DNA-Based Biomonitoring of Aquatic Ecosystems

A special issue of Water (ISSN 2073-4441). This special issue belongs to the section "Biodiversity and Functionality of Aquatic Ecosystems".

Deadline for manuscript submissions: closed (20 December 2022) | Viewed by 8654

Special Issue Editor


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Guest Editor
School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, China
Interests: environmental DNA; biological monitoring; aquatic ecosystems

Special Issue Information

Dear Colleagues,

Human-induced environmental changes threaten water security and the survival of species. Recently, it is estimated that the Living Planet Index (LPI) of freshwater vertebrates such as fish and amphibians dropped to one-third of that recorded in 1970. Therefore, monitoring aquatic biodiversity and species distribution across space and time is critical to mitigate biodiversity loss and ensure eco-environmental management. Recently, DNA-based biomonitoring (e.g., DNA barcoding or metabarcoding) has provided an unprecedented opportunity to allow for species identification and monitoring. In particular, the non-invasive attributes of environmental DNA (eDNA) metabarcoding provide a promising way to assess biodiversity within different environments, including soil, sediment, water, snow and air. Although DNA-based detection to monitor aquatic biodiversity has rapidly increased and been used to detect complete biodiversity and target species (e.g., endangered, invasive or rare species), there are numerous obstacles to solving the basic and applied problems surrounding this method, for example, the establishing of standardized application methods for DNA-based biomonitoring, eDNA dynamic processes in aquatic ecosystems, and how to use this new tool to identify key stressors in ecosystems.

This Special Issue will provide a platform for research that highlights the utility and diversity of DNA-based research for biodiversity assessments and provides specific implications for stakeholders and governors to enhance eco-environmental management. Therefore, we expect to collect experimental, methodological, and application studies. The topics covered by this Special Issue will include, but are not limited to, the following:

  • DNA-based biodiversity surveys, including single- and multi-species detection, abundance estimates, occurrence and spatiotemporal patterns;
  • eDNA dynamics in aquatic ecosystems, including eDNA degradation, transport and shedding;
  • DNA-based impact assessment, including the ecological risk of pollutants and ecosystem changes under multiple stressors.

Prof. Dr. Yuan Zhang
Guest Editor

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Keywords

  • eDNA
  • biomonitoring
  • biodiversity
  • bioassessment
  • aquatic ecosystem
  • water management

Published Papers (3 papers)

