TY - JOUR

T1 - Aquatic environmental DNA

T2 - A review of the macro-organismal biomonitoring revolution

AU - Takahashi, Miwa

AU - Saccò, Mattia

AU - Kestel, Joshua H.

AU - Nester, Georgia

AU - Campbell, Matthew A.

AU - van der Heyde, Mieke

AU - Heydenrych, Matthew J.

AU - Juszkiewicz, David J.

AU - Nevill, Paul

AU - Dawkins, Kathryn L.

AU - Bessey, Cindy

AU - Fernandes, Kristen

AU - Miller, Haylea

AU - Power, Matthew

AU - Mousavi-Derazmahalleh, Mahsa

AU - Newton, Joshua P.

AU - White, Nicole E.

AU - Richards, Zoe T.

AU - Allentoft, Morten E.

N1 - Publisher Copyright: © 2023

PY - 2023

Y1 - 2023

N2 - Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species and community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this is only possible with an in-depth overview of the technological advancements and a discussion of the pros and cons of available methods. We therefore conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021. We observed a gradual increase in the annual number of publications from four (2012) to 28 (2018), followed by a rapid growth to 124 publications in 2021. This was mirrored by a tremendous diversification of methods in all aspects of the eDNA workflow. For example, in 2012 only freezing was applied to preserve filter samples, whereas we recorded 12 different preservation methods in the 2021 literature. Despite an ongoing standardisation debate in the eDNA community, the field is seemingly moving fast in the opposite direction and we discuss the reasons and implications. Moreover, by compiling the largest PCR-primer database to date, we provide information on 522 and 141 published species-specific and metabarcoding primers targeting a wide range of aquatic organisms. This works as a user-friendly ‘distillation’ of primer information that was hitherto scattered across hundreds of papers, but the list also reflects which taxa are commonly studied with eDNA technology in aquatic environments such as fish and amphibians, and reveals that groups such as corals, plankton and algae are under-studied. Efforts to improve sampling and extraction methods, primer specificity and reference databases are crucial to capture these ecologically important taxa in future eDNA biomonitoring surveys. In a rapidly diversifying field, this review synthetises aquatic eDNA procedures and can guide eDNA users towards best practice.

AB - Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species and community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this is only possible with an in-depth overview of the technological advancements and a discussion of the pros and cons of available methods. We therefore conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021. We observed a gradual increase in the annual number of publications from four (2012) to 28 (2018), followed by a rapid growth to 124 publications in 2021. This was mirrored by a tremendous diversification of methods in all aspects of the eDNA workflow. For example, in 2012 only freezing was applied to preserve filter samples, whereas we recorded 12 different preservation methods in the 2021 literature. Despite an ongoing standardisation debate in the eDNA community, the field is seemingly moving fast in the opposite direction and we discuss the reasons and implications. Moreover, by compiling the largest PCR-primer database to date, we provide information on 522 and 141 published species-specific and metabarcoding primers targeting a wide range of aquatic organisms. This works as a user-friendly ‘distillation’ of primer information that was hitherto scattered across hundreds of papers, but the list also reflects which taxa are commonly studied with eDNA technology in aquatic environments such as fish and amphibians, and reveals that groups such as corals, plankton and algae are under-studied. Efforts to improve sampling and extraction methods, primer specificity and reference databases are crucial to capture these ecologically important taxa in future eDNA biomonitoring surveys. In a rapidly diversifying field, this review synthetises aquatic eDNA procedures and can guide eDNA users towards best practice.

KW - Biodiversity

KW - eDNA

KW - Freshwater

KW - Marine

KW - Primers

KW - Standardisation

U2 - 10.1016/j.scitotenv.2023.162322

DO - 10.1016/j.scitotenv.2023.162322

M3 - Review

C2 - 36801404

AN - SCOPUS:85149420183

VL - 873

JO - Science of the Total Environment

JF - Science of the Total Environment

SN - 0048-9697

M1 - 162322

ER -