scholarly journals Monthly eDNA Monitoring of an Invasive Bryozoan, Bugulina californica, in Seawater Using Species-Specific Markers

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1966
Author(s):  
Philjae Kim ◽  
Tae-Joong Yoon ◽  
Sook Shin
Keyword(s):  
Invasive Species ◽  
Dna Analysis ◽  
Early Stage ◽  
Environmental Dna ◽  
Pcr Analysis ◽  
Monitoring Method ◽  
Ship Hulls ◽  
Seawater Samples ◽  
Species Specific ◽  
Invasive Bryozoan

Environmental DNA (eDNA) method used by many ecologists as effective investigation tool can detect endangered species, rare species, and invasive species. In case of invasive species, eDNA method help to monitor the target species when the species was hard to detect through the traditional survey such as the early stage of invasion, low abundance, and larva or juvenile stage. The bryozoan, Bugulina californica, was known as a marine fouling invasive species in Korea since its first reported in 1978. This species expanded nationwide, and damages to ascidian aquaculture through attached on the ship hulls and artificial facilities. To monitor the distribution and biomass of invasive bryozoan, B. californica, the qPCR analysis of environmental DNA was performed on seawater samples from 12 harbors. In this study, we designed species-specific markers which can calculate the detected DNA copies of B. californica, and the presence and monitoring of this species can be more accurately estimated by environmental DNA analysis than by traditional survey, in which it is difficult to identify the species. Real-time PCR analysis using environmental DNA is an effective monitoring method that can determine both the distribution and the monthly change in biomass of B. californica in Korea.

scholarly journals Environmental DNA and Specific Primers for Detecting the Invasive Species Ectopleura crocea (Hydrozoa: Anthoathecata) in Seawater Samples

2020 ◽  
Vol 12 (6) ◽  
pp. 2360 ◽  
Author(s):  
Philjae Kim ◽  
Tae Joong Yoon ◽  
Sook Shin
Keyword(s):  
Invasive Species ◽  
Survey Methods ◽  
Environmental Dna ◽  
Visual Assessment ◽  
Molecular Techniques ◽  
Mitochondrial Cytochrome ◽  
Specific Primer ◽  
Specific Primers ◽  
Seawater Samples ◽  
Species Specific

In marine environments, environmental DNA (eDNA) can be effectively detected and possibly quantified when combined with molecular techniques, as demonstrated by several recent studies. In this study, we developed a species-specific primer set and a probe to detect the distribution and biomass of an invasive hydrozoan in South Korea, Ectopleura crocea. These molecular markers were designed to amplify a 187 bp region based on mitochondrial cytochrome c oxidase subunit I (COI) of E. crocea and were tested on seawater samples from 35 Korean harbors in 2017. Of the 35 sites we investigated, only nine harbors returned positive detections when using traditional survey methods, while surveys based on the use of eDNA techniques detected E. crocea DNA in all seawater samples. These results suggest that eDNA surveys based on molecular techniques are more effective at identifying species distribution and estimating biomass than traditional surveys based on visual assessment of morphology.

Combining species-specific COI primers with environmental DNA analysis for targeted detection of rare freshwater species

2013 ◽  
Vol 5 (4) ◽  
pp. 971-975 ◽  
Author(s):  
Jennifer E. Bronnenhuber ◽  
Chris C. Wilson
Keyword(s):  
Dna Analysis ◽  
Environmental Dna ◽  
Freshwater Species ◽  
Species Specific ◽  
Targeted Detection

scholarly journals Environmental DNA (eDNA) detection of marine aquatic invasive species (AIS) in Eastern Canada using a targeted species-specific qPCR approach

2020 ◽  
Vol 11 (2) ◽  
pp. 201-217
Author(s):  
Francis LeBlanc ◽  
Valérie Belliveau ◽  
Erica Watson ◽  
Chantal Coomber ◽  
Nathalie Simard ◽  
...  
Keyword(s):  
Invasive Species ◽  
Environmental Dna ◽  
Aquatic Invasive Species ◽  
Eastern Canada ◽  
Species Specific

scholarly journals Challenges in eDNA Detection of the Invasive European Green Crab, Carcinus Maenas

2021 ◽  
Author(s):  
Ariella M. Danziger ◽  
Markus Frederich
Keyword(s):  
Invasive Species ◽  
Visual Detection ◽  
Gulf Of Maine ◽  
Carcinus Maenas ◽  
Environmental Dna ◽  
Green Crab ◽  
Local Fauna ◽  
Irreversible Damage ◽  
European Green Crab ◽  
Species Specific

