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Animals
Special Issues
Environmental DNA for Biodiversity Assessment and Monitoring: Challenges and Perspectives
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Environmental DNA for Biodiversity Assessment and Monitoring: Challenges and Perspectives

A special issue of Animals (ISSN 2076-2615).

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 5762

Special Issue Editor

Dr. Richard C. Edmunds

E-Mail Website
Guest Editor
Reef Restoration and Adaptation Program, Australian Institute of Marine Science, Townsville, QLD 4811, Australia
Interests: environmental DNA; assay development; candidate gene expression; functional genomics; ecotoxicology; developmental transcriptomics

Special Issue Information

Dear Colleagues,

The conservation and management of global ecosystems are critical to the interest of all humans, nations, and governments. Our current knowledge regarding the inherent biodiversity of global ecosystems and the impacts of natural and anthropogenic stressors on the current biodiversity is far from complete. Environmental DNA (eDNA) is a contemporary molecular genetic tool that has shown great promise over the past decade for advancing our collective knowledge about the biodiversity of global ecosystems and how these ecosystems are changing in response to natural and anthropogenic stressors. However, the development of new molecular tools (e.g., targeted, metabarcoding, and eRNA assays) is not without unexpected challenges and unanticipated perspectives. This Special Issue aims to publish a diverse range of original research, review, rapid communication, and methodology articles that collectively advance our understanding about the challenges and perspectives of eDNA-based biodiversity assessment and monitoring.

In this Special Issue, original research articles, reviews, rapid communications, and methodologies are welcome. Research areas may include (but are not limited to) the following: 

  1. Detection of endangered, invasive, or problematic species for biodiversity assessment (targeted or metabarcoding);
  2. Assessment of baseline population diversity and/or abundance for long-term conservation management monitoring;
  3. Monitoring biosecurity threats in imported goods and ports (including invertebrates, parasites, bacteria, and viruses);
  4. Monitoring recovery or decline of ecosystem health (including population size and genetic diversity);
  5. Monitoring aquaculture systems for health/stress, productivity, infestations, and diseases (including eRNA);
  6. Development of novel methodologies for improved efficiency, sensitivity, throughput, or logistics (including eRNA) .

Dr. Richard C. Edmunds
Guest Editor

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. Animals is an international peer-reviewed open access semimonthly 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 2400 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
  • environmental RNA
  • ecosystem assessment
  • biodiversity
  • conservation management
  • invasive species
  • endangered species
  • aquaculture
  • biosecurity
  • preservation

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Published Papers (2 papers)

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Research

14 pages, 2893 KiB  
Article
Heterogeneity of Fish Taxonomic and Functional Diversity Evaluated by eDNA and Gillnet along a Mangrove–Seagrass–Coral Reef Continuum
by Shuting Qiu, Jillian Lean Sim Ooi, Weilin Chen, Sze-Wan Poong, Han Zhang, Weiyi He, Shangke Su, Hao Luo, Wenjia Hu, Yang Amri Affendi, Jianguo Du and Kar-Hoe Loh
Animals 2023, 13(11), 1777; https://doi.org/10.3390/ani13111777 - 26 May 2023
Cited by 2 | Viewed by 2967
Abstract
The effective and reliable monitoring of fish communities is important for the management and protection of marine ecosystems. Environmental DNA (eDNA) metabarcoding is a relatively new method that has been widely used in recent years, while traditional sampling via fish catching (i.e., gillnets) [...] Read more.
The effective and reliable monitoring of fish communities is important for the management and protection of marine ecosystems. Environmental DNA (eDNA) metabarcoding is a relatively new method that has been widely used in recent years, while traditional sampling via fish catching (i.e., gillnets) is one of the most common and reliable fish monitoring methods used to date. We compared the taxonomic and functional diversity of fish detected within a mangrove–seagrass–coral reef continuum using both survey methods. One liter seawater and gillnet samples were collected in August 2021 from mangrove forests, seagrass meadows and coral reef habitats (n = 3 each) in Hainan, China. Surveys using eDNA and gillnets identified 139 genera belonging to 66 families and 58 genera belonging to 42 families, respectively. Regardless of the survey method, fish detected in mangrove, seagrass and coral reef habitats were heterogeneous in their communities; however, the shared species between habitats suggest some degree of connectivity. There were no significant differences between habitats in terms of taxonomic and functional diversity, but a higher taxonomic diversity was detected using eDNA. Both methods were able to distinguish fish assemblages between different habitats; however, gillnet surveys performed better than eDNA surveys for distinguishing mangrove from seagrass assemblages. Therefore, the concurrent use of eDNA and gillnet survey methods provides a more comprehensive approach to understanding the heterogeneity of fish taxonomic and functional diversity along mangrove–seagrass–coral reef continuums. Full article
(This article belongs to the Special Issue Environmental DNA for Biodiversity Assessment and Monitoring: Challenges and Perspectives)
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11 pages, 1122 KiB  
Article
Detection of the Endangered Siamese Bat Catfish (Oreoglanis siamensis Smith, 1933) in Doi Inthanon National Park Using Environmental DNA
by Thanatrinan Rodpai, Chatmongkon Suwannapoom and Maslin Osathanunkul
Animals 2023, 13(3), 538; https://doi.org/10.3390/ani13030538 - 3 Feb 2023
Cited by 3 | Viewed by 2099
Abstract
Siamese bat catfish (Oreoglanis siamensis Smith, 1993) has been listed as an endangered species, and its abundance has been severely declining due to habitat degradation and overfishing. To establish an appropriate management strategy, it is crucial to gain information about the distribution [...] Read more.
Siamese bat catfish (Oreoglanis siamensis Smith, 1993) has been listed as an endangered species, and its abundance has been severely declining due to habitat degradation and overfishing. To establish an appropriate management strategy, it is crucial to gain information about the distribution of this endangered species. As O. siamensis live under rocks in streams, detecting their presence is difficult. Recently, environmental DNA (eDNA)–based detection has been demonstrated to be a valid tool for monitoring rare species, such as O. siamensis. Therefore, this study developed an eDNA assay targeting a 160 bp fragment of the COI region to detect the presence of this species in its natural habitat. An amount of 300 mL of water samples (0.7 μm filtered) were collected from 15 sites in the Mae Klang sub-basin, where this fish species was visually detected at two locations. O. siamensis eDNA was detected at 12 of the 15 sites sampled with varying concentrations (0.71–20.27 copies/mL), including at the sites where this species was visually detected previously. The developed O. siamensis eDNA assay was shown to be effective for detecting the presence of this endangered species in the Klang Phat and Klang Rivers within the Doi Inthanon National Park. Full article
(This article belongs to the Special Issue Environmental DNA for Biodiversity Assessment and Monitoring: Challenges and Perspectives)
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