Detection of fish sedimentary <scp>DNA</scp> in aquatic systems: A review of methodological challenges and future opportunities

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  • Grayson P. Huston
    School of Biology and Ecology University of Maine Maine Orono USA
  • Mark Louie D. Lopez
    Department of Biochemistry & Microbiology University of Victoria British Columbia Victoria Canada
  • Yuanyu Cheng
    Department of Biology McGill University Quebec Montreal Canada
  • Leighton King
    Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology Centre for Ecology, Evolution and Biogeochemistry Kastanienbaum Switzerland
  • Lucinda C. Duxbury
    School of Physics, Chemistry and Earth Sciences The University of Adelaide Adelaide Australia
  • Maïlys Picard
    Cawthron Institute Nelson New Zealand
  • Georgia Thomson‐Laing
    Cawthron Institute Nelson New Zealand
  • Erika Myler
    Department of Integrative Biology, College of Biological Science University of Guelph Ontario Guelph Canada
  • Caren C. Helbing
    Department of Biochemistry & Microbiology University of Victoria British Columbia Victoria Canada
  • Michael T. Kinnison
    School of Biology and Ecology University of Maine Maine Orono USA
  • Jasmine E. Saros
    School of Biology and Ecology University of Maine Maine Orono USA
  • Irene Gregory‐Eaves
    Department of Biology McGill University Quebec Montreal Canada
  • Marie‐Eve Monchamp
    Department of Biology McGill University Quebec Montreal Canada
  • Susanna A. Wood
    Cawthron Institute Nelson New Zealand
  • Linda Armbrecht
    Institute for Marine and Antarctic Studies University of Tasmania Tasmania Battery Point Australia
  • Gentile Francesco Ficetola
    Department of Environmental Sciences and Policy University of Milan Milan Italy
  • Lenka Kurte
    Núcleo Milenio INVASAL University of Concepción Concepción Chile
  • Jordan Von Eggers
    Department of Geology and Geophysics University of Wyoming Wyoming Laramie USA
  • Janice Brahney
    Watershed Sciences and Ecology Center Utah State University Utah Logan USA
  • Genevieve Parent
    Laboratory of Genomics, Maurice Lamontagne Institute Fisheries and Oceans Canada Quebec Mont‐Joli Canada
  • Masayuki K. Sakata
    Research Faculty of Agriculture Hokkaido University Hokkaido Japan
  • Hideyuki Doi
    Graduate School of Informatics Kyoto University Kyoto Japan
  • Eric Capo
    Department of Ecology and Environmental Science Umeå University Umeå Sweden

書誌事項

公開日
2023-08-28
資源種別
journal article
権利情報
  • http://creativecommons.org/licenses/by-nc-nd/4.0/
DOI
  • 10.1002/edn3.467
公開者
Wiley

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説明

<jats:title>Abstract</jats:title><jats:p>Environmental DNA studies have proliferated over the last decade, with promising data describing the diversity of organisms inhabiting aquatic and terrestrial ecosystems. The recovery of DNA present in the sediment of aquatic systems (sedDNA) has provided short‐ and long‐term data on a wide range of biological groups (e.g., photosynthetic organisms, zooplankton species) and has advanced our understanding of how environmental changes have affected aquatic communities. However, substantial challenges remain for recovering the genetic material of macro‐organisms (e.g., fish) from sediments, preventing complete reconstructions of past aquatic ecosystems, and limiting our understanding of historic, higher trophic level interactions. In this review, we outline the biotic and abiotic factors affecting the production, persistence, and transport of fish DNA from the water column to the sediments, and address questions regarding the preservation of fish DNA in sediment. We identify sources of uncertainties around the recovery of fish sedDNA arising during the sedDNA workflow. This includes methodological issues related to experimental design, DNA extraction procedures, and the selected molecular method (quantitative PCR, digital PCR, metabarcoding, metagenomics). By evaluating previous efforts (published and unpublished works) to recover fish sedDNA signals, we provide suggestions for future research and propose troubleshooting workflows for the effective detection and quantification of fish sedDNA. With further research, the use of sedDNA has the potential to be a powerful tool for inferring fish presence over time and reconstructing their population and community dynamics.</jats:p>

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