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

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.

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

2021 ◽  
Author(s):  
Hiroki Mizumoto ◽  
Osamu Kishida ◽  
Kotaro Takai ◽  
Naru Matsuura ◽  
Hitoshi Araki
Keyword(s):  
Invasive Species ◽  
River Basin ◽  
Water Samples ◽  
Environmental Dna ◽  
Watershed Scale ◽  
Efficient Tool ◽  
Occupancy Model ◽  
Wide Range ◽  
Powerful Means ◽  
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.

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

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.

scholarly journals Rapid Invasive Species Detection by Combining Environmental DNA with Light Transmission Spectroscopy

2013 ◽  
Vol 6 (6) ◽  
pp. 402-409 ◽  
Author(s):  
Scott P. Egan ◽  
Matthew A. Barnes ◽  
Ching-Ting Hwang ◽  
Andrew R. Mahon ◽  
Jeffery L. Feder ◽  
...  
Keyword(s):  
Invasive Species ◽  
Light Transmission ◽  
Environmental Dna ◽  
Species Detection ◽  
Transmission Spectroscopy

scholarly journals Matching a snail’s pace: Successful use of environmental DNA techniques to detect early stages of invasion by the destructive New Zealand mud snail

2020 ◽  
Author(s):  
James D. Woodell ◽  
Maurine Neiman ◽  
Edward P. Levri
Keyword(s):  
Invasive Species ◽  
New Zealand ◽  
Low Cost ◽  
Environmental Dna ◽  
Invasive Population ◽  
Effective Response ◽  
Mud Snail ◽  
Species Specific ◽  
New Zealand Mud Snail ◽  
And Control

ABSTRACTEarly detection of invasive species allows for a more rapid and effective response. Restoration of the native ecosystem after an invasive population has established is expensive and difficult but more likely to succeed when invasions are detected early in the invasion process. Containment efforts to prevent the spread of known invasions also benefit from earlier knowledge of invaded sites. Environmental DNA (eDNA) techniques have emerged as a tool that can identify invasive species at a distinctly earlier time point than traditional methods of detection. Due to expected range expansion in eastern North America, we focus on the destructive New Zealand Mud Snail Potamopyrgus antipodarum (NZMS) invasion. We collected water samples from eight sites that prior evidence indicated were not yet invaded by the NZMS. After filtering these samples to collect eDNA, we used a species-specific probe with qPCR to identify NZMS eDNA. We found evidence for NZMS invasion at five of the eight sites, with later physical confirmation of mud snails at one of these sites. This study is the first example of successful detection of a previously unidentified invasive population of NZMS, setting the stage for further monitoring of at-risk sites to detect and control new invasions of this destructive snail. This study also shows potential opportunities for invasion monitoring offered by using low-cost efforts and methods that are adaptable for citizen science.

scholarly journals Simultaneous detection of native and invasive crayfish and Aphanomyces astaci from environmental DNA samples in a wide range of habitats in Central Europe

NeoBiota ◽  
2020 ◽  
Vol 58 ◽  
pp. 1-32 ◽  
Author(s):  
Johannes C. Rusch ◽  
Michaela Mojžišová ◽  
David A. Strand ◽  
Jitka Svobodová ◽  
Trude Vrålstad ◽  
...  
Keyword(s):  
Central Europe ◽  
Western Europe ◽  
Low Cost ◽  
Simultaneous Detection ◽  
Environmental Dna ◽  
Aphanomyces Astaci ◽  
Wide Range ◽  
Species Specific ◽  
Native Crayfish ◽  
Crayfish Species

Crayfish of North American origin are amongst the most prominent high-impact invasive invertebrates in European freshwaters. They contribute to the decline of European native crayfish species by spreading the pathogen causing crayfish plague, the oomycete Aphanomyces astaci. In this study we validated the specificity of four quantitative PCR (qPCR) assays, either published or newly developed, usable for environmental DNA (eDNA) screening for widely distributed native and non-native crayfish present in Central Europe: Astacus astacus, Pacifastacus leniusculus, Faxonius limosus and Procambarus virginalis. We then conducted an eDNA monitoring survey of these crayfish as well as the crayfish plague pathogen in a wide variety of habitat types representative for Central and Western Europe. The specificity of qPCR assays was validated against an extensive collection of crayfish DNA isolates, containing most crayfish species documented from European waters. The three assays developed in this study were sufficiently species-specific, but the published assay for F. limosus displayed a weak cross-reaction with multiple other crayfish species of the family Cambaridae. In the field study, we infrequently detected eDNA of A. astaci together with the three non-native crayfish species under examination. We never detected eDNA from A. astaci together with native crayfish, but in a few locations eDNA from both native and non-native crayfish was captured, due either to passive transport of eDNA from upstream populations or co-existence in the absence of infected crayfish carriers of A. astaci. In the study, we evaluated a robust, easy-to-use and low-cost version of the eDNA sampling equipment, based mostly on items readily available in garden stores and hobby markets, for filtering relatively large (~5 l) water samples. It performed just as well as the far more expensive equipment industrially designed for eDNA water sampling, thus opening the possibility of collecting suitable eDNA samples to a wide range of stakeholders. Overall, our study confirms that eDNA-based screening for crayfish and their associated pathogen is a feasible alternative to traditional monitoring.

scholarly journals DNA metabarcoding potentially reveals multi-assemblage eutrophication responses in an eastern North American river

