scholarly journals Targeting the invaders – targeted detection of four priority freshwater invasive non-native species using environmental DNA

2018 ◽  
Author(s):  
Rosetta C Blackman ◽  
Marco Benucci ◽  
Robert Donnelly ◽  
Bernd Hänfling ◽  
Lynsey R Harper ◽  
...  
Keyword(s):  
Invasive Species ◽  
Native Species ◽  
Environmental Dna ◽  
Single Species ◽  
Pcr Primers ◽  
Field Trials ◽  
Morphological Identification ◽  
Mussel Species ◽  
The Uk ◽  
Monitoring Protocols

Early detection is paramount for attempts to remove invasive non-native species (INNS). Traditional methods rely on physical sampling and morphological identification, which can be problematic when species are in low densities and/or are cryptic. The use of environmental DNA (eDNA) as a monitoring tool in freshwater systems is becoming increasingly acceptable and widely used for the detection of single species. Here we demonstrate the development and application of standard PCR primers for the detection of four freshwater invasive species which are high priority for monitoring in the UK and elsewhere: Dreissenid mussels; Dreissena rostriformis bugensis (Andrusov, 1987) and D. polymorpha (Pallas, 1771), and Gammarid shrimps; Dikerogammarus villosus (Sowinsky, 1984) and D. haemobaphes (Eichwald, 1843). We carried out a rigorous validation process for testing the new primers, including DNA detection and degradation rate experiments in mesocosm, and a field comparison with traditional monitoring protocols. We successfully detected all four target species in mesocosms, but success was higher for mussels than shrimps. eDNA from single individuals of both mussel species could be detected within four hours of the start of the experiment. By contrast, shrimp were only consistently detected at higher densities (20 individuals). In field trials, the two mussel species and D. haemobaphes were detected at all sites where the species are known to be present, and eDNA consistently outperformed traditional kick sampling for species detection. However, D. villosus eDNA was only detected in one of five sites where the species was confirmed by kick sampling. These results demonstrate the applicability of standard PCR for eDNA detection of freshwater invasive species, but also highlight the importance of differences between taxa in terms of the detection ability.

scholarly journals Targeting the invaders – targeted detection of four priority freshwater invasive non-native species using environmental DNA

2018 ◽  
Author(s):  
Rosetta C Blackman ◽  
Marco Benucci ◽  
Robert Donnelly ◽  
Bernd Hänfling ◽  
Lynsey R Harper ◽  
...  
Keyword(s):  
Invasive Species ◽  
Native Species ◽  
Environmental Dna ◽  
Single Species ◽  
Pcr Primers ◽  
Field Trials ◽  
Morphological Identification ◽  
Mussel Species ◽  
The Uk ◽  
Monitoring Protocols

Early detection is paramount for attempts to remove invasive non-native species (INNS). Traditional methods rely on physical sampling and morphological identification, which can be problematic when species are in low densities and/or are cryptic. The use of environmental DNA (eDNA) as a monitoring tool in freshwater systems is becoming increasingly acceptable and widely used for the detection of single species. Here we demonstrate the development and application of standard PCR primers for the detection of four freshwater invasive species which are high priority for monitoring in the UK and elsewhere: Dreissenid mussels; Dreissena rostriformis bugensis (Andrusov, 1987) and D. polymorpha (Pallas, 1771), and Gammarid shrimps; Dikerogammarus villosus (Sowinsky, 1984) and D. haemobaphes (Eichwald, 1843). We carried out a rigorous validation process for testing the new primers, including DNA detection and degradation rate experiments in mesocosm, and a field comparison with traditional monitoring protocols. We successfully detected all four target species in mesocosms, but success was higher for mussels than shrimps. eDNA from single individuals of both mussel species could be detected within four hours of the start of the experiment. By contrast, shrimp were only consistently detected at higher densities (20 individuals). In field trials, the two mussel species and D. haemobaphes were detected at all sites where the species are known to be present, and eDNA consistently outperformed traditional kick sampling for species detection. However, D. villosus eDNA was only detected in one of five sites where the species was confirmed by kick sampling. These results demonstrate the applicability of standard PCR for eDNA detection of freshwater invasive species, but also highlight the importance of differences between taxa in terms of the detection ability.

scholarly journals Potensi Environmental DNA (e-DNA) Untuk Pemantauan dan Konservasi Keanekaragaman Hayati

2021 ◽  
Vol 11 (1) ◽  
pp. 75
Author(s):  
Siti Marfuah ◽  
Beivy Jonathan Kolondam ◽  
Trina Ekawati Tallei
Keyword(s):  
Invasive Species ◽  
Molecular Markers ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Native Species ◽  
Biological Diversity ◽  
Secondary Data ◽  
Environmental Dna ◽  
Review Article ◽  
Oxidase Subunit

