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Fishes
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Mapping and Monitoring Aquatic Biodiversity in Hotspot Habitat Areas Using...
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Mapping and Monitoring Aquatic Biodiversity in Hotspot Habitat Areas Using Environmental DNA (eDNA)

A special issue of Fishes (ISSN 2410-3888). This special issue belongs to the section "Biology and Ecology".

Deadline for manuscript submissions: 31 October 2025 | Viewed by 2819

Special Issue Editors

Dr. Yanjun Shen

E-Mail Website
Guest Editor
Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing 401331, China
Interests: fish diversity; community structure; adaptive evolution; evolution of diversity patterns; stress evolution of aquatic biodiversity
Prof. Dr. Wenping He

E-Mail Website
Guest Editor
College of Fisheries, Southwest University, Chongqing 400715, China
Interests: fish diversity; community structure
Special Issues, Collections and Topics in MDPI journals
Dr. Xiuhui Ma

E-Mail Website
Guest Editor
College of Animal Science, Guizhou University, Guiyang 550025, China
Interests: eDNA metabacoding; fish adaptive evolution

Special Issue Information

Dear Colleagues,

Environmental DNA technology is changing the way that biological data are obtained. The use of environmental DNA to monitor and quantify biodiversity has been one of the most important technological advances in the field of ecology in recent years and is now commonly used as a non-invasive means of monitoring species and communities.

To this end, this Special Issue will explore the new insights that environmental DNA data have provided for basic research in ecology and environmental sciences, including the following

  1. Theoretical and methodological studies related to environmental DNA technology;
  2. A wide range of research studies and applications of environmental DNA technology for target species monitoring, biodiversity assessment, biomass estimation, and aquatic ecosystem health assessment in aquatic ecosystems;
  3. Comparative studies between environmental DNA technology and other relevant aquatic biodiversity research methods.

Dr. Yanjun Shen
Prof. Dr. Wenping He
Dr. Xiuhui Ma
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

  • eDNA
  • aquatic biodiversity
  • fish diversity
  • community structure
  • diversity patterns
  • habitat destruction

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (4 papers)

