scholarly journals Quantification of Environmental DNA (eDNA) shedding and decay rates for three commercially harvested fish species and comparison between eDNA detection and trawl catches

2021 ◽  
Author(s):  
Anish Kirtane ◽  
Daniel Wieczorek ◽  
Thomas Noji ◽  
Liza Baskin ◽  
Claire Ober ◽  
...  
Keyword(s):  
Fish Species ◽  
Environmental Dna ◽  
Decay Rates ◽  
Trawl Catches

scholarly journals Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tatsuhiko Hoshino ◽  
Ryohei Nakao ◽  
Hideyuki Doi ◽  
Toshifumi Minamoto
Keyword(s):  
Fish Species ◽  
High Throughput Sequencing ◽  
Correlation Coefficients ◽  
Environmental Dna ◽  
Digital Pcr ◽  
Absolute Quantification ◽  
Taqman Probe ◽  
Individual Species ◽  
Natural Environments ◽  
Target Sequence

AbstractThe combination of high-throughput sequencing technology and environmental DNA (eDNA) analysis has the potential to be a powerful tool for comprehensive, non-invasive monitoring of species in the environment. To understand the correlation between the abundance of eDNA and that of species in natural environments, we have to obtain quantitative eDNA data, usually via individual assays for each species. The recently developed quantitative sequencing (qSeq) technique enables simultaneous phylogenetic identification and quantification of individual species by counting random tags added to the 5′ end of the target sequence during the first DNA synthesis. Here, we applied qSeq to eDNA analysis to test its effectiveness in biodiversity monitoring. eDNA was extracted from water samples taken over 4 days from aquaria containing five fish species (Hemigrammocypris neglectus, Candidia temminckii, Oryzias latipes, Rhinogobius flumineus, and Misgurnus anguillicaudatus), and quantified by qSeq and microfluidic digital PCR (dPCR) using a TaqMan probe. The eDNA abundance quantified by qSeq was consistent with that quantified by dPCR for each fish species at each sampling time. The correlation coefficients between qSeq and dPCR were 0.643, 0.859, and 0.786 for H. neglectus, O. latipes, and M. anguillicaudatus, respectively, indicating that qSeq accurately quantifies fish eDNA.

scholarly journals Environmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood

Biology ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 1132
Author(s):  
Hung-Tai Lee ◽  
Cheng-Hsin Liao ◽  
Te-Hua Hsu
Keyword(s):  
Species Diversity ◽  
Species Identification ◽  
Fish Species ◽  
Large Scale ◽  
Environmental Dna ◽  
Universal Primers ◽  
Similar Species ◽  
Operational Taxonomic Units ◽  
Fish Market ◽  
Fish Species Identification

Seafood, especially in traditional food Taiwan, is rarely sourced from a fixed species and routinely from similar species depending on their availability. Hence, the species composition of seafood can be complicated. While a DNA-based approach has been routinely utilized for species identification, a large scale of seafood identification in fish markets and restaurants could be challenging (e.g., elevated cost and time-consuming only for a limited number of species identification). In the present study, we aimed to identify the majority of fish species potentially consumed in fish markets and nearby seafood restaurants using environmental DNA (eDNA) metabarcoding. Four eDNA samplings from a local fish market and nearby seafood restaurants were conducted using Sterivex cartridges. Nineteen universal primers previously validated for fish species identification were utilized to amplify the fragments of mitochondrial DNA (12S, COI, ND5) of species in eDNA samples and sequenced with NovaSeq 6000 sequencing. A total of 153 fish species have been identified based on 417 fish related operational taxonomic units (OTUs) generated from 50,534,995 reads. Principal Coordinate Analysis (PCoA) further showed the differences in fish species between the sampling times and sampling sites. Of these fish species, 22 chondrichthyan fish, 14 Anguilliformes species, and 15 Serranidae species were respectively associated with smoked sharks, braised moray eels, and grouper fish soups. To our best knowledge, this work represents the first study to demonstrate the feasibility of a large scale of seafood identification using eDNA metabarcoding approach. Our findings also imply the species diversity in traditional seafood might be seriously underestimated and crucial for the conservation and management of marine resources.

scholarly journals Monitoring spawning migrations of potamodromous fish species via eDNA

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Bettina Thalinger ◽  
Elisabeth Wolf ◽  
Michael Traugott ◽  
Josef Wanzenböck
Keyword(s):  
Fish Species ◽  
Anthropogenic Impacts ◽  
Environmental Dna ◽  
Signal Strength ◽  
Digital Pcr ◽  
Freshwater Ecosystems ◽  
Non Invasive ◽  
River Stretch ◽  
Daily Discharge ◽  
Invasive Techniques

Abstract Potamodromous fish are considered important indicators of habitat connectivity in freshwater ecosystems, but they are globally threatened by anthropogenic impacts. Hence, non-invasive techniques are necessary for monitoring during spawning migrations. The use of environmental DNA (eDNA) potentially facilitates these efforts, albeit quantitative examinations of spawning migrations remain so far mostly uncharted. Here, we investigated spawning migrations of Danube bleak, Alburnus mento, and Vimba bream, Vimba vimba, and found a strong correlation between daily visual fish counts and downstream eDNA signals obtained from filtered water samples analysed with digital PCR and end-point PCR coupled with capillary electrophoresis. By accounting for daily discharge fluctuations, it was possible to predict eDNA signal strength from the number of migrating fish: first, the whole spawning reach was taken into account. Second, the model was validated using eDNA signals and fish counts obtained from the upper half of the examined river stretch. Consequently, fish counts and their day-to-day changes could be described via an eDNA-based time series model for the whole migration period. Our findings highlight the capability of eDNA beyond delivering simple presence/absence data towards efficient and informative monitoring of highly dynamic aquatic processes such as spawning migrations of potamodromous fish species.

