Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Program, Nanyang Technological Universitygrid.59025.3b, Singapore.
School of Civil and Environmental Engineering, Nanyang Technological Universitygrid.59025.3b, Singapore.
Appl Environ Microbiol. 2022 Feb 8;88(3):e0184521. doi: 10.1128/AEM.01845-21. Epub 2021 Nov 24.
Environmental DNA, i.e., DNA extracted directly from environmental samples, has been used to understand microbial communities in the environment and to monitor contemporary biodiversity in the conservation context. Environmental DNA often contains both intracellular DNA (iDNA) and extracellular DNA (eDNA). eDNA can persist in the environment and complicate environmental DNA sequencing-based analyses of microbial communities and biodiversity. Although several studies acknowledged the impact of eDNA on DNA-based profiling of environmental communities, eDNA is still being neglected or ignored in most studies dealing with environmental samples. In this article, we summarize key findings on eDNA in environmental samples and discuss the methods used to extract and quantify eDNA as well as the importance of eDNA on the interpretation of experimental results. We then suggested several factors to consider when designing experiments and analyzing data to negate or determine the contribution of eDNA to environmental DNA-based community analyses. This field of research will be driven forward by (i) carefully designing environmental DNA extraction pipelines by taking into consideration technical details in methods for eDNA extraction/removal and membrane-based filtration and concentration; (ii) quantifying eDNA in extracted environmental DNA using multiple methods, including qPCR and fluorescent DNA binding dyes; (iii) carefully interpreting the effect of eDNA on DNA-based community analyses at different taxonomic levels; and (iv) when possible, removing eDNA from environmental samples for DNA-based community analyses.
环境 DNA，即直接从环境样本中提取的 DNA，已被用于了解环境中的微生物群落，并在保护背景下监测当代生物多样性。环境 DNA 通常包含细胞内 DNA（iDNA）和细胞外 DNA（eDNA）。eDNA 可以在环境中持续存在，并使基于环境 DNA 测序的微生物群落和生物多样性分析变得复杂。尽管有几项研究承认了 eDNA 对基于 DNA 的环境群落分析的影响，但在大多数涉及环境样本的研究中，eDNA 仍然被忽视或忽略。在本文中，我们总结了环境样本中 eDNA 的关键发现，并讨论了提取和定量 eDNA 的方法，以及 eDNA 对实验结果解释的重要性。然后，我们建议了在设计实验和分析数据时需要考虑的几个因素，以否定或确定 eDNA 对基于环境 DNA 的群落分析的贡献。这一研究领域将通过以下几个方面得到推动：（i）在设计环境 DNA 提取方案时，仔细考虑 eDNA 提取/去除方法以及基于膜的过滤和浓缩的技术细节；（ii）使用包括 qPCR 和荧光 DNA 结合染料在内的多种方法，对提取的环境 DNA 中的 eDNA 进行定量；（iii）仔细解释 eDNA 对不同分类水平上基于 DNA 的群落分析的影响；（iv）在可能的情况下，从环境样本中去除 eDNA 以进行基于 DNA 的群落分析。
