Evaluation of an Environmental DNA Method as a Potential Tool for Monitoring Salmonid Fishes in the Wild

AbstractUnderstanding the distribution of invasive species and their reproductive area is crucial for their managements after invasion. While catch and observation surveys are still embraced, environmental DNA (eDNA) has been increasingly utilized as an efficient tool for identifying these species in the wild. In this study, we developed a Bufo-specific eDNA assay for detecting an invasive, toxic, and terrestrial toad species Bufo japonicus formosus in Hokkaido, Japan, and applied it to their reproductive area at watershed scale. The eDNA assay was field-validated in ponds where B. japonicus were observed, as well as in rivers downstream of the reproductive ponds. Thus, the assay provided us an opportunity to screen watersheds that include their reproductive area by collecting downstream water samples. Applying it to the Ishikari river basin, the largest river basin in Hokkaido (c.a., 14,330 km2), we detected toad eDNA at 32 out of 73 sampling sites. They are composed of eleven sites with species observation records nearby (all the sites with observation records within a 500 m radius) and 21 sites without such records. And those eDNA detections were from twelve out of 31 river systems in the entire river basin. A Bayesian, multiscale occupancy model supported high eDNA detectability among those sites. These results suggest that the eDNA assay can efficiently estimate the presence of reproductive area of the terrestrial toad even from a distant downstream of the watershed, and that it provides a powerful means of detecting new reproductive area and monitoring further spread of invasive species.

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Utilizing environmental DNA for wide-range distributions of reproductive area of an invasive terrestrial toad in Ishikari river basin in Japan

10.21203/rs.3.rs-246449/v1 ◽

2021 ◽

Author(s):

Hiroki Mizumoto ◽

Osamu Kishida ◽

Kotaro Takai ◽

Hitoshi Araki

Keyword(s):

Invasive Species ◽

River Basin ◽

Water Samples ◽

Detection System ◽

Environmental Dna ◽

Watershed Scale ◽

Efficient Tool ◽

Wide Range ◽

Powerful Means ◽

In The Wild

Abstract Understanding the distribution of invasive species and their reproductive area is crucial for their managements after invasion. While catch and observation surveys are still embraced, environmental DNA (eDNA) has been increasingly utilized as an efficient tool for identifying these species in the wild. In this study, we developed an eDNA detection system for an invasive, toxic, and terrestrial toad species Bufo japonicus in Hokkaido, Japan, and applied it to their reproductive area at watershed scale. We found that our system successfully detected their eDNA not only in ponds where their larvae were observed, but also in rivers downstream of the reproductive ponds. Thus, the system provided us an opportunity to estimate watersheds that include their reproductive area by collecting downstream water samples. Applying it to the Ishikari river basin, the largest river basin in Hokkaido (c.a., 14,330 km2), we detected their eDNA at 32 out of 73 river sampling sites. They are composed of eleven sites with species observation records nearby (all the sites with observation records within a 500 m radius) and21 sites without such records. And those eDNA detections were from 14 out of 31 river systems, and they were widespread across the river basin. These results suggest that the eDNA detection system can efficiently estimate the presence of reproductive area of the terrestrial toad even from a distant downstream of the watershed, and that it provides a powerful means of detecting new reproductive area and monitoring further spread of invasive species.

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Idea paper: Monitoring and databasing non-native species to manage establishment debt in aquatic ecosystems

10.32942/osf.io/y975g ◽

2022 ◽

Author(s):

Takumi Saito

Keyword(s):

Native Species ◽

Social Issues ◽

Environmental Dna ◽

Management Approach ◽

Pet Trade ◽

Country Level ◽

Urgent Task ◽

Dna Metabarcoding ◽

In The Wild ◽

Invasion Pathway

In the era of globalization, biological invasions are one of the most serious social issues. Thus, managing its impact is an urgent task. It is essential to control non-native species before they become established. However, it is insufficient to address establishment debt, which occurs when a non-native species has been introduced into an area but has not yet been established in the wild. In particular, unintentionally introduced or contaminated organisms of the aquatic ornamental pet trade are referred to as “hitchhikers” and have not received much attention in the context of establishment debt. To understand the nature of establishment debt, including that of aquatic hitchhikers, I propose the monitoring of non-native species inhabiting artificial isolated waters, such as indoor aquariums, and the construction of a database using environmental DNA metabarcoding. This idea would be an effective non-regulatory management approach when implemented broadly, at the country level. Furthermore, implementation of this strategy in combination with border biosecurity and field monitoring may promote accurate prioritization, rapid species identification, and effective invasion pathway assessment.

