Literature DB >> 31744434

Predicting the fate of eDNA in the environment and implications for studying biodiversity.

Jori B Harrison1, Jennifer M Sunday2, Sean M Rogers1.   

Abstract

Environmental DNA (eDNA) applications are transforming the standard of characterizing aquatic biodiversity via the presence, location and abundance of DNA collected from environmental samples. As eDNA studies use DNA fragments as a proxy for the presence of organisms, the ecological properties of the complex and dynamic environments from which eDNA is sampled need to be considered for accurate biological interpretation. In this review, we discuss the role that differing environments play on the major processes that eDNA undergoes between organism and collection, including shedding, decay and transport. We focus on a mechanistic understanding of these processes and highlight how decay and transport models are being developed towards more accurate and robust predictions of the fate of eDNA. We conclude with five recommendations for eDNA researchers and practitioners, to advance current best practices, as well as to support a future model of eDNA spatio-temporal persistence.

Entities:  

Keywords:  aquatic biodiversity; biodiversity; eDNA decay; eDNA transport; environmental DNA; taphonomy

Mesh:

Substances:

Year:  2019        PMID: 31744434      PMCID: PMC6892050          DOI: 10.1098/rspb.2019.1409

Source DB:  PubMed          Journal:  Proc Biol Sci        ISSN: 0962-8452            Impact factor:   5.349


  80 in total

1.  Stream Transport and Retention of Environmental DNA Pulse Releases in Relation to Hydrogeomorphic Scaling Factors.

Authors:  Alexander K Fremier; Katherine M Strickler; Joseph Parzych; Stephen Powers; Caren S Goldberg
Journal:  Environ Sci Technol       Date:  2019-06-04       Impact factor: 9.028

2.  Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula.

Authors:  Dominique A Cowart; Katherine R Murphy; C-H Christina Cheng
Journal:  Mar Genomics       Date:  2017-12-06       Impact factor: 1.710

3.  Capture enrichment of aquatic environmental DNA: A first proof of concept.

Authors:  Taylor M Wilcox; Katherine E Zarn; Maxine P Piggott; Michael K Young; Kevin S McKelvey; Michael K Schwartz
Journal:  Mol Ecol Resour       Date:  2018-08-11       Impact factor: 7.090

4.  Environmental DNA (eDNA) Detection Probability Is Influenced by Seasonal Activity of Organisms.

Authors:  Lesley S de Souza; James C Godwin; Mark A Renshaw; Eric Larson
Journal:  PLoS One       Date:  2016-10-24       Impact factor: 3.240

5.  A systematic approach to evaluate the influence of environmental conditions on eDNA detection success in aquatic ecosystems.

Authors:  Bernhard C Stoeckle; Sebastian Beggel; Alexander F Cerwenka; Elena Motivans; Ralph Kuehn; Juergen Geist
Journal:  PLoS One       Date:  2017-12-08       Impact factor: 3.240

6.  Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance.

Authors:  Satsuki Tsuji; Masayuki Ushio; Sho Sakurai; Toshifumi Minamoto; Hiroki Yamanaka
Journal:  PLoS One       Date:  2017-04-27       Impact factor: 3.240

7.  Shedding light on eDNA: neither natural levels of UV radiation nor the presence of a filter feeder affect eDNA-based detection of aquatic organisms.

Authors:  Elvira Mächler; Maslin Osathanunkul; Florian Altermatt
Journal:  PLoS One       Date:  2018-04-06       Impact factor: 3.240

8.  Potential of Environmental DNA to Evaluate Northern Pike (Esox lucius) Eradication Efforts: An Experimental Test and Case Study.