scholarly journals Salinity stress increases the severity of ranavirus epidemics in amphibian populations

2020 ◽  
Vol 287 (1926) ◽  
pp. 20200062 ◽  
Author(s):  
Emily M. Hall ◽  
Jesse L. Brunner ◽  
Brandon Hutzenbiler ◽  
Erica J. Crespi
Keyword(s):  
Salinity Stress ◽  
Negative Relationship ◽  
Environmental Dna ◽  
Transmission Efficiency ◽  
Decay Rates ◽  
Mass Mortality ◽  
Population Declines ◽  
Elevated Salinity ◽  
Chronic Stressor ◽  
Small Change

The stress-induced susceptibility hypothesis, which predicts chronic stress weakens immune defences, was proposed to explain increasing infectious disease-related mass mortality and population declines. Previous work characterized wetland salinization as a chronic stressor to larval amphibian populations. Thus, we combined field observations with experimental exposures quantifying epidemiological parameters to test the role of salinity stress in the occurrence of ranavirus-associated mass mortality events. Despite ubiquitous pathogen presence (94%), populations exposed to salt runoff had slightly more frequent ranavirus related mass mortality events, more lethal infections, and 117-times greater pathogen environmental DNA. Experimental exposure to chronic elevated salinity (0.8–1.6 g l −1 Cl − ) reduced tolerance to infection, causing greater mortality at lower doses. We found a strong negative relationship between splenocyte proliferation and corticosterone in ranavirus-infected larvae at a moderate elevation of salinity, supporting glucocorticoid-medicated immunosuppression, but not at high salinity. Salinity alone reduced proliferation further at similar corticosterone levels and infection intensities. Finally, larvae raised in elevated salinity had 10 times more intense infections and shed five times as much virus with similar viral decay rates, suggesting increased transmission. Our findings illustrate how a small change in habitat quality leads to more lethal infections and potentially greater transmission efficiency, increasing the severity of ranavirus epidemics.

scholarly journals Pilot Study on Fish Species Composition Using Environmental DNA in Marine Sediment

2021 ◽  
Vol 44 (4) ◽  
pp. 79-84
Author(s):  
Tomohiro SHIRAGAKI ◽  
Taku INOUE ◽  
Hideki FUKUDA ◽  
Masayuki USHIO ◽  
Miki KUSAKA ◽  
...  
Keyword(s):  
Pilot Study ◽  
Species Composition ◽  
Fish Species ◽  
Marine Sediment ◽  
Environmental Dna ◽  
Fish Species Composition

Environmental DNA (eDNA) metabarcoding protocol for fish species v2 (protocols.io.bar4id8w)

protocols.io ◽  
2019 ◽  
Author(s):  
Omneya Ahmed ◽  
Tomas Larsson ◽  
Mats T ◽  
Alexander Eiler
Keyword(s):  
Fish Species ◽  
Environmental Dna

scholarly journals Improving the detection of rare native fish species in environmental DNA metabarcoding surveys

2021 ◽  
Author(s):  
Jack Rojahn ◽  
Dianne M. Gleeson ◽  
Elise Furlan ◽  
Tim Haeusler ◽  
Jonas Bylemans
Keyword(s):  
Fish Species ◽  
Environmental Dna ◽  
Native Fish ◽  
Dna Metabarcoding

scholarly journals New findings of light dusky rockfish Sebastes variabilis (Sebastidae) at the eastern coast of Kamchatka

2020 ◽  
Vol 200 (4) ◽  
pp. 895-906
Author(s):  
Yu. K. Kurbanov
Keyword(s):  
Body Weight ◽  
Body Length ◽  
Fish Species ◽  
Bottom Topography ◽  
Water Dynamics ◽  
Eastern Coast ◽  
Migration Routes ◽  
New Findings ◽  
Rare Fish ◽  
Trawl Catches

Light dusky rockfish Sebastes variabilis is a rare fish species in the waters at East Kamchatka, rarely recorded in trawl catches. They aggregate in the areas with complicated bottom topography and active water dynamics with the depth from 118 to 316 m. Their maximum catches are recorded off Capes Gowen, Olyutorsky, and Kronotsky. The light dusky rockfish body length varies from 34 to 50 cm, and body weight — from 0.53 to 1.78 kg. Some issues related to the migration routes of this species to the shores of Kamchatka are discussed.

scholarly journals Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves

2021 ◽  
Vol 288 (1949) ◽  
Author(s):  
Emilie Boulanger ◽  
Nicolas Loiseau ◽  
Alice Valentini ◽  
Véronique Arnal ◽  
Pierre Boissery ◽  
...  
Keyword(s):  
Species Richness ◽  
Fish Species ◽  
Fish Assemblages ◽  
Marine Reserves ◽  
Marked Change ◽  
Environmental Dna ◽  
Biodiversity Loss ◽  
Conclusive Evidence ◽  
Anthropogenic Pressure ◽  
Local Species Richness

Although we are currently experiencing worldwide biodiversity loss, local species richness does not always decline under anthropogenic pressure. This conservation paradox may also apply in protected areas but has not yet received conclusive evidence in marine ecosystems. Here, we survey fish assemblages in six Mediterranean no-take reserves and their adjacent fishing grounds using environmental DNA (eDNA) while controlling for environmental conditions. We detect less fish species in marine reserves than in nearby fished areas. The paradoxical gradient in species richness is accompanied by a marked change in fish species composition under different managements. This dissimilarity is mainly driven by species that are often overlooked by classical visual surveys but detected with eDNA: cryptobenthic, pelagic, and rare fishes. These results do not negate the importance of reserves in protecting biodiversity but shed new light on how under-represented species groups can positively react to fishing pressure and how conservation efforts can shape regional biodiversity patterns.

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