Abstract The early detection of invasive species is essential to cease the spread of the species before it can cause irreversible damage to the environment. The analysis of environmental DNA (eDNA) has emerged as a non-harmful method to detect the presence of a species before visual detection and is a promising approach to monitor invasive species. Few studies have investigated the use of eDNA for arthropods, as their exoskeleton is expected to limit the release of eDNA into the environment. We tested published primers for the invasive European green crab, Carcinus maenas, in the Gulf of Maine and found them not species-specific enough for reliable use outside of the area for which they were designed for. We then designed new primers, tested them against a broad range of local faunal species, and validated these primers in a field study. We demonstrate that eDNA analyses can be used for crustaceans with an exoskeleton and suggest that primers and probe sequences must be tested on local fauna at each location of use to ensure no positive amplification of these other species.

scholarly journals Application of environmental DNA for monitoring and management of aquatic biological invasions: Emerging trends and advancements towards best practice

2021 ◽  
Vol 4 ◽  
Author(s):  
Emily Chen
Keyword(s):  
Invasive Species ◽  
Experimental Design ◽  
Native Species ◽  
Best Practice ◽  
Environmental Dna ◽  
Extraction Methods ◽  
Indigenous Species ◽  
Recent Emergence ◽  
Species Specific ◽  
Sampling Procedures

Introduction Aquatic Invasive Species (AIS) are a growing concern for global biodiversity as humans continue to accelerate the transport of non-indigenous species beyond their natural range. These species may possess traits that allow them to thrive in new environmental conditions such as non-selective feeding and high reproductive output, causing ecological harm through competition with native species for limited local resources. Consequently, environmental DNA (eDNA) has come to the forefront of AIS management in recent years as a promising method to detect or monitor invasive species using rapid and non-invasive sampling to complement traditional surveying. As eDNA’s potential is explored and beginning to be adopted for a variety of applications around the world, it is increasingly important to synthesize the trends in field and laboratory protocols from different working groups to establish guidelines that will allow greater comparability between studies and improve experimental design. Methodology and Results This meta-analytic study collated and reviewed information from previously published eDNA studies that targeted AIS in freshwater and marine environments to recognize current patterns in sampling techniques, laboratory protocols, and potential geographic or taxonomic biases. A total of 492 records from 192 full-text articles were used in the analysis, composed of 408 species-specific and 84 metabarcoding records. With regards to sampling procedures, many studies were not explicit enough for true replicability, lacking critical information such as the volume of filtered water and details of storage conditions. There was no observable trend for eDNA extraction methods in either species-specific or metabarcoding approaches, with choice of extraction method being mostly arbitrary among laboratories as well as influenced by the recent emergence of dedicated commercial kits . Discussion This analysis revealed a wide variety of choices for collecting and processing eDNA samples, so it is recommended that there should be some sort of standardized workflow diagram or decision tree for every stage of the experimental design in order for researchers to determine what approaches best meet their research objectives. There is also a clear need for improving metadata reporting guidelines; although the relevance of some criteria depends on the goals and limitations of specific projects, there should be a standardized minimum set of parameters to be reported for each eDNA study, from environmental variables to decontamination practices to PCR conditions. This will increase consistency and transparency through all stages of eDNA research, which is key to collectively improving methodologies and moving forward in this field.

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.

Species-specific detection of the endangered piscivorous cyprinid fish Opsariichthys uncirostris uncirostris, three-lips, using environmental DNA analysis

2018 ◽  
Vol 33 (5) ◽  
pp. 1075-1078 ◽  
Author(s):  
Hiroki Yamanaka ◽  
Daiki Takao ◽  
Atsushi Maruyama ◽  
Akio Imamura
Keyword(s):  
Dna Analysis ◽  
Environmental Dna ◽  
Cyprinid Fish ◽  
Specific Detection ◽  
Species Specific

Application of mitochondrial DNA analysis for microbial source tracking purposes in shellfish harvesting waters

2010 ◽  
Vol 61 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Craig Baker-Austin ◽  
Rachel Rangdale ◽  
James Lowther ◽  
David N. Lees
Keyword(s):  
Mitochondrial Dna ◽  
Real Time ◽  
Real Time Pcr ◽  
Dna Analysis ◽  
Pcr Amplification ◽  
Source Tracking ◽  
Pcr Analysis ◽  
Taqman Probes ◽  
Faecal Matter ◽  
Species Specific

We present a method for the reliable detection and source characterisation of faecal pollution in water and shellfish matrices, utilising real-time PCR analysis of mitochondrial DNA targets. In this study we designed real-time PCR (TaqMan) probes to target human, bovine, ovine and swine mtDNA. PCR amplification using species-specific TaqMan probes on faecal matter and mixed effluent slurries revealed no cross-reactions between species of interest and other vertebrate faecal matter. Performed as a single blind experiment we were able to correctly identify faecal material in 17/20 effluents (85% correct). mtDNA degrades relatively quickly in faecally-spiked water samples (∼2 weeks), a similar timeframe of environmental persistence to several bacterial faecal indictors, highlighting its applicability. The procedure described here is specific, rapid (<5 hours) and sensitive. These results confirm the suitability of using species-specific mtDNA as an indicator in source tracking studies in surface waters, shellfish harvesting areas and shellfish matrices.

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