Authors:  Kristine J Dunker; Adam J Sepulveda; Robert L Massengill; Jeffrey B Olsen; Ora L Russ; John K Wenburg; Anton Antonovich
Journal:  PLoS One       Date:  2016-09-14       Impact factor: 3.240

9.  An analytical framework for estimating aquatic species density from environmental DNA.

Authors:  Thierry Chambert; David S Pilliod; Caren S Goldberg; Hideyuki Doi; Teruhiko Takahara
Journal:  Ecol Evol       Date:  2018-02-25       Impact factor: 2.912

10.  Mitochondrial inner membrane permeabilisation enables mtDNA release during apoptosis.

Authors:  Joel S Riley; Giovanni Quarato; Catherine Cloix; Jonathan Lopez; Jim O'Prey; Matthew Pearson; James Chapman; Hiromi Sesaki; Leo M Carlin; João F Passos; Ann P Wheeler; Andrew Oberst; Kevin M Ryan; Stephen Wg Tait
Journal:  EMBO J       Date:  2018-07-26       Impact factor: 11.598

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  30 in total

1.  Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle.

Authors:  Jean-Baptiste Juhel; Rizkie S Utama; Virginie Marques; Indra B Vimono; Hagi Yulia Sugeha; Laurent Pouyaud; Tony Dejean; David Mouillot; Régis Hocdé
Journal:  Proc Biol Sci       Date:  2020-07-08       Impact factor: 5.349

2.  Using eDNA techniques to find the endangered big-headed turtle (Platysternon megacephalum).

Authors:  Ivan P Y Lam; Yik-Hei Sung; Jonathan J Fong
Journal:  PLoS One       Date:  2022-02-07       Impact factor: 3.240

3.  Can nuclear aquatic environmental DNA be a genetic marker for the accurate estimation of species abundance?

Authors:  Toshiaki S Jo; Kenji Tsuri; Hiroki Yamanaka
Journal:  Naturwissenschaften       Date:  2022-07-21

Review 4.  Priorities for ocean microbiome research.

Authors: 
Journal:  Nat Microbiol       Date:  2022-06-30       Impact factor: 30.964

5.  eDNA metabarcoding as a promising conservation tool to monitor fish diversity in Beijing water systems compared with ground cages.

Authors:  Mei Shen; Nengwen Xiao; Ziyi Zhao; Ningning Guo; Zunlan Luo; Guang Sun; Junsheng Li
Journal:  Sci Rep       Date:  2022-06-30       Impact factor: 4.996

6.  Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding.

Authors:  Laetitia Mathon; Virginie Marques; David Mouillot; Camille Albouy; Marco Andrello; Florian Baletaud; Giomar H Borrero-Pérez; Tony Dejean; Graham J Edgar; Jonathan Grondin; Pierre-Edouard Guerin; Régis Hocdé; Jean-Baptiste Juhel; Eva Maire; Gael Mariani; Matthew McLean; Andrea Polanco F; Laurent Pouyaud; Rick D Stuart-Smith; Hagi Yulia Sugeha; Alice Valentini; Laurent Vigliola; Indra B Vimono; Loïc Pellissier; Stéphanie Manel
Journal:  Proc Biol Sci       Date:  2022-04-20       Impact factor: 5.530

7.  Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves.

Authors:  Emilie Boulanger; Nicolas Loiseau; Alice Valentini; Véronique Arnal; Pierre Boissery; Tony Dejean; Julie Deter; Nacim Guellati; Florian Holon; Jean-Baptiste Juhel; Philippe Lenfant; Stéphanie Manel; David Mouillot
Journal:  Proc Biol Sci       Date:  2021-04-28       Impact factor: 5.349

8.  Quantification of marine benthic communities with metabarcoding.

Authors:  Lise Klunder; Judith D L van Bleijswijk; Loran Kleine Schaars; Henk W van der Veer; Pieternella C Luttikhuizen; Allert I Bijleveld
Journal:  Mol Ecol Resour       Date:  2021-11-01       Impact factor: 8.678

9.  Using environmental DNA methods to survey for rare groundwater fauna: Detection of an endangered endemic cave crayfish in northern Alabama.

Authors:  Spencer H Boyd; K Denise Kendall Niemiller; Katherine E Dooley; Jennifer Nix; Matthew L Niemiller
Journal:  PLoS One       Date:  2020-12-10       Impact factor: 3.240

10.  Environmental DNA metabarcoding primers for freshwater fish detection and quantification: In silico and in tanks.

Authors:  Lu Shu; Arne Ludwig; Zuogang Peng
Journal:  Ecol Evol       Date:  2021-05-16       Impact factor: 2.912

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