Monitoring seasonal distribution of an endangered anadromous sturgeon in a large river using environmental DNA

Xu, Nanfei; Zhu, Bofeng; Shi, Fu-Ming; Shao, Kai; Que, Yanfu; Li, Weitao; Li, Wei; Jiao, Wenzhe; Tian, Hua; Xu, Dongmei; Chang, Junjun

doi:10.1007/s00114-018-1587-4

Cited by 20 publications

(23 citation statements)

References 17 publications

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“…In this study, peaks in eDNA read abundance were observed for 19 species among the 60 most abundant species for both ports. Although uncertainty exists about the relationship between eDNA abundance and species ecology, several studies observed peaks of read abundance corresponding to breeding or larval hatch in the freshwater environment (Buxton et al., 2018; Erickson et al., 2016; Laramie et al., 2015; Spear et al., 2015; Tillotson et al., 2018; Xu et al., 2018). Peaks in eDNA were also observed in Chinook Salmon ( Oncorhynchus tshawytscha ), Sockeye Salmon ( Oncorhynchus nerka ), and Bighead Carps ( Hypophthalmichthys spp.)…”

Section: Discussionmentioning

confidence: 99%

“…Here, we hypothesize that this type of winter activity in the Arctic marine environment could be detected through eDNA metabarcoding. For instance, several studies in freshwater environments have detected peaks of eDNA corresponding to breeding or larval hatching (Buxton et al., 2018; Erickson et al., 2016; Laramie et al., 2015; Spear et al., 2015; Tillotson et al., 2018; Xu et al., 2018).…”

Section: Introductionmentioning

confidence: 99%

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Detecting community change in Arctic marine ecosystems using the temporal dynamics of environmental DNA

et al. 2020

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Detecting community change in Arctic marine ecosystems using the temporal dynamics of environmental DNA

et al. 2020

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“…eDNA analysis can screen the presence or absence of rare fish species in water samples; thus, it has become very useful for monitoring and conserving vulnerable species. eDNA sampling has also become a common tool for surveying at-risk species because of its non-invasive nature and cost-effectiveness, such as for evaluating Green sturgeon [10,11] in the United States, Chinese sturgeon [71], and Mekong giant catfish [9] in Asia. In addition to the absence-presence detection of single species, estimating the species richness of fish communities is important for management and conservation.…”

Section: Edna Detectionmentioning

confidence: 99%

Standards for Methods Utilizing Environmental DNA for Detection of Fish Species

Shu

Ludwig

Peng

2020

Genes

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Environmental DNA (eDNA) techniques are gaining attention as cost-effective, non-invasive strategies for acquiring information on fish and other aquatic organisms from water samples. Currently, eDNA approaches are used to detect specific fish species and determine fish community diversity. Various protocols used with eDNA methods for aquatic organism detection have been reported in different eDNA studies, but there are no general recommendations for fish detection. Herein, we reviewed 168 papers to supplement and highlight the key criteria for each step of eDNA technology in fish detection and provide general suggestions for eliminating detection errors. Although there is no unified recommendation for the application of diverse eDNA in detecting fish species, in most cases, 1 or 2 L surface water collection and eDNA capture on 0.7-μm glass fiber filters followed by extraction with a DNeasy Blood and Tissue Kit or PowerWater DNA Isolation Kit are useful for obtaining high-quality eDNA. Subsequently, species-specific quantitative polymerase chain reaction (qPCR) assays based on mitochondrial cytochrome b gene markers or eDNA metabarcoding based on both 12S and 16S rRNA markers via high-throughput sequencing can effectively detect target DNA or estimate species richness. Furthermore, detection errors can be minimized by mitigating contamination, negative control, PCR replication, and using multiple genetic markers. Our aim is to provide a useful strategy for fish eDNA technology that can be applied by researchers, advisors, and managers.

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“…This can be used to analyze the distributional characteristics of target fish species. The eDNA method has progressed in aspects of fish resource management, like gathering the information of endangered fish [16,17], investigating invasive species [18], and evaluating fish diversity [19] and fish prey diversity [20]. Despite advantages of the eDNA method compared to conventional fish survey methods, it should be very careful for an interpretation of eDNA data [21].…”

Section: Introductionmentioning

confidence: 99%

Using Optimal Environmental DNA Method to Improve the Fish Diversity Survey—From Laboratory to Aquatic Life Reserve

Liu

Guo

et al. 2021

Water

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Conserving aquatic ecosystems requires efficient tools to accurately assess the biodiversity of aquatic species. However, existing knowledge is insufficient in terms of the reliability and the comparability of methods measuring fish diversity. Environmental DNA (eDNA), as a promising method, was used to detect fish taxa in this study. We optimized the eDNA method in the laboratory, and applied the optimal eDNA method to survey fish diversity in a natural aquatic life reserve. We simulated necessary steps of the eDNA method in the lab to increase the confidence of the field survey. Specifically, we compared different eDNA sampling, extraction, and sequencing strategies for accurately capturing fish species of the target area. We found that 1L water samples were sufficient for sampling eDNA information of the majority taxa. The filtration was more effective than the centrifugal precipitation for the eDNA extraction. The cloning sequencing was better than the high-throughput sequencing. The field survey showed that the Shannon–Wiener diversity index of fish taxa was the highest in Huairou Reservoir. The diversity index also showed seasonal changes. The accuracy rate of detecting fish taxa was positively correlated with the eDNA concentration. This study provides a scientific reference for an application of the eDNA method in terms of surveying and estimating the biodiversity of aquatic species.

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Monitoring seasonal distribution of an endangered anadromous sturgeon in a large river using environmental DNA

Cited by 20 publications

References 17 publications

Detecting community change in Arctic marine ecosystems using the temporal dynamics of environmental DNA

Detecting community change in Arctic marine ecosystems using the temporal dynamics of environmental DNA

Standards for Methods Utilizing Environmental DNA for Detection of Fish Species

Using Optimal Environmental DNA Method to Improve the Fish Diversity Survey—From Laboratory to Aquatic Life Reserve

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