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An Environmental DNA Primer for Microbial and Restoration Ecology

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Abstract

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.

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Acknowledgements

Thanks are due to those who restore habitats and make the world a better place. MRB thanks Peter Kingsley-Smith, Gary Sundin, Michael Hodges, and Graham Wagner of the South Carolina Department of Natural Resources SCORE (South Carolina Oyster Recycling and Enhancement) Program for installing oyster-based living shorelines.

Funding

Funding for the oyster reef eDNA project was generously provided by the Spring Island Trust (Director: Chris Marsh), the Office of Coastal Management/NOAA/DOC via an operations award to the North Inlet-Winyah Bay National Estuarine Research Reserve (PI Erik Smith of the Baruch Institute for Marine & Coastal Sciences; Grant #NA20NOS4200030), and the University of South Carolina Beaufort.

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Tessler, M., Cunningham, S.W., Ingala, M.R. et al. An Environmental DNA Primer for Microbial and Restoration Ecology. Microb Ecol 85, 796–808 (2023). https://doi.org/10.1007/s00248-022-02168-5

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