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Diversity
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Applications of Environmental DNA for Fish and Aquatic Biodiversity Assessment
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Applications of Environmental DNA for Fish and Aquatic Biodiversity Assessment

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Biodiversity Conservation".

Deadline for manuscript submissions: 31 July 2026 | Viewed by 1712

Special Issue Editors

Dr. Cristina Nardi

E-Mail Website
Guest Editor
Instituto de Ciencias Polares, Recursos Naturales yAmbientes, Universidad Nacional de Tierra del Fuego (ICPA-UNTDF-CONICET), Fuegia Basket 251, Ushuaia V9410, Argentina
Interests: ecology; fish; eDNA
Dr. Maurizio Pinna

E-Mail Website
Guest Editor
Department of Biological and Environmental Sciences and Technologies, DiSTeBA, University of Salento, Via Monteroni 165, 73100 Lecce, Italy
Interests: aquatic ecosystems; biodiversity; benthic communities; fish fauna; litter decomposition; macroinvertebrates
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Environmental DNA (eDNA) analysis has transformed the detection and monitoring of aquatic biodiversity through non-invasive sampling of water bodies. This Special Issue aims to showcase innovative applications of eDNA for assessing fish diversity alongside other aquatic organisms across diverse environments, including marine, freshwater, and brackish systems. While fish are the key focus, studies exploring broader aquatic communities and their interactions are also welcome. Special attention will be given to cryptic, endemic, and poorly studied species that are often overlooked by traditional survey methods, as well as populations in remote and understudied locations. Additionally, this Special Issue will address the role of eDNA in detecting and monitoring biological invasions. Methodological optimisations and technical advances in eDNA applications will be considered. However, particular emphasis will be placed on studies where eDNA is employed as a tool to answer specific ecological or conservation questions. Aligned with the aims and scope of Diversity, this Special Issue seeks to promote interdisciplinary research that advances our understanding and supports the sustainable monitoring of aquatic ecosystems through the use of eDNA-based biodiversity assessments.

Dr. Cristina Nardi
Dr. Maurizio Pinna
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 250 words) can be sent to the Editorial Office for assessment.

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. Diversity 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 2100 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

  • eDNA metabarcoding
  • targeted eDNA
  • aquatic biodiversity
  • biological invasions
  • biodiversity monitoring

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Published Papers (2 papers)

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18 pages, 10471 KB  
Article
Environmental DNA Metabarcoding Reveals Hidden Fish Diversity and Strong Habitat Partitioning Across Coastal Ecosystems in the Con Dao Archipelago, Vietnam
by Hung Manh Pham, Jacques Panfili, Huy Duc Hoang, Monique Simier, Masaki Miya and Jean-Dominique Durand
Diversity 2026, 18(5), 255; https://doi.org/10.3390/d18050255 - 26 Apr 2026
Viewed by 649
Abstract
The Con Dao archipelago hosts the oldest MPA in Vietnam and is recognized as a regional marine biodiversity hotspot. Here, we applied environmental DNA (eDNA) metabarcoding to assess coastal fish diversity across four major habitat types: coral reefs, seagrass beds, mangroves, and a [...] Read more.
The Con Dao archipelago hosts the oldest MPA in Vietnam and is recognized as a regional marine biodiversity hotspot. Here, we applied environmental DNA (eDNA) metabarcoding to assess coastal fish diversity across four major habitat types: coral reefs, seagrass beds, mangroves, and a harbour in the Con Dao archipelago. Using MiFish-U 12S primers at eight stations, we detected 282 operational taxonomic units, corresponding to 144 fish taxa. Fish assemblages exhibited strong habitat structuring: community composition differed markedly among habitats, with minimal overlap. Only three species were shared across all habitats. Multivariate analyses confirmed that habitat type, rather than spatial distance among sites, was the primary driver of community differentiation. Mangrove and seagrass supported distinct assemblages that were underrepresented in existing species checklists and MPA management frameworks. Notably, eDNA detected cryptic and non-commercial species overlooked by conventional survey methods. These results substantially expand the known fish diversity of the Con Dao Archipelago and highlight the need to incorporate habitat heterogeneity, particularly non-reef ecosystems, into MPA design and monitoring. Although eDNA metabarcoding is subject to amplification biases and limited taxonomic resolution in reference databases, it offers a powerful complement to traditional surveys for characterizing under-sampled habitats. Full article
(This article belongs to the Special Issue Applications of Environmental DNA for Fish and Aquatic Biodiversity Assessment)
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17 pages, 6711 KB  
Article
Mapping the Research Landscape of Environmental DNA in China: Evidence from the CNKI Database
by Peng Hou, Xin Ma, Li Liu, Ying Men, Ding Yang and Chuntian Zhang
Diversity 2026, 18(2), 108; https://doi.org/10.3390/d18020108 - 8 Feb 2026
Viewed by 587
Abstract
Environmental DNA (eDNA) serves as the material foundation for biodiversity research. As a revolutionary biomonitoring tool, eDNA technology offers significant advantages such as being non-invasive, efficient, and cost-effective. Understanding the eDNA research landscape in China is important for global scholars, both for tracking [...] Read more.
Environmental DNA (eDNA) serves as the material foundation for biodiversity research. As a revolutionary biomonitoring tool, eDNA technology offers significant advantages such as being non-invasive, efficient, and cost-effective. Understanding the eDNA research landscape in China is important for global scholars, both for tracking progress in this field and for observing how an advanced biodiversity monitoring technology is systematically validated and applied in a major biodiversity-rich country. This study employs the CiteSpace bibliometric analysis tool, based on 304 publications from the CNKI database, to systematically map the research landscape in this field. The results indicate a consistent upward trend in the number of publications within China’s eDNA research domain, which has evolved through three stages. The field involves numerous researchers, with the top three prolific authors being Xiao-wei Zhang, Jiang-hua Yang, and Zhi Chen. Some research institutions have formed clusters, but a close cross-institutional collaborative network has yet to be established. Chinese eDNA research is oriented toward technological application and addressing ecological issues, with current hotspots focusing on applying eDNA technology to biodiversity studies through biomonitoring, biomass assessment, and biological community structure analysis, targeting phytoplankton, benthic animals, fish, and environmental microorganisms, among others. However, it also faces common global challenges. This study provides a reference for environmental DNA-related research and contributes Chinese experience and insights to global biodiversity monitoring. Full article
(This article belongs to the Special Issue Applications of Environmental DNA for Fish and Aquatic Biodiversity Assessment)
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