Dr Miwa Takahashi1, Dr Mattia Sacco1, Dr Matthew Campbell1, Dr Mieke Van Der Heyde1, Mr Joshua Kestel1, Dr Paul Nevill1, Dr Kat Dawkins1, Dr Mahsa Mousavi-Derazmahalleh1, Dr Cindy Bessey2, Ms Kristen Fernandes1, Dr Haylea Miller2, Mr Matthew Power1, Mr Josh Newton1, Ms Georgia Nester1, Mr David Juszkiewicz1, Mr Matt Heydenrych3, Prof. Morten Allentoft1
1Curtin University, Bentley, Australia, 2CSIRO, Crawley, Australia, 3University of Western Australia, Crawley, Australia
The use of environmental DNA (eDNA) is by far the fastest growing biomonitoring tool, fuelled by time efficiency, sensitivity and accuracy. We conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021 to overview the technological advancements, and identify the pros and cons of the available methods, knowledge gaps and future directions. The number of publications gradually increased from four in 2012 to 28 in 2018, followed by a rapid growth to 124 publications in 2021. Our analyses uncovered a tremendous diversification of available methods in all aspects of the eDNA workflow. For example, in 2012 freezing was the only method applied to preserve filter samples, whereas we recorded 12 different preservation methods in 2021 including ethanol, RNA later, lysis buffer and desiccation, all of which allow ambient temperature storage. Our review revealed several knowledge gaps related to a lack of comprehensive method comparison studies, insufficient validation and optimisation, particularly for recently developed methods, and missing detailed method description. Moreover, we compiled the PCR-primer database, providing information on 529 and 168 sets of species-specific and metabarcoding primers, respectively, targeting DNA of a wide range of macroorganisms. This list reflects commonly studied taxa (i.e., fish and amphibian) as well as severely under-studied taxa (i.e., corals, planktons, algae) despite their ecological importance. In a field that is rapidly diversifying methodologically, this review serves as an updated encyclopedia of aquatic eDNA procedures and can guide eDNA users towards optimal methods and primers for their future studies.
Biography:
Miwa is a marine biologist interested in marine ecology, fishery science, metabarcoding and species distribution modelling. She did her undergraduate studies at James Cook University, followed by a PhD at Curtin University. She is now working at eDNA frontiers and at CSIRO, both based in Perth, being involved in eDNA methods innovation and leading a community engagement program.