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Research

13 pages, 2796 KiB  
Article
Revealing the Structure and Biodiversity Patterns of Fish Communities in River Networks Based on Environmental DNA
by Ziyu Liu, Yongsheng Wu, Wenhui You, Shuxin Li, Ge Shi and Chen Zhang
Fishes 2025, 10(4), 175; https://doi.org/10.3390/fishes10040175 - 13 Apr 2025
Viewed by 253
Abstract
Revealing taxonomic, functional, and phylogenetic dimensions of biodiversity is critical for the effective conservation and management of aquatic organisms in freshwater ecosystems subjected to multiple threats. Fish biodiversity patterns in river ecosystems exhibit complex spatiotemporal variation influenced by hydrological connectivity and the dispersal [...] Read more.
Revealing taxonomic, functional, and phylogenetic dimensions of biodiversity is critical for the effective conservation and management of aquatic organisms in freshwater ecosystems subjected to multiple threats. Fish biodiversity patterns in river ecosystems exhibit complex spatiotemporal variation influenced by hydrological connectivity and the dispersal ability of species within the river network. This study utilized eDNA metabarcoding to investigate fish communities in three subtropical mountain rivers, aiming to uncover the community structure and spatiotemporal dynamics of the multidimensional biodiversity of fish communities across varying positions within the river network. The three biodiversity indices of the fish communities at the confluence were significantly greater than those of the mainstream community in the dry season, whereas the phylogenetic diversity of the fish community at the tributaries during the wet season was significantly greater than that in the mainstream. This likely reflected the unique spatial configuration of confluences and the seasonal dispersal of fish in the river network. The results of this study highlighted the important role of confluences and tributaries in river networks and the fact that they need to be prioritized to conserve riverine fish diversity. Full article
(This article belongs to the Special Issue Mapping and Monitoring Aquatic Biodiversity in Hotspot Habitat Areas Using Environmental DNA (eDNA))
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14 pages, 2579 KiB  
Article
Environmental DNA Was Utilized to Assess Fish Diversity and Community Structure in the Qingshui River
by Fujiang Huang, Ruiyuan Zhang, Zhengyu Lv, Yan Xiang, Wenwu Min, Xue Wang, Wei Liu, Wei Wang and Sheng Zeng
Fishes 2025, 10(4), 165; https://doi.org/10.3390/fishes10040165 - 8 Apr 2025
Viewed by 283
Abstract
An accurate assessment of fish stocks is crucial for maintaining the health and stability of aquatic ecosystems. To understand the characteristics of fish diversity in the Qingshui River, this study utilized high-throughput sequencing data obtained through environmental DNA macrobarcoding technology (eDNA). The research [...] Read more.
An accurate assessment of fish stocks is crucial for maintaining the health and stability of aquatic ecosystems. To understand the characteristics of fish diversity in the Qingshui River, this study utilized high-throughput sequencing data obtained through environmental DNA macrobarcoding technology (eDNA). The research explored differences in fish diversity and community characteristics in the Qingshui River by analyzing fish community structure, α diversity, β diversity, and the redundancy of environmental factors. This analysis aims to provide data support for water ecological monitoring and management. The results were as follows: (1) A total of 91 species of fishes from 18 families and seven orders were detected in the eDNA survey, and the dominant species was Cypriniformes, accounting for 72.5%. (2) There were significant differences in α diversity analysis in the Qingshui River (p < 0.05). (3) The fish community structure was similar in β diversity analysis. (4) In the redundancy analysis of environmental factors, pH, DO, TN, TP, NO2− and MnO4− have the greatest impact on the Qingshui River Basin. eDNA technology has the advantages of high efficiency and low harm and can be used for water ecological monitoring and management. It provides a scientific basis for fish protection and a valuable reference for fish monitoring in the future. Full article
(This article belongs to the Special Issue Mapping and Monitoring Aquatic Biodiversity in Hotspot Habitat Areas Using Environmental DNA (eDNA))
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33 pages, 2651 KiB  
Article
Ichthyofaunal Metabarcoding in the Southern Appalachians: Use of eDNA Metabarcoding in Fish Surveys in Lotic Systems of the Great Smoky Mountains National Park with Comparisons to Historic Electrofishing Data
by Ben F. Brammell, Sara A. Brewer, Karsner S. Fetter, Lauren E. Slone, Matt A. Kulp and Ben R. S. McLaughlin
Fishes 2025, 10(4), 145; https://doi.org/10.3390/fishes10040145 - 22 Mar 2025
Viewed by 523
Abstract
eDNA appears well positioned to play a significant role in the future of biomonitoring, and the need to assess the efficacy of eDNA-based surveys in a variety of habitats is increasing. We conducted an eDNA metabarcoding-based survey of fish communities in the Great [...] Read more.
eDNA appears well positioned to play a significant role in the future of biomonitoring, and the need to assess the efficacy of eDNA-based surveys in a variety of habitats is increasing. We conducted an eDNA metabarcoding-based survey of fish communities in the Great Smoky Mountains National Park (GSMNP), located in eastern Tennessee and western North Carolina. The GSMNP, widely recognized as a biodiversity hotspot, encompasses 211,419 hectares of the Southern Appalachian Mountains with elevations up to 2205 meters and is home to approximately 73 species of fish, including 12 families and three species classified as endangered or threatened. We collected 50 water samples in first to sixth order streams at elevations of 336 to 1462 meters, including all major watersheds found in the park. eDNA was amplified utilizing two primer sets which each target differing regions of the 12S mitochondrial gene and generate amplicons of varying size (97 and 225 bp, respectively), and sequencing was conducted to an expected read depth of 400,000 reads per sample per marker. We detected a total of 40 fish species; of these, 36 were detected with the primer set which produces a 97 bp amplicon, and 12 of these 36 were detected only by this primer set. Species assemblages varied between stream orders, and species richness decreased with increasing elevation and increased with increasing stream order. Significant correlations were observed between biomass data from electrofishing monitoring (1984–2023) and eDNA metabarcoding read counts in five of seven species examined, including all salmonids. eDNA metabarcoding was demonstrated to be effective in assessing fish communities in high-elevation lotic systems in the Southern Appalachians, and our results suggest that primers targeting shorter amplicons may exhibit greater efficacy in these ecosystems. Full article
(This article belongs to the Special Issue Mapping and Monitoring Aquatic Biodiversity in Hotspot Habitat Areas Using Environmental DNA (eDNA))
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11 pages, 1590 KiB  
Article
Study on Fish Species Diversity in the Pingzhai Reservoir Based on Environmental DNA Technology
by Jingjing Yuan, Jing Wen, Qiuhong Kong and Xianjun Zhou
Fishes 2024, 9(10), 382; https://doi.org/10.3390/fishes9100382 - 27 Sep 2024
Cited by 1 | Viewed by 1185
Abstract
This study elucidated the composition and diversity characteristics of the main fish species in the Pingzhai Reservoir by collecting and analyzing environmental DNA (eDNA) samples from the reservoir and comparing them with data from traditional fishery resource surveys. The results showed that eDNA [...] Read more.
This study elucidated the composition and diversity characteristics of the main fish species in the Pingzhai Reservoir by collecting and analyzing environmental DNA (eDNA) samples from the reservoir and comparing them with data from traditional fishery resource surveys. The results showed that eDNA technology detected 43 fish species spanning 37 genera, 5 orders, and 11 families. Importantly, no significant difference in fish diversity was observed among the surveyed sites, and the potential of eDNA technology in studying fish diversity in the Pingzhai Reservoir was discussed. A total of 29 species distributed across 18 genera, 3 families, and 3 orders were captured using traditional resource surveys. Overall, 21 fish species were detected using both methods, constituting 48.8% of the total fish population. Cypriniformes were the most prominently detected order in both methods. Among all the fish species, the most abundant in the Pingzhai Reservoir were the free-range fish species Hypophthalmichthys molitrix and Hypophthalmichthys nobilis, which have the largest sequence abundance in the eDNA investigation, in addition to the detection of exotic species, such as Micropterus salmoides and Oreochromis niloticus. Compared with traditional investigation methods, eDNA technology offers several advantages, including high sensitivity, minimal ecological impact, superior data accuracy, and low cost, making it suitable for fish diversity research in fishery resources investigations. This study enhances our understanding of fish diversity in the Pingzhai Reservoir and provides crucial basic information to support the ecosystem management and restoration efforts of the reservoir. Full article
(This article belongs to the Special Issue Mapping and Monitoring Aquatic Biodiversity in Hotspot Habitat Areas Using Environmental DNA (eDNA))
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