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Fishes
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Application of Environmental DNA Technology in Fishery Resources
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Application of Environmental DNA Technology in Fishery Resources

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

Deadline for manuscript submissions: closed (21 September 2022) | Viewed by 16142

Special Issue Editors

Dr. Catherine A. Richter

E-Mail Website
Guest Editor
Columbia Environmental Research Center, USGS, 4200 E New Haven Rd, Columbia, MO 65201, USA
Interests: aquatic toxicology; gene expression; environmental DNA; invasive aquatic species; freshwater mussels; thiamine deficiency
Dr. Richard F. Lance

E-Mail Website
Guest Editor
Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS, USA
Interests: environmental DNA; environmental RNA; DNA metabarcoding; DNA barcoding; noninvasive genetics; invasive species; threatened and endangered species; ecological networks; bat ecology and genetics

Special Issue Information

Dear Colleagues,

The journal Fishes is preparing a Special Issue entitled “Application of Environmental DNA Technology in Fishery Resources”. Analysis of environmental DNA (eDNA) has emerged as a powerful and versatile tool to inform decisions in the management of fisheries resources, including commercial, subsistence, and recreational fisheries as well as ecological services dependent on healthy and abundant fish populations. Monitoring with eDNA is especially well-suited to studies of rare species, either for early detection of aquatic invaders, or for the investigation of species of conservation concern. This Special Issue will highlight studies that utilize the unique advantages of eDNA analysis in non-invasive detection, species specificity, sensitivity of detection, and ease of sampling to answer questions and solve problems in fisheries management. Studies of innovative approaches to sampling and detection are also welcome.

Dr. Catherine A. Richter
Dr. Richard F. Lance
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

  • environmental DNA
  • environmental RNA
  • aquatic invasive species
  • threatened and endangered fish species
  • management of fishery resources
  • improved methodology
  • eDNA innovations

Published Papers (6 papers)