(Article History: Received January 6, 2021; Revised February 12, 2021; Accepted February 28, 2021) ABSTRAK Hilangnya spesies dan adanya spesies invasif dalam suatu habitat dapat menjadi ancaman bagi spesies asli dalam satu ekosistem. Untuk itu diperlukan teknik terkini yang mampu mendeteksi keberadaan suatu organisme. Salah satu teknik yang dapat mendeteksi organisme target di lingkungan secara cepat dan akurat yaitu environmental DNA (e-DNA).Tujuan dari ulasan artikel ini yaitu untuk mengeksplorasi kemampuan e-DNA secara ekogenomik untuk pemantauan dan konservasi keanekaragaman hayati. Ulasan artikel ini menggunakan data sekunder yang diperoleh dari berbagai database yang berbasis dalam jaringan. Hasil analisis memperlihatkan bahwa dengan menggunakan pendekatan e-DNA pemantauan dan konsevasi keanekaragaman hayati dapat dideteksi sesuai dengan taksonomi organisme dan penanda molekuler. Penanda molekuler Cytochrome c Oxidase subunit 1 (COI) mampu mendeteksi berbagai spesies baik langka dan invasif. Dengan demikian dapat disimpulkan bahwa pendekatan e-DNA dapat dijadikan sebagai metode untuk pemantauan dan konsevasi keanekaragaman hayati pada berbagai ekosistem.Kata - kata kunci: environmental DNA; keanekaragaman hayati dan konservasi; penanda molekuler  ABSTRACTThe loss of species and the presence of invasive species in a habitat can be a threat to native species in an ecosystem. So we need the latest techniques that are able to detect the presence of an organism. One technique that can detect target organisms in the environment quickly and accurately is environmental DNA (e-DNA). The purpose of this review article is to explore the ecogenomic ability of e-DNA for monitoring and conservation of biodiversity. This article reviews using secondary data obtained from various network-based databases. The results of the analysis show that by using the e-DNA approach, monitoring and conservation of biological diversity can be detected according to the taxonomy of organisms and molecular markers. Cytochrome c Oxidase subunit 1 (COI) molecular markers are capable of detecting a variety of both rare and invasive species. Thus it can be concluded that the e-DNA approach can be used as a method for monitoring and conservation of biological diversity in various ecosystems.Keywords: environmental DNA; biodiversity and conservation; molecular markers

scholarly journals The amount of environmental DNA increases with freshwater crayfish density and over time

2021 ◽  
Vol 4 ◽  
Author(s):  
Corinna Wallinger ◽  
Daniela Sint ◽  
Bernhard Kolp ◽  
Leopold Füreder ◽  
Michael Traugott
Keyword(s):  
Invasive Species ◽  
Native Species ◽  
Laboratory Experiments ◽  
High Sensitivity ◽  
Environmental Dna ◽  
Freshwater Crayfish ◽  
Population Densities ◽  
Non Invasive ◽  
Crayfish Population ◽  
The Relationship

eDNA analysis is ideally suited to monitor the occurrence of endangered or invasive species because of its non-invasive nature and high sensitivity. European freshwater crayfish are threatened across the whole continent. Classical crayfish monitoring is challenging and time consuming due to their nocturnal activity and hidden lifestyle. Therefore, eDNA-based monitoring of native as well as invasive species seems to be of great benefit for the conservation of the native species and it has indeed been increasingly applied in recent years. Nevertheless, comparably little is known on the relationship between eDNA concentration and crayfish population densities, a prerequisite for estimating population size based on eDNA measurements. Here, we performed laboratory experiments to investigate the relationship between the concentration of crayfish eDNA and population densities - measured as crayfish size and biomass. There was a strong correlation between the two measurements. Moreover, the amount of eDNA increased at least during the first three days after crayfish stocking in the aquarium. The experiments also indicate, that crayfish activity might have a strong influence on the eDNA signal strength. Our findings will significantly contribute to an optimization of the monitoring of freshwater crayfish via the analysis of eDNA and therefore be important for the conservation of these threatened 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.

Active and passive environmental DNA surveillance of aquatic invasive species

2016 ◽  
Vol 73 (1) ◽  
pp. 76-83 ◽  
Author(s):  
Megan Simmons ◽  
Andrew Tucker ◽  
W. Lindsay Chadderton ◽  
Christopher L. Jerde ◽  
Andrew R. Mahon
Keyword(s):  
Invasive Species ◽  
Active Surveillance ◽  
High Throughput Sequencing ◽  
Environmental Dna ◽  
Single Species ◽  
Bighead Carp ◽  
Passive Surveillance ◽  
Molecular Surveillance ◽  
River Watershed ◽  
Channa Argus

