Department of Biology, St. Francis College, Brooklyn, NY, USA.
Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.
Microb Ecol. 2023 Apr;85(3):796-808. doi: 10.1007/s00248-022-02168-5. Epub 2023 Feb 3.
Environmental DNA (eDNA) sequencing-DNA collected from the environment from living cells or shed DNA-was first developed for working with microbes and has greatly benefitted microbial ecologists for decades since. These tools have only become increasingly powerful with the advent of metabarcoding and metagenomics. Most new studies that examine diverse assemblages of bacteria, archaea, protists, fungi, and viruses lean heavily into eDNA using these newer technologies, as the necessary sequencing technology and bioinformatic tools have become increasingly affordable and user friendly. However, eDNA methods are rapidly evolving, and sometimes it can feel overwhelming to simply keep up with the basics. In this review, we provide a starting point for microbial ecologists who are new to DNA-based methods by detailing the eDNA methods that are most pertinent, including study design, sample collection and storage, selecting the right sequencing technology, lab protocols, equipment, and a few bioinformatic tools. Furthermore, we focus on how eDNA work can benefit restoration and what modifications are needed when working in this subfield.
环境 DNA（eDNA）测序——从环境中采集的来自活细胞或脱落 DNA 的 DNA——最初是为研究微生物而开发的，自那时以来，几十年来一直使微生物生态学家受益匪浅。随着代谢组学和宏基因组学的出现，这些工具的功能变得越来越强大。大多数研究不同细菌、古菌、原生生物、真菌和病毒组合的新研究都大量使用 eDNA 这些新技术，因为必要的测序技术和生物信息学工具变得越来越便宜和用户友好。然而，eDNA 方法正在迅速发展，有时仅仅跟上基础知识就会让人感到不知所措。在这篇综述中，我们通过详细介绍最相关的 eDNA 方法，为刚开始使用基于 DNA 的方法的微生物生态学家提供了一个起点，包括研究设计、样本采集和存储、选择合适的测序技术、实验室方案、设备以及一些生物信息学工具。此外，我们还重点介绍了 eDNA 工作如何有益于恢复，以及在该子领域工作时需要进行哪些修改。