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Research

15 pages, 1933 KiB  
Article
Round Goby Detection in Lakes Huron and Michigan—An Evaluation of eDNA and Fish Catches
by Kasia J. Przybyla-Kelly, Ashley M. Spoljaric and Meredith B. Nevers
Fishes 2023, 8(1), 41; https://doi.org/10.3390/fishes8010041 - 6 Jan 2023
Cited by 6 | Viewed by 2288 | Correction
Abstract
Aquatic surveys for fish in large water bodies (e.g., Laurentian Great Lakes of North America) often require a flexible approach using multiple methods, surveying different depths, and sampling across seasons, especially when the target species is elusive in its natural habitat. The round [...] Read more.
Aquatic surveys for fish in large water bodies (e.g., Laurentian Great Lakes of North America) often require a flexible approach using multiple methods, surveying different depths, and sampling across seasons, especially when the target species is elusive in its natural habitat. The round goby (Neogobius melanostomus) is an invasive, bottom-dwelling fish inhabiting rocky areas of all five Great Lakes. While trawl surveys are typically used for abundance assessments, angling has been demonstrated as a means of supplementing surveys with additional data. Yet, round goby abundance and distribution is still not well described. Recently, with considerable success, scientists have explored sampling environmental DNA (eDNA) to complement traditional monitoring techniques for population abundance estimates, early detection of invasive species, and spawning or migration events. Therefore, we collected eDNA from water samples alongside bottom trawls and hook and line angling in Lakes Huron and Michigan to detect round goby. eDNA samples were analyzed by both droplet digital PCR (ddPCR) and quantitative PCR (qPCR) to maximize the likelihood of detection. Overall, round goby was captured in 23% of the trawls, but the eDNA based methods detected round goby in 74% and 66% of samples by ddPCR and qPCR, respectively, mostly in samples collected at <30 m depths, and mostly in the fall. More studies comparing eDNA based methods to traditional monitoring, especially trawls in large open waters, may contribute to a better understanding of using eDNA in population assessments. Full article
(This article belongs to the Special Issue Application of Environmental DNA Technology in Fishery Resources)
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18 pages, 1632 KiB  
Article
Validation of a Portable eDNA Detection Kit for Invasive Carps
by Stacie A. Kageyama, Matthew R. Hoogland, Tariq Tajjioui, Theresa M. Schreier, Richard A. Erickson and Christopher M. Merkes
Fishes 2022, 7(6), 363; https://doi.org/10.3390/fishes7060363 - 30 Nov 2022
Cited by 6 | Viewed by 3295
Abstract
Loop-mediated isothermal amplification (LAMP) is a rapid molecular detection technique that has been used as a diagnostic tool for detecting human and animal pathogens for over 20 years and is promising for detecting environmental DNA shed by invasive species. We designed a LAMP [...] Read more.
Loop-mediated isothermal amplification (LAMP) is a rapid molecular detection technique that has been used as a diagnostic tool for detecting human and animal pathogens for over 20 years and is promising for detecting environmental DNA shed by invasive species. We designed a LAMP assay to detect the invasive carps, silver carp (Hypophthalmichthys molitrix), bighead carp (Hypophthalmichthys nobilis), black carp (Mylopharyngodon piceus), and grass carp (Ctenopharyngodon idella). To determine the sensitivity of the LAMP assay, we determined limit of detection (LOD) for each invasive carp species and compared with the performance of a grass carp quantitative PCR (qPCR) assay in LOD and in a mesocosm study. We used two grass carp densities, 3 juvenile grass carp in one mesocosm and 33 juvenile grass carp in the other. Prior to adding grass carp to the mesocosms, we added 68 kg of fathead minnows (Pimephales promelas) to each mesocosm to simulate farm ponds used for raising bait fish. We filtered 500 mL of water per sample to compare LAMP and qPCR analysis, and we collected 50 mL grab samples that were only analyzed using qPCR to gain additional data using a higher-throughput method to monitor environmental DNA (eDNA) levels throughout the study period. No eDNA for any of the four invasive carp species was detected in water collected from the mesocosms during the three days prior to adding grass carp. Forty-eight hours after grass carp addition to mesocosms, we detected grass carp eDNA in the mesocosm containing 33 grass carp using the LAMP assay. However, we failed to detect any grass carp DNA in the mesocosm containing 3 grass carp with the LAMP assay throughout the study. We analyzed the data using an occupancy model and found that the 500 mL filter samples yielded a higher eDNA capture probability than 50 mL grab samples in the mesocosm containing three grass carp but had similar eDNA capture probability in the mesocosm containing 33 grass carp. Both LAMP and qPCR reliably detected grass carp eDNA 2 days after grass carp addition, but detections were more consistent with qPCR. The LAMP assay may have utility for certain niche uses because it can be used to rapidly analyze eDNA samples and is robust to inhibition, despite having some limitations. Full article
(This article belongs to the Special Issue Application of Environmental DNA Technology in Fishery Resources)
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19 pages, 1370 KiB  
Article
Establishing the Signal above the Noise: Accounting for an Environmental Background in the Detection and Quantification of Salmonid Environmental DNA
by Morgan D. Hocking, Jeffrey C. MacAdams, Michael J. Allison, Lauren C. Bergman, Robert Sneiderman, Ben F. Koop, Brian M. Starzomski, Mary L. Lesperance and Caren C. Helbing
Fishes 2022, 7(5), 266; https://doi.org/10.3390/fishes7050266 - 29 Sep 2022
Cited by 4 | Viewed by 2339
Abstract
A current challenge for environmental DNA (eDNA) applications is how to account for an environmental (or false-positive) background in surveys. We performed two controlled experiments in the Goldstream Hatchery in British Columbia using a validated coho salmon (Oncorhynchus kisutch) eDNA assay [...] Read more.
A current challenge for environmental DNA (eDNA) applications is how to account for an environmental (or false-positive) background in surveys. We performed two controlled experiments in the Goldstream Hatchery in British Columbia using a validated coho salmon (Oncorhynchus kisutch) eDNA assay (eONKI4). In the density experiment at high copy number, eDNA in 2 L water samples was measured from four 10 kL tanks containing 1 to 65 juvenile coho salmon. At these densities, we obtained a strong positive 1:1 relationship between predicted copy number/L and coho salmon biomass (g/L). The dilution experiment simulated a situation where fish leave a pool environment, and water from upstream continues to flow through at rates of 141–159 L/min. Here, three coho salmon were placed in four 10 kL tanks, removed after nine days, and the amount of remaining eDNA was measured at times coinciding with dilutions of 20, 40, 80, 160, and 1000 kL. The dilution experiment demonstrates a novel method using Binomial–Poisson distributions to detect target species eDNA at low copy number in the presence of an environmental background. This includes determination of the limit of blank with background (LOB-B) with a controlled false positive rate, and limit of detection with background (LOD-B) with a controlled false negative rate, which provides a statistically robust “Detect” or “No Detect” assessment for eDNA surveys. Full article