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Environmental DNA detects Critically Endangered largetooth sawfish in the wild

Endangered Species Research ◽

10.3354/esr00731 ◽

2016 ◽

Vol 30 ◽

pp. 109-116 ◽

Cited By ~ 34

Author(s):

CA Simpfendorfer ◽

PM Kyne ◽

TH Noble ◽

J Goldsbury ◽

RK Basiita ◽

...

Keyword(s):

Environmental Dna ◽

Critically Endangered ◽

In The Wild

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Fieldable Environmental DNA Sequencing to Assess Jellyfish Biodiversity in Nearshore Waters of the Florida Keys, United States

Frontiers in Marine Science ◽

10.3389/fmars.2021.640527 ◽

2021 ◽

Vol 8 ◽

Author(s):

Cheryl Lewis Ames ◽

Aki H. Ohdera ◽

Sophie M. Colston ◽

Allen G. Collins ◽

William K. Fitt ◽

...

Keyword(s):

Dna Sequencing ◽

Real Time ◽

Environmental Dna ◽

Florida Keys ◽

Gene Profiling ◽

Rrna Gene ◽

Laboratory Equipment ◽

Molecular Sequencing ◽

Mitochondrial Cytochrome Oxidase ◽

Potential Tool

Recent advances in molecular sequencing technology and the increased availability of fieldable laboratory equipment have provided researchers with the opportunity to conduct real-time or near real-time gene-based biodiversity assessments of aquatic ecosystems. In this study, we developed a workflow and portable kit for fieldable environmental DNA sequencing (FeDS) and tested its efficacy by characterizing the breadth of jellyfish (Medusozoa) taxa in the coastal waters of the Upper and Lower Florida Keys. Environmental DNA was isolated from seawater collection events at eight sites and samples were subjected to medusozoan 16S rRNA gene and metazoan mitochondrial cytochrome oxidase 1 gene profiling via metabarcoding onsite. In total, FeDS yielded 175,326 processed sequence reads providing evidence for 53 medusozoan taxa. Our most salient findings revealed eDNA from: (1) two venomous box jellyfish (Cubozoa) species, including taxa whose stings cause the notorious Irukandji envenomation syndrome; (2) two species of potentially introduced stalked jellyfish (Staurozoa); and (3) a likely cryptic species of upside-down jellyfish (Scyphozoa). Taken together, the results of this study highlight the merits of FeDS in conducting biodiversity surveys of endemic and introduced species, and as a potential tool for assessing envenomation and/or conservation-related threats.

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Culturing Putatively Obligate Epizoic Diatoms: Insights for the Evolution and Ecology of Diatoms and Their Host

10.21203/rs.3.rs-1041030/v1 ◽

2021 ◽

Author(s):

Matt Ashworth ◽

Roksana Majewska ◽

Thomas A Frankovich ◽

Michael Sullivan ◽

Sunčica Bosak ◽

...

Keyword(s):

Dna Sequences ◽

Cultured Cells ◽

Sequence Data ◽

Environmental Dna ◽

Sea Turtle ◽

Reference Sequence ◽

Generalist Species ◽

In The Wild ◽

Host Ecology ◽

Marine Megafauna

Abstract Background: Our understanding of the importance of microbiomes on large aquatic animals—such as whales, sea turtles and manatees—has advanced considerably in recent years. Recent activity describing the epizoic diatoms growing on marine vertebrates suggests that these epibiotic diatom communities constitute diverse, polyphyletic, and compositionally stable assemblages that include both putatively obligate epizoic and generalist species. Here, we outline a successful attempt to culture putatively obligate epizoic diatoms without their hosts and propose further applications and research avenues in this growing area of study. Results: We cultured cells of epizoic diatoms from multiple host species sampled in the wild and captivity. Analyzing the DNA sequences of these cultures, we found that several unique diatom taxa have independently evolved to occupy in epibiotic habitats. We created a library of reference sequence data for use in metabarcoding surveys of sea turtle and manatee microbiomes that will further facilitate the use of environmental DNA for studying host specificity in epizoic diatoms and the utility of diatoms as indicators of host ecology and health. Conclusions: Our discovery that epizoic diatoms can be cultured independently from their hosts raises several questions about the nature of the interaction between these diatom species and their hosts. We encourage the interdisciplinary community working with marine megafauna to consider including diatom sampling and diatom analysis into their routine practices.