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Research

13 pages, 2487 KiB  
Article
Next-Generation DNA Barcoding for Fish Identification Using High-Throughput Sequencing in Tai Lake, China
by Yawen Mu, Chao Song, Jianghua Yang, Yong Zhang and Xiaowei Zhang
Water 2023, 15(4), 774; https://0-doi-org.brum.beds.ac.uk/10.3390/w15040774 - 16 Feb 2023
Viewed by 2463
Abstract
Tai Lake, an important biodiversity hotspot of the lower reaches of the Yangtze River in China, possesses its characteristic fish fauna. Barcoding on native species is important for species identification and biodiversity assessment with molecular-based methods, such as environmental DNA (eDNA) metabarcoding. Here, [...] Read more.
Tai Lake, an important biodiversity hotspot of the lower reaches of the Yangtze River in China, possesses its characteristic fish fauna. Barcoding on native species is important for species identification and biodiversity assessment with molecular-based methods, such as environmental DNA (eDNA) metabarcoding. Here, DNA-barcoding coupled with high-throughput sequencing (HTS) and traditional Sanger sequencing was introduced to barcoding 180 specimens belonging to 33 prior morphological species, including the most majority of fish fauna in Tai Lake. HTS technology, on the one hand, significantly enhances the capture of barcode sequences of fish. The successful rate of fish barcoding was 74% and 91% in Sanger and HTS, respectively. On the other hand, the HTS output has a large number (64%) of insertions and deletions, which require strict bioinformatics processing to ensure that the ‘‘true’’ barcode sequence is captured. Cross-contamination and parasites were the primary error sources that compromised attempts at the DNA barcoding of fish species. The barcode gap analysis was 100% successful at delimiting species in all specimens. The automatic barcode gap discovery (ABGD) method grouped barcode sequences into 34 OTUs, and some deep divergence and closed species failed to obtain corresponding OTUs. Overall, the local species barcode library established by HTS barcoding here is anticipated to shed new light on conserving fish diversity in Tai Lake. Full article
(This article belongs to the Special Issue DNA-Based Biomonitoring of Aquatic Ecosystems)
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16 pages, 4892 KiB  
Article
Fish Biomonitoring and Ecological Assessment in the Dianchi Lake Basin Based on Environmental DNA
by Han Meng, Yuanyuan Lin, Wenjun Zhong, Zheng Zhao, Liang Shen, Zhen Ling, Kaisong Zhao and Shan Xu
Water 2023, 15(3), 399; https://0-doi-org.brum.beds.ac.uk/10.3390/w15030399 - 18 Jan 2023
Cited by 4 | Viewed by 2714
Abstract
Fish are among the main target groups when conducting biomonitoring and ecological assessment of aquatic environments. Environmental DNA (eDNA) metabarcoding provides a unique opportunity to enhance biomonitoring throughput, precision, and standardization. However, few fish monitoring studies based on eDNA metabarcoding have been conducted [...] Read more.
Fish are among the main target groups when conducting biomonitoring and ecological assessment of aquatic environments. Environmental DNA (eDNA) metabarcoding provides a unique opportunity to enhance biomonitoring throughput, precision, and standardization. However, few fish monitoring studies based on eDNA metabarcoding have been conducted at the basin scale. Taking Dianchi Lake and the three inflowing rivers (Panlong River, Baoxiang River, and Chai River) as research objects, this study monitored fish diversity via eDNA metabarcoding, and the Fish Index of Biological Integrity (F-IBI) was constructed and applied for the ecological assessment of the aquatic environment. Here, we detected 41 species belonging to 9 orders, 15 families, and 35 genera in the sampling areas, including 17 native fish species such as Hemiculter leucisculus, Cyprinus carpio, and Silurus soldatovi. Distinct diversity patterns were observed among Dianchi Lake and the three inflowing rivers. Particularly, the fish diversity of Panlong River was richer than that of Dianchi Lake, Baoxiang River, and Chai River. Water temperature (WT), chemical oxygen demand (COD), total nitrogen (TN), and total phosphorus (TP) significantly influenced the distribution of fish communities in most sampling sites of the Dianchi Lake basin (p < 0.05). Moreover, according to the F-IBI assessment system, 25% of the sampling sites were defined as ‘fine’ or above, and 75% were ‘impaired’ or below. This study provided insights into the ecological restoration and precise management of the aquatic environment of the Dianchi Lake basin. Full article
(This article belongs to the Special Issue DNA-Based Biomonitoring of Aquatic Ecosystems)
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12 pages, 1259 KiB  
Article
eDNA Biomonitoring of Macroinvertebrate Communities for the Bioassessment of a River’s Ecological Status
by Feifei Wu, Yanting Zou, Shan Qin, Feilong Li and Yuan Zhang
Water 2023, 15(2), 308; https://0-doi-org.brum.beds.ac.uk/10.3390/w15020308 - 11 Jan 2023
Cited by 3 | Viewed by 2810
Abstract
Environmental DNA (eDNA) becomes a promising technology for macroinvertebrate monitoring worldwide. In recent decades, with increasing humanization processes, such as water pollution and habitat fragmentation, the richness and abundance of macroinvertebrates show a dramatic decline, which is particularly evident in tropical or subtropical [...] Read more.
Environmental DNA (eDNA) becomes a promising technology for macroinvertebrate monitoring worldwide. In recent decades, with increasing humanization processes, such as water pollution and habitat fragmentation, the richness and abundance of macroinvertebrates show a dramatic decline, which is particularly evident in tropical or subtropical rivers. The high-throughput and rapid monitoring of species’ survival and the ecological status of their habitats are relevant to river management. Here, we used the eDNA technology to detect macroinvertebrates in the Dongjiang River—a typical subtropical river in Southern China, to assess the ecological status, based on eDNA datasets. Our data showed a total of 640 OTUs detected by eDNA technology, belonging to three phyla, five classes, 13 orders, 33 families and 71 genera of macroinvertebrates, and these taxa had a 36.6% coverage rate with historical data at the genus level. The traditional water quality index (WQI) showed that the upstream of Dongjiang River were mainly levels I~II, the middle stream were levels II~III, and the downstream were levels IV~V. The eDNA-based biotic indices showed almost the same findings, that is, the overall ecological status of Dongjiang River was: upstream > middle reaches > downstream. Overall, this study provides important datasets and technical support for eDNA technology in macroinvertebrate monitoring and ecosystem management in the subtropical rivers. Full article
(This article belongs to the Special Issue DNA-Based Biomonitoring of Aquatic Ecosystems)
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