An Environmental DNA Primer for Microbial and Restoration Ecology.

Michael Tessler, Seth W Cunningham, Melissa R Ingala, Sally D Warring, Mercer R Brugler

Microbial ecology 2023 Apr

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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. © 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.

Citation

Michael Tessler, Seth W Cunningham, Melissa R Ingala, Sally D Warring, Mercer R Brugler. An Environmental DNA Primer for Microbial and Restoration Ecology. Microbial ecology. 2023 Apr;85(3):796-808