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

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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Environmental DNA detection of endangered and invasive species in Kejimkujik National Park and Historic Site

Genome ◽

10.1139/gen-2020-0042 ◽

2020 ◽

Author(s):

Tzitziki Loeza-Quintana ◽

Steven Crookes ◽

Pei Yuan Li ◽

Darrin P Reid ◽

Matthew Smith ◽

...

Keyword(s):

Invasive Species ◽

Water Samples ◽

National Park ◽

Sampling Site ◽

Environmental Dna ◽

Smallmouth Bass ◽

Historic Site ◽

Blanding's Turtle ◽

Kejimkujik National Park ◽

Blanding’S Turtle

The use of environmental DNA (eDNA) allows the early detection of aquatic species at low densities (e.g. elusive and invasive species), which otherwise could be challenging to monitor using conventional techniques. Here, we assess the ability of eDNA sampling to detect the presence/absence of one species-at-risk (Blanding’s Turtle) and two invasive species (Chain Pickerel and Smallmouth Bass) in Kejimkujik National Park and National Historic site, Nova Scotia, where the aquatic system is highly acidic and rich in organic compounds. Five replicates of 1L water samples were taken per sampling site. Water filtration and eDNA extractions were performed on-site, while qPCR reactions were performed in the laboratory using species-specific assays. Samples were treated with an inhibition removal kit and analyzed pre- and post-inhibition removal. Despite the low pH and PCR inhibitors in water samples, our results showed positive eDNA detections in almost all expected positive sites (except in one site for Blanding’s Turtle). Detections of the target species were also observed at sites where their presence was previously unknown. Our study supports the advantage of eDNA to monitor species at low densities, revealing new distributions or recently invaded areas. We also demonstrate how eDNA can directly instruct management strategies in Kejimkujik.

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In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River

10.1101/027235 ◽

2015 ◽

Cited By ~ 1

Author(s):

M.V. Cannon ◽

J. Hester ◽

A. Shalkhauser ◽

E.R. Chan ◽

K. Logue ◽

...

Keyword(s):

High Throughput ◽

Dna Sequences ◽

Water Samples ◽

High Throughput Sequencing ◽

Biological Diversity ◽

Pcr Amplification ◽

Environmental Dna ◽

Asian Carp ◽

Broad Perspective ◽

Wide Range

Analysis of environmental DNA (eDNA) enables the detection of species of interest from water and soil samples, typically using species-specific PCR. Here, we describe a method to characterize the biodiversity of a given environment by amplifying eDNA using primer pairs targeting a wide range of taxa and high-throughput sequencing for species identification. We tested this approach on 91 water samples of 40 mL collected along the Cuyahoga River (Ohio, USA). We amplified eDNA using 12 primer pairs targeting mammals, fish, amphibians, birds, bryophytes, arthropods, copepods, plants and several microorganism taxa and sequenced all PCR products simultaneously by high-throughput sequencing. Overall, we identified DNA sequences from 15 species of fish, 17 species of mammals, 8 species of birds, 15 species of arthropods, one turtle and one salamander. Interestingly, in addition to aquatic and semiaquatic animals, we identified DNA from terrestrial species that live near the Cuyahoga River. We also identified DNA from one Asian carp species invasive to the Great Lakes but that had not been previously reported in the Cuyahoga River. Our study shows that analysis of eDNA extracted from small water samples using wide-range PCR amplification combined with high-throughput sequencing can provide a broad perspective on biological diversity.

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Applications of eDNA Metabarcoding for Vertebrate Diversity Studies in Northern Colombian Water Bodies

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2020.617948 ◽

2021 ◽

Vol 8 ◽

Author(s):

Juan Diego Lozano Mojica ◽

Susana Caballero

Keyword(s):