Environmental DNA (eDNA) is useful for delimiting species ranges in aquatic systems, whereby water samples are screened for the presence of DNA from a single species. However, DNA from many species is collected in every sample, and high-throughput sequencing approaches allow for more passive surveillance where a community of species is identified. In this study, we use active (targeted) and passive molecular surveillance approaches to detect species in the Muskingum River Watershed in Ohio, USA. The presence of bighead carp (Hypophthalmichthys nobilis) eDNA in the Muskingum River Watershed was confirmed with active surveillance using digital droplet polymerase chain reaction (ddPCR). The passive surveillance method detected the presence of eDNA from northern snakehead (Channa argus), which was further confirmed with active ddPCR. Whereas active surveillance may be more sensitive to detecting rare DNA, passive surveillance has the capability of detecting unexpected invasive species. Deploying both active and passive surveillance approaches with the same eDNA samples is beneficial for invasive species management.

scholarly journals Metabarcoding with MinION: Speeding up the detection of invasive aquatic species using environmental DNA and nanopore sequencing

2021 ◽  
Vol 4 ◽  
Author(s):  
Bastian Egeter ◽  
Joana Veríssimo ◽  
Manuel Lopes-Lima ◽  
catia chaves ◽  
Joana Pinto ◽  
...  
Keyword(s):  
Invasive Species ◽  
Environmental Dna ◽  
Morphological Identification ◽  
Nanopore Sequencing ◽  
Sequencing Technology ◽  
Bioinformatic Tools ◽  
Invasive Bivalves ◽  
Multiple Species ◽  
High Level ◽  
Laboratory Protocol

Traditional detection of aquatic invasive species, via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more widely accessible and to substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools to increase the reliability of nanopore sequencing to detect invasive species, and we test its application using invasive bivalves. We sampled water from sites with pre-existing bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. We extracted, amplified and sequenced eDNA with a turnaround of 3.5 days. The majority of processed reads were ≥ 99 % identical to reference sequences. There were no taxa detected other than those known to occur. The lack of detections of some species at some sites could be explained by their known low abundances. The approach is now being tested on other target taxa such as fish and other vertebrates.

scholarly journals Speeding up the detection of invasive aquatic species using environmental DNA and nanopore sequencing

2020 ◽  
Author(s):  
Bastian Egeter ◽  
Joana Veríssimo ◽  
Manuel Lopes-Lima ◽  
Cátia Chaves ◽  
Joana Pinto ◽  
...  
Keyword(s):  
Invasive Species ◽  
Health Assessment ◽  
Environmental Dna ◽  
Aquatic Invasive Species ◽  
Morphological Identification ◽  
Nanopore Sequencing ◽  
Sequencing Technology ◽  
Bioinformatic Tools ◽  
Invasive Bivalves ◽  
High Level

AbstractTraditional detection of aquatic invasive species, via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more widely accessible and to substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools to increase the reliability of nanopore sequencing to detect invasive species, and we test its application using invasive bivalves. We sampled water from sites with pre-existing bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. We extracted, amplified and sequenced eDNA with a turnaround of 3.5 days. The majority of processed reads were ≥ 99 % identical to reference sequences. There were no taxa detected other than those known to occur. The lack of detections of some species at some sites could be explained by their known low abundances. This is the first reported use of MinION to detect aquatic invasive species from eDNA samples. The approach can be easily adapted for other metabarcoding applications, such as biodiversity assessment, ecosystem health assessment and diet studies.

High predatory efficiency and abundance drive expected ecological impacts of a marine invasive fish

2020 ◽  
Vol 637 ◽  
pp. 195-208 ◽  
Author(s):  
EM DeRoy ◽  
R Scott ◽  
NE Hussey ◽  
HJ MacIsaac
Keyword(s):  
Invasive Species ◽  
Native Species ◽  
Ecological Impact ◽  
Marine Species ◽  
Ecological Impacts ◽  
Negative Effects ◽  
Marine Predator ◽  
Eastern Gulf Of Mexico ◽  
Red Grouper ◽  
Per Capita

The ecological impacts of invasive species are highly variable and mediated by many factors, including both habitat and population abundance. Lionfish Pterois volitans are an invasive marine species which have high reported detrimental effects on prey populations, but whose effects relative to native predators are currently unknown for the recently colonized eastern Gulf of Mexico. We used functional response (FR) methodology to assess the ecological impact of lionfish relative to 2 functionally similar native species (red grouper Epinephelus morio and graysby grouper Cephalopholis cruentata) foraging in a heterogeneous environment. We then combined the per capita impact of each species with their field abundance to obtain a Relative Impact Potential (RIP). RIP assesses the broader ecological impact of invasive relative to native predators, the magnitude of which predicts community-level negative effects of invasive species. Lionfish FR and overall consumption rate was intermediate to that of red grouper (higher) and graysby grouper (lower). However, lionfish had the highest capture efficiency of all species, which was invariant of habitat. Much higher field abundance of lionfish resulted in high RIPs relative to both grouper species, demonstrating that the ecological impact of lionfish in this region will be driven mainly by high abundance and high predator efficiency rather than per capita effect. Our comparative study is the first empirical assessment of lionfish per capita impact and RIP in this region and is one of few such studies to quantify the FR of a marine predator.

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