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Fishes
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Detection and Monitoring of Aquatic Pathogens by Using Environmental DNA...
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Detection and Monitoring of Aquatic Pathogens by Using Environmental DNA (eDNA)

A special issue of Fishes (ISSN 2410-3888). This special issue belongs to the section "Welfare, Health and Disease".

Deadline for manuscript submissions: closed (31 October 2024) | Viewed by 1565

Special Issue Editors

Prof. Dr. Rodolphe Elie Gozlan

E-Mail Website
Guest Editor
ISEM, Université de Montpellier, CNRS, IRD, EPHE, 34095 Montpellier, France
Interests: biodiversity conservation; emerging infectious diseases; invasive species; aquatic ecosystems; one health
Dr. Marine Combe

E-Mail Website
Guest Editor
ISEM (Institute of Evolutionary Science) of Montpellier, Université de Montpellier, CNRS, IRD, EPHE, 31095 Montpellier, France
Interests: emerging infectious diseases; biodiversity; bacteriology; virology; parasitology; aquatic ecosystems; invasive species; one health
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The journal Fishes is preparing a Special Issue entitled “Detection and monitoring of aquatic pathogens using environmental DNA”. Environmental DNA (eDNA) is an exciting tool for rapid biodiversity surveys and conservation and management strategies, allowing rapid targeted or multispecies detection by using DNA derived from an environmental sample in combination with high-throughput sequencing technologies. Importantly, eDNA-based biodiversity monitoring provides a non-destructive and non-invasive way to sample DNA from aquatic organisms, making it a more ethical tool for biodiversity monitoring. Increasingly, bacterial, fungal, and animal communities from diverse aquatic environments are being efficiently sampled using eDNA, allowing early detection of pathogen introduction and emergence. This special issue seeks to gather together studies that aim to develop eDNA assays to improve the detection and monitoring of all aquatic pathogens (including bacteria, viruses, and fungi) and parasites for biodiversity assessments, invasion biology studies, fisheries management and/or conservation strategies. A wide range of aspects are welcome, from innovative sampling strategies and molecular improvements to issues and questions regarding species specificities, sensitivity of detection, interpretation of results, etc.

Prof. Dr. Rodolphe Elie Gozlan
Dr. Marine Combe
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Fishes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • environmental DNA/RNA
  • aquatic pathogens and parasites
  • aquatic host-pathogens association
  • aquatic animal diseases
  • eDNA-based innovations.

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Published Papers (1 paper)

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Research

17 pages, 8321 KiB  
Article
Ease and Limitations in Using Environmental DNA to Track the Spread of Invasive Host–Parasite Complexes: A Case Study of the Freshwater Fish Pseudorasbora parva and the Cryptic Fungal Parasite Sphaerothecum destruens
by Théo Deremarque, Rodolphe Elie Gozlan, Ravo Ravaozafindrasoa, Giuliano Mucci, Lucie Delalex, Jean-Michel Foissy, Michaël Cagnant, Mathieu Clair, Justina Givens, Fabienne Justy, Alice Valentini, Delphine Nicolas, Pascal Contournet, Claire Tetrel, Marc Thibault and Marine Combe
Fishes 2024, 9(12), 477; https://doi.org/10.3390/fishes9120477 - 26 Nov 2024
Viewed by 1202
Abstract
The spread of non-native species threatens biodiversity and exacerbates societal challenges like food security. To address this, effective conservation programs require detection methods that are easy to implement, accurate, and non-invasive. Over the past 15 years, environmental DNA (eDNA) techniques have gained popularity, [...] Read more.
The spread of non-native species threatens biodiversity and exacerbates societal challenges like food security. To address this, effective conservation programs require detection methods that are easy to implement, accurate, and non-invasive. Over the past 15 years, environmental DNA (eDNA) techniques have gained popularity, surpassing traditional sampling methods. In this context, our study focused on tracking the invasive host–pathogen complex Pseudorasbora parva and Sphaerothecum destruens using eDNA metabarcoding. We collected water samples from freshwater canals over five months in the Camargue region, and once in Corsica Island, both in southern France. Total DNA was extracted from filtered water samples, and PCR-amplicons were sequenced using Illumina or Nanopore technologies. Our results revealed a high detection rate of P. parva in lentic ecosystems, aligning with habitat preferences of this small freshwater fish. Additionally, the detection rate in Camargue increased in May and June, likely due to the peak of the spawning season, which leads to more DNA being released into the environment (i.e., concentration and interaction of individuals). While eDNA successfully detected this invasive fish, we were unable to detect its cryptic fungal parasite, S. destruens, highlighting the challenges of identifying intracellular and cryptic fungal pathogens through eDNA methods. Full article
(This article belongs to the Special Issue Detection and Monitoring of Aquatic Pathogens by Using Environmental DNA (eDNA))
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