Invasive Species ◽

Low Cost ◽

Environmental Dna ◽

River Basins ◽

Water Bodies ◽

Species Detection ◽

Main River ◽

Wide Range ◽

Elusive Species ◽

Diversity Studies

Environmental DNA metabarcoding is a tool with increasing use worldwide. The uses of such technology have been validated several times for diversity census, invasive species detection, and endangered/cryptic/elusive species detection and monitoring. With the help of this technology, water samples collected (n = 37) from several main river basins and other water bodies of the northern part of Colombia, including the Magdalena, Sinú, Atrato, and San Jorge river basins, were filtered and analyzed and processed using universal 12S primers for vertebrate fauna and NGS. Over 200 native taxa were detected, the majority of them being fish species but also including amphibia, reptiles, and several non-aquatic species of birds and mammals (around 78, 3, 2, 9, and 8%, respectively). Among the matches, vulnerable, and endangered species such as the catfish Pseudoplatystoma magdaleniatum and the Antillean manatee (Trichechus manatus) were detected. The manual revision of the data revealed some geographical incongruencies in classification. No invasive species were detected in the filters. This is, to our knowledge, the first time this technique is used in rivers of the country and this tool promises to bring advances in monitoring and conservation efforts, since its low cost and fast deployment allows for sampling in small periods of time, together with the fact that it can detect a wide range of species, allows for a new way of censing the vertebrate diversity in Colombia. Diversity analysis showed how the species identified using this method point to expected community structure although still much needs to be improved in rates of detection and genomic reference databases. This technique could be used in citizen science projects involving local communities in these regions.

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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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Development of an environmental DNA method for monitoring fish communities: ground truthing in diverse lakes with characterised fish faunas

10.1101/394718 ◽

2018 ◽

Author(s):

Jianlong Li ◽

Tristan W. Hatton-Ellis ◽

Lori-Jayne Lawson Handley ◽

Helen S. Kimbell ◽

Marco Benucci ◽

...

Keyword(s):

Water Samples ◽

Fish Communities ◽

Environmental Dna ◽

Quantitative Information ◽

12S Rrna ◽

Similar Species ◽

List Type ◽

Large Lakes ◽

Non Invasive ◽

Wide Range

AbstractAccurate, cost-effective monitoring of fish is required to assess the quality of lakes under the European Water Framework Directive (WFD). Recent studies have shown that environmental DNA (eDNA) metabarcoding is an effective and non-invasive method, which can provide semi-quantitative information on fish communities in large lakes.This study further investigated the potential of eDNA metabarcoding as a tool for WFD status assessment by collecting and analysing water samples from eight Welsh lakes and six meres in Cheshire, England, with well described fish faunas. Water samples (N = 252) were assayed using two mitochondrial DNA regions (Cytb and 12S rRNA).eDNA sampling indicated the presence of very similar species in the lakes compared to those expected on the basis of existing and historical information. In total, 24 species were detected with a total of 111 species occurrences in the lakes studied using eDNA. Secondly, there was a significant positive correlation between expected faunas and eDNA data in terms of confidence of species occurrence (Spearman’s r = 0.74, df = 109, p <; 0.001). Thirdly, eDNA data can estimate relative abundance with the standard five-level classification scale (“DAFOR”). Lastly, four ecological fish communities were characterised using eDNA data which agrees with the pre-defined lake types according to environmental characteristics.Synthesis and applications. This study provides further evidence that eDNA metabarcoding could be a powerful and non-invasive monitoring tool for WFD purpose in a wide range of lake types, considerably outperforming other methods for community level analysis.

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An Improved Membrane Filtration Method for Enumeration of Faecal Coliforms and E. Coli by a Fluorogenic β-Glucuronidase Assay

Water Science & Technology ◽

10.2166/wst.1993.0357 ◽

1993 ◽

Vol 27 (3-4) ◽

pp. 267-270 ◽

Cited By ~ 4

Author(s):

M. T. Augoustinos ◽

N. A. Grabow ◽

B. Genthe ◽

R. Kfir

Keyword(s):

Escherichia Coli ◽

Water Samples ◽

Membrane Filtration ◽

Faecal Coliforms ◽

Environmental Waters ◽

Filtration Method ◽

E Coli ◽

Wide Range ◽

Pure Cultures ◽

Glucuronidase Assay

A fluorogenic β-glucuronidase assay comprising membrane filtration followed by selective enumeration on m-FC agar at 44.5°C and further confirmation using tlie 4-metliylumbelliferyl-β-D-glucuronide (MUG) containing medium was evaluated for the detection of Escherichia coli in water. A total of 200 typical blue and non-typical blue colonies were isolated from sea and fresh water samples using initial selective enumeration on m-FC agar. Pure cultures of the selected colonies were further tested using the MUG assay and identified using the API 20E method. Of the colonies tested which were shown to be positive using the MUG assay 99.4% were Escherichia coli. The results of this study indicate the combination of the m-FC method followed by the MUG assay to be highly efficient for the selection and confirmation of E. coli from a wide range of environmental waters.

