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Biology
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Environmental DNA (eDNA) for Assessment of Coastal Marine Biodiversity
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Environmental DNA (eDNA) for Assessment of Coastal Marine Biodiversity

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Ecology".

Deadline for manuscript submissions: 15 December 2025 | Viewed by 1936

Special Issue Editors

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
Dr. Valeria Specchia

E-Mail Website
Guest Editor
Department of Biological and Environmental Sciences and Technologies, DiSTeBA, University of Salento, Via Monteroni 165, 73100 Lecce, Italy
Interests: eDNA metabarcoding; genomics; genetics

Special Issue Information

Dear Colleagues,

This Special Issue aims to collect research papers and reviews that present studies on the topic of eDNA metabarcoding, ranging from methodological aspects to applications in marine coastal ecosystems.

Environmental DNA (eDNA) metabarcoding is an innovative approach used to assess biodiversity in aquatic ecosystems. eDNA metabarcoding can provide a comprehensive overview of community composition, revealing insights into ecosystem health, species interactions, and the response of ecosystems to environmental change. Moreover, eDNA metabarcoding can address key ecological questions, contribute to the assessment of biological and genetic diversity, and support management decisions in aquatic environments. However, challenges such as the need for standardized protocols and the potential inability of this technology to determine species remain important considerations for researchers in the field. Overall, eDNA metabarcoding is a powerful tool that can be utilized to study aquatic ecosystems and enhance our understanding of biodiversity.

This Special Issue welcomes the submission of papers that explore methodologies and applications related to genetic and ecological questions, with a particular focus on coastal marine ecosystems.

Dr. Maurizio Pinna
Dr. Valeria Specchia
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. Biology 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 2700 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
  • coastal marine ecosystems
  • biodiversity
  • genetic distances
  • ecological indicators

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Published Papers (2 papers)

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16 pages, 4426 KB  
Article
Monitoring Fish Biodiversity in the Pelagic Zone of the Western Indian Ocean Using Environmental DNA Metabarcoding
by Ding Lyu, Rihong Xu, Yue Jin, Yulong Hu, Mianyu Liu, Guanzheng Lyu, Xiujuan Shan and Weiji Wang
Biology 2025, 14(9), 1194; https://doi.org/10.3390/biology14091194 - 4 Sep 2025
Viewed by 499
Abstract
The Indian Ocean is globally significant in terms of capture fisheries, and understanding the species composition of fish in the Indian Ocean is of great importance for the protection and development of its fishery resources. While coastal fish communities in the Indian Ocean [...] Read more.
The Indian Ocean is globally significant in terms of capture fisheries, and understanding the species composition of fish in the Indian Ocean is of great importance for the protection and development of its fishery resources. While coastal fish communities in the Indian Ocean are relatively well-documented, studies on pelagic zones remain sparse, especially for non-target species constituting fishery bycatch. Traditional biodiversity surveys rely on labor-intensive, inefficient trawling methods. To address these limitations, this study aims to apply environmental DNA (eDNA) metabarcoding for a species diversity survey in the Western Indian Ocean, offering a more reliable, efficient, and non-invasive alternative to traditional methods. The results will provide important insights into the region’s fish biodiversity, supporting sustainable management and conservation of fisheries resources in the area. Samples were collected from 130 stations in different water layers in the Western Indian Ocean, and species diversity was analyzed through 12S rRNA gene amplicon sequencing. The results showed that 98 fish species were detected from 176 seawater eDNA samples, belonging to two classes (Actinopteri and Chondrichthyes), 20 orders, 35 families, and 60 genera. Within a depth range of 300 m, there were no significant differences in species diversity parameters among samples from different depths. The orders with the highest relative abundance detected include Scombriformes, Aulopiformes, and Myctophiformes. The species with the highest relative abundance include Thunnus albacares, Alepisaurus ferox, Xiphias gladius, Diaphus fragilis, Decapterus macarellus, Thunnus maccoyii, and Platycephalus cultellatus. The species composition and relative abundance of economic species observed in this study showed, as expected, differences from fishery catch statistics. These results suggest that eDNA technology can not only monitor marine fish diversity more efficiently but also complement the lack of fisheries data. Integrating eDNA technology into routine monitoring in the Western Indian Ocean in the future could promote sustainable management of fisheries resources in the region. Full article
(This article belongs to the Special Issue Environmental DNA (eDNA) for Assessment of Coastal Marine Biodiversity)
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20 pages, 2851 KB  
Article
A Study on the Community and Ecological Characteristics of Benthic Invertebrates in the Ulungu River, Xinjiang, via eDNA Metabarcoding and Morphological Methods
by Qiang Huo, Yuying Ma, Linghui Hu, Qi Liu, Chengxin Wang, Jiaxuan Liu, Daoquan Ren, Zhichao Wang, Baoqiang Wang, Honghui Zeng, Yong Song and Sheng’ao Chen
Biology 2025, 14(4), 410; https://doi.org/10.3390/biology14040410 - 12 Apr 2025
Viewed by 772
Abstract
eDNA metabarcoding has been used for the biomonitoring of benthic invertebrates, but the correct steps to achieve its effectiveness, the stability of the results, and comparisons with morphological methods are still understudied. In this study, morphology and eDNA were studied for benthic invertebrate [...] Read more.
eDNA metabarcoding has been used for the biomonitoring of benthic invertebrates, but the correct steps to achieve its effectiveness, the stability of the results, and comparisons with morphological methods are still understudied. In this study, morphology and eDNA were studied for benthic invertebrate samples collected at six sites in the Ulungu River Basin. A Mantel test and NMDS analyses were used to test the correlations of the communities obtained via the two methods, the Shannon index was calculated to evaluate the ecological status, and the correlation of the evaluation results was analyzed. The results revealed that eDNA metabarcoding did not detect a greater number of species than the morphological method, that the results from the two methods shared fewer taxa at the family level and below, and that only five taxa were shared at the genus level. The Mantel test and NMDS analyses revealed very significant differences between the communities monitored by the two methods (PERMANOVA, p = 0.0056), but eDNA metabarcoding provided richness and abundance data for species that are difficult to identify morphologically, and these findings can be used to supplement the morphological data. The cor.test revealed that there was no significant correlation between the diversity and ecological assessment results of the two methods, and the ecological assessment results of eDNA metabarcoding cannot represent accurate and true ecological conditions. The water sample eDNA-based method and morphological method exhibited low consistency and high complementarity in monitoring benthic invertebrate communities and diversity. More research is still needed on the key links of eDNA sampling, the control of the degradation rate, data utilization, and index development to provide more environmentally friendly and effective monitoring methods for ecological protection, more reliable support for ecological decision-making, and to more adequately respond to the challenges of global environmental change. Full article
(This article belongs to the Special Issue Environmental DNA (eDNA) for Assessment of Coastal Marine Biodiversity)
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