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

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

Huston, Grayson P. (författare): School of Biology and Ecology, University of Maine, ME, Orono, United States; Maine Center for Genetics in the Environment, University of Maine, ME, Orono, United States

Lopez, Mark Louie D. (författare): Department of Biochemistry & Microbiology, University of Victoria, BC, Victoria, Canada

Cheng, Yuanyu (författare): Department of Biology, McGill University, QC, Montreal, Canada; Groupe de recherche interuniversitaire en limnologie (GRIL), Canada

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King, Leighton (författare): Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland; Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland

Duxbury, Lucinda C. (författare): School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, Australia; ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), The University of Adelaide, Adelaide, Australia

Picard, Maïlys (författare): Cawthron Institute, Nelson, New Zealand; Department of Biological Sciences, School of Biological Sciences, University of Waikato, Hamilton, New Zealand

Thomson-Laing, Georgia (författare): Cawthron Institute, Nelson, New Zealand; School of Geography, Environment, and Earth Sciences, Victoria University of Wellington, Wellington, New Zealand

Myler, Erika (författare): Department of Integrative Biology, College of Biological Science, University of Guelph, ON, Guelph, Canada

Helbing, Caren C. (författare): Department of Biochemistry & Microbiology, University of Victoria, BC, Victoria, Canada

Kinnison, Michael T. (författare): School of Biology and Ecology, University of Maine, ME, Orono, United States; Maine Center for Genetics in the Environment, University of Maine, ME, Orono, United States

Saros, Jasmine E. (författare): School of Biology and Ecology, University of Maine, ME, Orono, United States; Climate Change Institute, University of Maine, ME, Orono, United States

Gregory-Eaves, Irene (författare): Department of Biology, McGill University, QC, Montreal, Canada; Groupe de recherche interuniversitaire en limnologie (GRIL), Canada

Monchamp, Marie-Eve (författare): Department of Biology, McGill University, QC, Montreal, Canada; Groupe de recherche interuniversitaire en limnologie (GRIL), Canada

Wood, Susanna A. (författare): Cawthron Institute, Nelson, New Zealand

Armbrecht, Linda (författare): Institute for Marine and Antarctic Studies, University of Tasmania, TAS, Battery Point, Australia

Ficetola, Gentile Francesco (författare): Department of Environmental Sciences and Policy, University of Milan, Milan, Italy; Laboratoire d'Ecologie Alpine (LECA), CNRS, Université Grenoble Alpes and Université Savoie Mont Blanc, Grenoble, France

Kurte, Lenka (författare): Núcleo Milenio INVASAL, University of Concepción, Concepción, Chile

Von Eggers, Jordan (författare): Department of Geology and Geophysics, University of Wyoming, WY, Laramie, United States

Brahney, Janice (författare): Watershed Sciences and Ecology Center, Utah State University, UT, Logan, United States

Parent, Genevieve (författare): Laboratory of Genomics, Maurice Lamontagne Institute, Fisheries and Oceans Canada, QC, Mont-Joli, Canada

Sakata, Masayuki K. (författare): Research Faculty of Agriculture, Hokkaido University, Hokkaido, Japan

Doi, Hideyuki (författare): Graduate School of Informatics, Kyoto University, Kyoto, Japan

Capo, Eric (författare): Umeå universitet,Institutionen för ekologi, miljö och geovetenskap,Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain

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John Wiley & Sons, 2023
2023
Engelska.
Ingår i: Environmental DNA. - : John Wiley & Sons. - 2637-4943. ; 5:6, s. 1449-1472

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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.

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NATURVETENSKAP: NATURVETENSKAP; och Biologi; och Ekologi

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

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