2017 ◽  
Author(s):  
Joseph M. Craine ◽  
Matthew V. Cannon ◽  
Andrew J. Elmore ◽  
Steven M. Guinn ◽  
Noah Fierer
Keyword(s):  
Water Quality ◽  
Environmental Dna ◽  
Nutrient Concentrations ◽  
Marker Genes ◽  
Full Potential ◽  
Aquatic Biodiversity ◽  
Main River ◽  
Wide Range ◽  
Relative Abundances ◽  
Taxonomic Groups

AbstractFreshwater aquatic ecosystems provide a wide range of ecosystem services, yet provision of these services is increasingly threatened by human activities. Directly quantifying freshwater biotic assemblages has long been a proxy for assessing changing environmental conditions, yet traditional aquatic biodiversity assessments are often time consuming, expensive, and limited to only certain habitats and certain taxa. Sequencing aquatic environmental DNA via metabarcoding has the potential to remedy these deficiencies. Such an approach could be used to quantify changes in the relative abundances of a broad suite of taxa along environmental gradients, providing data comparable to that obtained using more traditional bioassessment approaches. To determine the utility of metabarcoding for comprehensive aquatic biodiversity assessments, we sampled aquatic environmental DNA at 25 sites that spanned the full length of the Potomac River from its headwaters to the Potomac estuary. We measured dissolved nutrient concentrations and also sequenced amplified marker genes using primer pairs broadly targeting four taxonomic groups. The relative abundances of bacteria, phytoplankton, invertebrate, and vertebrate taxa were distinctly patterned along the river with significant differences in their abundances across headwaters, the main river, and the estuary. Within the main river, changes in the abundances of these broad taxonomic groups reflected either increasing river size or a higher degree of eutrophication. The larger and more eutrophic regions of the river were defined by high total dissolved phosphorus in the water, a unique suite of bacteria, phytoplankton such as species of the diatom Nitzschia, invertebrates like the freshwater snail Physella acuta, and high abundance of fish including the common carp (Cyprinus carpio). Taxonomic richness of phytoplankton and vertebrates increased downriver while it consistently decreased for bacteria. Given these results, multi-assemblage aquatic environmental DNA assessment of surface water quality is a viable tool for bioassessment. With minimal sampling effort, we were able to construct the equivalent of a freshwater water quality index, differentiate closely-related taxa, sample places where traditional monitoring would be difficult, quantify species that are difficult to detect with traditional techniques, and census taxa that are generally captured with more traditional bioassessment approaches. To realize the full potential of aquatic environmental DNA for bioassessment, research is still needed on primer development, a geographically broad set of reference sites need to be characterized, and reference libraries need to be further developed to improve taxonomic identification.

Identification of sibling species in the genus Eucyclops from water-bodies of Ukraine and Russia using crossbreeding studies

2014 ◽  
Vol 25 (1-2) ◽  
pp. 61-68 ◽  
Author(s):  
V. I. Monchenko ◽  
L. P. Gaponova ◽  
V. R. Alekseev
Keyword(s):  
Cryptic Species ◽  
River Basin ◽  
Black Sea ◽  
Species Complex ◽  
River Basins ◽  
Water Bodies ◽  
Similar Species ◽  
Basin Water ◽  
Different Populations ◽  
Baltic Sea Basin

Crossbreeding experiments were used to estimate cryptic species in water bodies of Ukraine and Russia because the most useful criterion in species independence is reproductive isolation. The problem of cryptic species in the genus Eucyclops was examined using interpopulation crosses of populations collected from Baltic Sea basin (pond of Strelka river basin) and Black Sea basin (water-reservoires of Dnieper, Dniester and Danube rivers basins). The results of reciprocal crosses in Eucyclops serrulatus-group are shown that E. serrulatus from different populations but from water bodies belonging to the same river basin crossed each others successfully. The interpopulation crosses of E. serrulatus populations collected from different river basins (Dnipro, Danube and Dniester river basins) were sterile. In this group of experiments we assigned evidence of sterility to four categories: 1) incomplete copulation or absence of copulation; 2) nonviable eggs; 3) absence of egg membranes or egg sacs 4) empty egg membranes. These crossbreeding studies suggest the presence of cryptic species in the E. serrulatus inhabiting ecologically different populations in many parts of its range. The same crossbreeding experiments were carries out between Eucyclops serrulatus and morphological similar species – Eucyclops macruroides from Baltic and Black Sea basins. The reciprocal crossings between these two species were sterile. Thus taxonomic heterogeneity among species of genus Eucyclops lower in E. macruroides than in E. serrulatus. The interpopulation crosses of E. macruroides populations collected from distant part of range were fertile. These crossbreeding studies suggest that E. macruroides species complex was evaluated as more stable than E. serrulatus species complex.

Assessment of the Influence of the Invasive Species Pistia stratiotes (Araceae) on Some Species of Submerged Macrophytes of Natural Water Bodies of Ukraine

2017 ◽  
Vol 53 (5) ◽  
pp. 75-84
Author(s):  
O. P. Olkhovich ◽  
N. Yu. Taran ◽  
N. B. Svetlova ◽  
L. M. Batsmanova ◽  
M. V. Aleksiyenko ◽  
...  
Keyword(s):  
Invasive Species ◽  
Natural Water ◽  
Submerged Macrophytes ◽  
Water Bodies ◽  
Pistia Stratiotes ◽  
Natural Water Bodies

The Biology of Mediterranean-Type Ecosystems

2018 ◽  
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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