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Danube River Basin: Progress with the Environmental Programme

Water Science & Technology ◽

10.2166/wst.1999.0495 ◽

1999 ◽

Vol 40 (10) ◽

pp. 1-8 ◽

Cited By ~ 3

Author(s):

T. Botterweg ◽

D. W. Rodda

Keyword(s):

River Basin ◽

Action Plan ◽

Waste Water Treatment ◽

Warning System ◽

Danube River ◽

The Black Sea ◽

Research Activity ◽

Global Environment Facility ◽

Major Activity ◽

Wide Range

An Internationally funded Programme, involving the European Commission, the Global Environment Facility managed by UN Development Programme, the World Bank and the European Bank for Reconstruction and Development, is addressing river basin problems in a unique situation. The solution of these should lead to the prevention of pollution and better water quality, protected ecosystems, sustainable water resources and more efficient sewerage and waste water treatment facilities for the 90 million population living in the region and the reduction of pollution impact on the Black Sea into which the Danube River flows. The paper introduces current Programme activities, the challenges being met and progress. Work is described for implementing a monitoring strategy, an accident emergency warning system and implementation of the 1994 Strategic Action Plan. The applied research activity is explained. The Programme is a major activity with many elements addressing a wide range of environmental problems in the catchment of a major international waterway.

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The Biology of Mediterranean-Type Ecosystems

10.1093/oso/9780198739135.001.0001 ◽

2018 ◽

Cited By ~ 7

Author(s):

Karen J. Esler ◽

Anna L. Jacobsen ◽

R. Brandon Pratt

Keyword(s):

Climate Change ◽

South Africa ◽

Invasive Species ◽

Habitat Loss ◽

Endemic Species ◽

Geographic Area ◽

Cutting Edge ◽

Wide Range ◽

The Mediterranean ◽

Mediterranean Type Ecosystems

The world’s mediterranean-type climate regions (including areas within the Mediterranean, South Africa, Australia, California, and Chile) have long been of interest to biologists by virtue of their extraordinary biodiversity and the appearance of evolutionary convergence between these disparate regions. Comparisons between mediterranean-type climate regions have provided important insights into questions at the cutting edge of ecological, ecophysiological and evolutionary research. These regions, dominated by evergreen shrubland communities, contain many rare and endemic species. Their mild climate makes them appealing places to live and visit and this has resulted in numerous threats to the species and communities that occupy them. Threats include a wide range of factors such as habitat loss due to development and agriculture, disturbance, invasive species, and climate change. As a result, they continue to attract far more attention than their limited geographic area might suggest. This book provides a concise but comprehensive introduction to mediterranean-type ecosystems. As with other books in the Biology of Habitats Series, the emphasis in this book is on the organisms that dominate these regions although their management, conservation, and restoration are also considered.

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Backpacking with the Saints

10.1093/oso/9780199927814.001.0001 ◽

2015 ◽

Author(s):

Belden C. Lane

Keyword(s):

American Southwest ◽

Spiritual Practice ◽

Spiritual Journey ◽

Human Response ◽

John Muir ◽

Hildegard Of Bingen ◽

Wide Range ◽

Thich Nhat Hanh ◽

In The Wild ◽

John Of The Cross

Carrying only basic camping equipment and a collection of the world's great spiritual writings, Belden C. Lane embarks on solitary spiritual treks through the Ozarks and across the American Southwest. For companions, he has only such teachers as Rumi, John of the Cross, Hildegard of Bingen, Dag Hammarskjöld, and Thomas Merton, and as he walks, he engages their writings with the natural wonders he encounters--Bell Mountain Wilderness with Søren Kierkegaard, Moonshine Hollow with Thich Nhat Hanh--demonstrating how being alone in the wild opens a rare view onto one's interior landscape, and how the saints' writings reveal the divine in nature. The discipline of backpacking, Lane shows, is a metaphor for a spiritual journey. Just as the wilderness offered revelations to the early Desert Christians, backpacking hones crucial spiritual skills: paying attention, traveling light, practicing silence, and exercising wonder. Lane engages the practice not only with a wide range of spiritual writings--Celtic, Catholic, Protestant, Buddhist, Hindu, and Sufi Muslim--but with the fascination of other lovers of the backcountry, from John Muir and Ed Abbey to Bill Plotkin and Cheryl Strayed. In this intimate and down-to-earth narrative, backpacking is shown to be a spiritual practice that allows the discovery of God amidst the beauty and unexpected terrors of nature. Adoration, Lane suggests, is the most appropriate human response to what we cannot explain, but have nonetheless learned to love. An enchanting narrative for Christians of all denominations, Backpacking with the Saints is an inspiring exploration of how solitude, simplicity, and mindfulness are illuminated and encouraged by the discipline of backcountry wandering, and of how the wilderness itself becomes a way of knowing-an ecology of the soul.

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