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Laboratory experiments for the detection of environmental DNA of crayfish: Examining the potential

Freshwater Crayfish ◽

10.5869/fc.2015.v21-1.159 ◽

2015 ◽

Vol 21 (1) ◽

pp. 159-163 ◽

Cited By ~ 6

Author(s):

Chester R. Figiel ◽

Sandra Bohn

Keyword(s):

Water Samples ◽

Dna Detection ◽

Environmental Dna ◽

Sampling Period ◽

Sediment Samples ◽

Target Dna ◽

Invasive Crayfish ◽

In The Wild ◽

Species Specific ◽

Crayfish Species

Abstract We examined methods for detecting environmental DNA of the invasive white river crayfish Procambarus zonangulus. In a laboratory experiment, we investigated detection capability in benthic sediment samples and in water samples in six flow-through tanks. Additionally we determined whether crayfish density (low = 0.67 or high = 2.69 crayfish·m-2) or crayfish time in tanks influenced DNA detectability (collection of samples on Days 2, 5, 8 and 15). Species-specific primers and probes were designed for P. zonangulus and their specificity was tested against other crayfish species. Limits of detection and quantification were specified for the target DNA sequence by means of quantitative PCR amplifications on dilution series of known amounts of P. zonangulus DNA. We detected crayfish DNA in 14 of the 24 benthic sediment samples and in two of the 24 water samples. DNA detection was found in benthic sediment samples in at least two tanks at every sampling period, while DNA detection was found in water samples only on Day 8. Crayfish DNA was detected in benthic sediment and water samples independently of crayfish density. Crayfish at both densities were observed to ‘explore’ all areas of the tank and move irrespective of diurnal time or conspecific presence. These behavior patterns were observed throughout the 15 day experiment and likely resulted in the positive detections, especially in benthic sediment samples. We believe that these methods could benefit monitoring of invasive crayfish species, although there is no doubt that further optimization and more research is needed to evaluate these techniques in the wild.

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Hemolysis of erythrocytes by the hemolytic system from the blood-feeding stable fly, Stomoxys calcitrans

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100123854 ◽

1992 ◽

Vol 50 (1) ◽

pp. 690-691

Author(s):

H. J. Kirch ◽

G. Spates ◽

R. Droleskey ◽

W.J. Kloft ◽

J.R. DeLoach

Keyword(s):

Blood Feeding ◽

Stomoxys Calcitrans ◽

Stable Fly ◽

Digestive Physiology ◽

Transmission Electron ◽

Erythrocyte Lysis ◽

Mammalian Blood ◽

Bovine Erythrocytes ◽

Potential Tool

Blood feeding insects have to rely on the protein content of mammalian blood to insure reproduction. A substantial quantity of protein is provided by hemoglobin present in erythrocytes. Access to hemoglobin is accomplished only via erythrocyte lysis. It has been shown that midgut homogenates from the blood feeding stable fly, Stomoxys calcitrans, contain free fatty acids and it was proposed that these detergent-like compounds play a major role as hemolysins in the digestive physiology of this species. More recently sphingomyelinase activity was detected in midgut preparations of this fly, which would provide a potential tool for the enzymatic cleavage of the erythrocyte's membrane sphingomyelin. The action of specific hemolytic factors should affect the erythrocyte's morphology. The shape of bovine erythrocytes undergoing in vitro hemolysis by crude midgut homogenates from the stable fly was examined by scanning and transmission electron microscopy.

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Freeze-substituted fungal cells of Nectria haematococca: A comparison of the macroconidial walls of the adhesion-competent wild type with an adhesion-reduced mutant

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100160996 ◽

1990 ◽

Vol 48 (3) ◽

pp. 688-689

Author(s):

Thecan Caesar-Ton That ◽

Lynn Epstein

Keyword(s):

Freeze Substitution ◽

Uranyl Acetate ◽

Wild Type ◽

Nectria Haematococca ◽

Fruit Extract ◽

Dialysis Tubing ◽

Tube Emergence ◽

Contrast Microscopy ◽

In The Wild ◽

Freeze Damage

Nectria haematococca mating population I (anamorph, Fusarium solani) macroconidia attach to its host (squash) and non-host surfaces prior to germ tube emergence. The macroconidia become adhesive after a brief period of protein synthesis. Recently, Hickman et al. (1989) isolated N. haematococca adhesion-reduced mutants. Using freeze substitution, we compared the development of the macroconidial wall in the wild type in comparison to one of the mutants, LEI.Macroconidia were harvested at 1C, washed by centrifugation, resuspended in a dilute zucchini fruit extract and incubated from 0 - 5 h. During the incubation period, wild type macroconidia attached to uncoated dialysis tubing. Mutant macroconidia did not attach and were collected on poly-L-lysine coated dialysis tubing just prior to freezing. Conidia on the tubing were frozen in liquid propane at 191 - 193C, substituted in acetone with 2% OsO4 and 0.05% uranyl acetate, washed with acetone, and flat-embedded in Epon-Araldite. Using phase contrast microscopy at 1000X, cells without freeze damage were selected, remounted, sectioned and post-stained sequentially with 1% Ba(MnO4)2 2% uranyl acetate and Reynold’s lead citrate. At least 30 cells/treatment were examined.

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