(This article belongs to the Special Issue Application of Environmental DNA Technology in Fishery Resources)
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20 pages, 2868 KiB  
Article
eDNA and Acoustic Tag Monitoring Reveal Congruent Overwintering Distributions of Striped Bass in a Hydrologically Complex Estuarine Environment
by Michaela Harris, Nathalie Brodeur, Francis LeBlanc, Scott Douglas, Paul Chamberland, Thomas Guyondet, Royce Steeves and Nellie Gagné
Fishes 2022, 7(4), 183; https://doi.org/10.3390/fishes7040183 - 23 Jul 2022
Cited by 3 | Viewed by 2520
Abstract
After collapsing in the late 1990s, the southern Gulf of St. Lawrence population of striped bass (Morone saxatilis) is recovering. Here, we evaluate the use of under-ice eDNA sampling to monitor the population and confirm overwintering locations. From 2018 to 2020, [...] Read more.
After collapsing in the late 1990s, the southern Gulf of St. Lawrence population of striped bass (Morone saxatilis) is recovering. Here, we evaluate the use of under-ice eDNA sampling to monitor the population and confirm overwintering locations. From 2018 to 2020, water samples were collected from transects spanning 35 km of the Miramichi River system, accounting for the effects of sampling site, month, sampling depth and tidal influence on eDNA concentration. We examined the distribution of eDNA in a complex tidal river system with a time series consisting of 12 h of continuous sampling throughout a tidal cycle, in conjunction with the use of artificial DNA tracers and acoustic Doppler current profiler flow measurements. The eDNA distribution correctly identified overwintering grounds based on acoustic tag data, including a perceptible upstream shift in 2020. Overall, there was no significant effect of year, sampling month (February or March), sampling depth or tidal phase on eDNA concentrations. The tidal time series revealed only weak patterns of eDNA recirculation. Monitoring eDNA concentration and distribution allows for a relative comparison of population size and location between years, and has the potential to be expanded to other river systems more easily than traditional acoustic fish tags and surveys. Full article
(This article belongs to the Special Issue Application of Environmental DNA Technology in Fishery Resources)
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9 pages, 607 KiB  
Article
Proof-of-Concept Studies Demonstrate That Food and Pheromone Stimuli Can Be Used to Attract Invasive Carp So Their Presence Can Be Readily Measured Using Environmental DNA
by Ratna Ghosal, Alison A. Coulter and Peter W. Sorensen
Fishes 2022, 7(4), 176; https://doi.org/10.3390/fishes7040176 - 20 Jul 2022
Viewed by 1935
Abstract
The utility of environmental DNA (eDNA) as a detection tool for fisheries management is limited by dilution and degradation, especially in areas of low fish abundance. This proof-of-concept study addressed these challenges by testing whether food or pheromones might be used to attract [...] Read more.
The utility of environmental DNA (eDNA) as a detection tool for fisheries management is limited by dilution and degradation, especially in areas of low fish abundance. This proof-of-concept study addressed these challenges by testing whether food or pheromones might be used to attract invasive carp so they can be measured more readily using eDNA. In two experiments, PIT-tagged carp were stocked into ponds (N = 3 for silver carp; N = 1 for common carp) while one of two stimuli (planktonic food [spirulina] for silver carp and a sex pheromone [prostaglandin F2α] for male common carp) was added to determine if we could attract fish to one side while measuring both fish presence (detections) and eDNA concentrations. The addition of spirulina increased detections of silver carp by 2–3 fold, while eDNA concentrations increased by 4-fold on the test side when compared to the side without the stimulus. The addition of the sex pheromone increased detections of common carp by ~25-fold, where a 6-fold increase in eDNA concentrations was measured (p < 0.05). A strong positive correlation was noted between fish presence and eDNA concentration for both species. These experiments demonstrate that food and pheromone stimuli could be used to attract invasive carp so they could be measured more easily and accurately. Full article
(This article belongs to the Special Issue Application of Environmental DNA Technology in Fishery Resources)
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16 pages, 1211 KiB  
Article
A Comparison of eDNA and Visual Survey Methods for Detection of Longnose Darter Percina nasuta in Missouri
by Jacob T. Westhoff, Leah K. Berkman, Katy E. Klymus, Nathan L. Thompson and Catherine A. Richter
Fishes 2022, 7(2), 70; https://doi.org/10.3390/fishes7020070 - 18 Mar 2022
Cited by 6 | Viewed by 2797
Abstract
The longnose darter Percina nasuta is a rare and cryptic fish that recently disappeared from much of its historic range. We developed and used an environmental DNA (eDNA) assay for longnose darter paired with visual surveys to better determine the species’ range and [...] Read more.
The longnose darter Percina nasuta is a rare and cryptic fish that recently disappeared from much of its historic range. We developed and used an environmental DNA (eDNA) assay for longnose darter paired with visual surveys to better determine the species’ range and compare detection probability between sampling approaches in an occupancy modeling framework. We detected longnose darter eDNA further upstream in the mainstem St. Francis River than previously reported and in a tributary for the first time. Our multi-scale occupancy approach compared models where detection was constant against a model that allowed detection to vary by survey method. The constant model received the most support indicating survey method was not a strong predictor and detection was estimated at 0.70 (0.45–0.86; 95% CI) across both methods. Our study produced effective longnose darter eDNA primers and demonstrated the application of eDNA for sampling small-bodied, cryptic fish. We detected longnose darter eDNA 27 km upstream of their known range and determined that snorkel surveys are the most efficient sampling method if water clarity allows. We recommend target sample sizes to achieve various detection goals for both sample methods and our results inform future design of distributional and monitoring efforts. Full article
(This article belongs to the Special Issue Application of Environmental DNA Technology in Fishery Resources)
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