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

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.

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Are Environmental DNA Methods Ready for Aquatic Invasive Species Management?

Trends in Ecology & Evolution ◽

10.1016/j.tree.2020.03.011 ◽

2020 ◽

Vol 35 (8) ◽

pp. 668-678 ◽

Cited By ~ 10

Author(s):

Adam J. Sepulveda ◽

Nanette M. Nelson ◽

Christopher L. Jerde ◽

Gordon Luikart

Keyword(s):

Invasive Species ◽

Environmental Dna ◽

Aquatic Invasive Species ◽

Invasive Species Management ◽

Species Management

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

Management of Biological Invasions ◽

10.3391/mbi.2020.11.2.03 ◽

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

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

10.7287/peerj.preprints.27284 ◽

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.

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

10.7287/peerj.preprints.27284v1 ◽

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.

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Quantifying Environmental DNA Signals for Aquatic Invasive Species Across Multiple Detection Platforms

Environmental Science & Technology ◽

10.1021/es5034052 ◽

2014 ◽

Vol 48 (21) ◽

pp. 12800-12806 ◽

Cited By ~ 109

Author(s):

Lucas M. Nathan ◽

Megan Simmons ◽

Benjamin J. Wegleitner ◽

Christopher L. Jerde ◽

Andrew R. Mahon

Keyword(s):

Invasive Species ◽

Environmental Dna ◽

Aquatic Invasive Species ◽

Multiple Detection

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Advanced molecular-based surveillance of quagga and zebra mussels: A review of environmental DNA/RNA (eDNA/eRNA) studies and considerations for future directions

NeoBiota ◽

10.3897/neobiota.66.60751 ◽

2021 ◽

Vol 66 ◽

pp. 117-159

Author(s):

Sheena M. Feist ◽

Richard F. Lance

Keyword(s):

Invasive Species ◽

Zebra Mussel ◽

High Throughput Sequencing ◽

Freshwater Mussel ◽

Environmental Dna ◽

Zebra Mussels ◽

Aquatic Invasive Species ◽

Quagga Mussel ◽

Future Directions ◽

Dreissena Rostriformis Bugensis

Sensitive methods, capable of rapidly and accurately detecting aquatic invasive species, are in demand. Molecular-based approaches, such as environmental DNA (eDNA) surveys, satisfy these requirements and have grown in popularity. As such, eDNA surveys could aid the effort to combat the colonisation and spread of two notoriously invasive freshwater mussel species, the quagga mussel (Dreissena rostriformis bugensis) and zebra mussel (D. polymorpha), through improved surveillance ability. Here, we provide a review of dreissenid eDNA literature (both grey and published), summarising efforts involved in the development of various assays for use in multiple different technologies (e.g. quantitative PCR, high-throughput sequencing and loop-mediated isothermal amplification) and sampling scenarios. We discuss important discoveries made along the way, including novel revelations involving environmental RNA (eRNA), as well as the advantages and limitations of available methods and instrumentation. In closing, we highlight critical remaining gaps, where further investigation could lead to advancements in dreissenid monitoring capacity.

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Forage palatability of Broussonetia papyrifera an invasive species in Ghana: Relative preference and palatability by sheep and goats

Journal of Energy and Natural Resource Management ◽

10.26796/jenrm.v2i0.46 ◽

2018 ◽

Vol 2 (2) ◽

pp. 63-70 ◽

Cited By ~ 1

Author(s):

R. Obour

Keyword(s):

Invasive Species ◽

Leucaena Leucocephala ◽

Condensed Tannin ◽

Block Design ◽

Wet Season ◽

Broussonetia Papyrifera ◽

Sheep And Goats ◽

Relative Preference ◽

Exotic Tree ◽

High Level

Broussonetia papyrifera is an exotic tree widely grown for paper production. Due to its prolific regeneration it has invaded forestcanopy gaps and degraded farmlands and has now become an invasive species in Ghana. In enhancing its value for use the plantwas evaluated as potential forage for grazing animals vis-à-vis other two existing forage plants: Ficus exasperata and Leucaenaleucocephala.The study assessed the palatability and preference of Broussonetia papyrifera using sheep and goats for the wet anddry seasons.The species were assessed in indoor pen feeding trials using eight-unit (3×3 m) pens with the cafeteria method.The amount of forage offered was 100g (fresh material) in all instances for each species and for ten minutes. Adesign basedon 3×2×2 factorial in Randomized Complete Block Design (RCBD) was used to test the differences in palatability betweenthe three forage species.Results revealed that palatability was higher (P<0.05) in Leucaena leucocephala compared with Ficusexasperata and Broussonetia papyrifera for sheep and goats across seasons. The trend shown might be the result of the effectsof familiarity with the Leucaena leucocephala since animals tend to select plants that are familiar than newly introduced andunfamiliar plants. The study also revealed high level of condensed tannin (CT) in Broussonetia papyrifera which might haveinterfered with forage intake by the animals.There were no significant differences in palatability of Broussonetia papyrifera forgoat in both dry and wet season interactions and Ficus exasperata for goat in both dry and wet season interactions (P>0.05).Thestudy concluded that Broussonetia papyrifera could be a potential feed for both sheep and goats across seasons.The researchrecommended that livestock farmers should incorporate Broussonetia papyrifera feed into their programmes for both sheep andgoats and should be introduced to animals from infancy so that it may become a familiar feed for them.

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Faculty Opinions recommendation of The risk of establishment of aquatic invasive species: joining invasibility and propagule pressure.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1089738.544031 ◽

2007 ◽

Author(s):

Kai Chan

Keyword(s):

Invasive Species ◽

Propagule Pressure ◽

Aquatic Invasive Species

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Long Term Interactions of Native and Invasive Species in a Marine Protected Area Suggest Complex Cascading Effects Challenging Conservation Outcomes

Diversity ◽

10.3390/d13020071 ◽

2021 ◽

Vol 13 (2) ◽

pp. 71

Author(s):

Charalampos Dimitriadis ◽

Ivoni Fournari-Konstantinidou ◽

Laurent Sourbès ◽

Drosos Koutsoubas ◽

Stelios Katsanevakis

Keyword(s):

Invasive Species ◽

Native Species ◽

High Performance ◽

Marine Protected Area ◽

Habitat Degradation ◽

Population Increase ◽

Rocky Reef ◽

Cascading Effects ◽

High Level

Understanding the interactions among invasive species, native species and marine protected areas (MPAs), and the long-term regime shifts in MPAs is receiving increased attention, since biological invasions can alter the structure and functioning of the protected ecosystems and challenge conservation efforts. Here we found evidence of marked modifications in the rocky reef associated biota in a Mediterranean MPA from 2009 to 2019 through visual census surveys, due to the presence of invasive species altering the structure of the ecosystem and triggering complex cascading effects on the long term. Low levels of the populations of native high-level predators were accompanied by the population increase and high performance of both native and invasive fish herbivores. Subsequently the overgrazing and habitat degradation resulted in cascading effects towards the diminishing of the native and invasive invertebrate grazers and omnivorous benthic species. Our study represents a good showcase of how invasive species can coexist or exclude native biota and at the same time regulate or out-compete other established invaders and native species.

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