto, Japan.

Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan.

出版信息

PeerJ. 2022 May 27;10:e13477. doi: 10.7717/peerj.13477. eCollection 2022.

DOI:10.7717/peerj.13477

PMID:35651749

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9150701/

Abstract

BACKGROUND

Environmental DNA (eDNA) metabarcoding is a common technique for efficient biodiversity monitoring, especially of microbes. Recently, the usefulness of aquatic eDNA in monitoring the diversity of both terrestrial and aquatic fungi has been suggested. In eDNA studies, different experimental factors, such as DNA extraction kits or methods, can affect the subsequent analyses and the results of DNA metabarcoding. However, few methodological studies have been carried out on eDNA of fungi, and little is known about how experimental procedures can affect the results of biodiversity analysis. In this study, we focused on the effect of DNA extraction method on fungal DNA metabarcoding using freshwater samples obtained from rivers and lakes.

METHODS

DNA was extracted from freshwater samples using the DNeasy PowerSoil kit, which is mainly used to extractmicrobial DNA from soil, and the DNeasy Blood & Tissue kit, which is commonly used for eDNA studies on animals. We then compared PCR inhibition and fungal DNA metabarcoding results; operational taxonomic unit (OTU) number and composition of the extracted samples.

RESULTS

No PCR inhibition was detected in any of the samples, and no significant differences in the number of OTUs and OTU compositions were detected between the samples processed using different kits. These results indicate that both DNA extraction kits may provide similar diversity results for the river and lake samples evaluated in this study. Therefore, it may be possible to evaluate the diversity of fungi using a unified experimental method, even with samples obtained for diversity studies on other taxa such as those of animals.

摘要

背景

环境 DNA（eDNA）宏条形码技术是一种高效的生物多样性监测技术，尤其适用于微生物。最近，水生 eDNA 在监测陆地和水生真菌多样性方面的有用性已被提出。在 eDNA 研究中，不同的实验因素，如 DNA 提取试剂盒或方法，可能会影响后续的分析和 DNA 宏条形码的结果。然而，关于真菌的 eDNA 方法学研究较少，对于实验程序如何影响生物多样性分析的结果知之甚少。在这项研究中，我们专注于使用从河流和湖泊中获得的淡水样本，研究 DNA 提取方法对真菌 DNA 宏条形码的影响。

方法

使用 DNeasy PowerSoil 试剂盒（主要用于从土壤中提取微生物 DNA）和 DNeasy Blood & Tissue 试剂盒（常用于动物 eDNA 研究）从淡水样本中提取 DNA。然后，我们比较了 PCR 抑制和真菌 DNA 宏条形码结果；提取样本的 OTU 数量和组成。

结果

在任何样本中均未检测到 PCR 抑制，并且使用不同试剂盒处理的样本之间的 OTU 数量和 OTU 组成没有显著差异。这些结果表明，对于本研究评估的河流和湖泊样本，两种 DNA 提取试剂盒可能提供相似的多样性结果。因此，即使使用用于评估其他类群（如动物）多样性研究的样本，也可以使用统一的实验方法评估真菌的多样性。