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

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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Quantifying the ecological niche overlap between two interacting invasive species: the zebra mussel(Dreissena polymorpha)and the quagga mussel(Dreissena rostriformis bugensis)

Aquatic Conservation Marine and Freshwater Ecosystems ◽

10.1002/aqc.2414 ◽

2013 ◽

Vol 24 (3) ◽

pp. 324-337 ◽

Cited By ~ 26

Author(s):

Alex Quinn ◽

Belinda Gallardo ◽

David C. Aldridge

Keyword(s):

Invasive Species ◽

Zebra Mussel ◽

Dreissena Polymorpha ◽

Ecological Niche ◽

Niche Overlap ◽

Quagga Mussel ◽

Dreissena Rostriformis Bugensis

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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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Watercraft Decontamination Practices to Reduce the Viability of Aquatic Invasive Species Implicated in Overland Transport.

10.21203/rs.3.rs-1021628/v1 ◽

2021 ◽

Author(s):

Shrisha Mohit ◽

Timothy B. Johnson ◽

Shelley E. Arnott

Keyword(s):

Invasive Species ◽

Dreissena Polymorpha ◽

High Pressures ◽

Water Pressure ◽

Myriophyllum Spicatum ◽

Zebra Mussels ◽

Hot Water ◽

Aquatic Invasive Species ◽

Air Drying ◽

Water Exposure

Abstract Recreational boating activities enable aquatic invasive species (AIS) dispersal among disconnected lakes, as invertebrates and plants caught on or contained within watercraft and equipment used in invaded waterbodies can survive overland transport. Resource management agencies worldwide recommend decontaminating watercraft and equipment using high water pressure, rinsing with hot water, or air-drying for up to seven days to inhibit this mode of secondary spread. There is a lack of studies on the efficacy of these methods under realistic conditions and considering feasibility for recreational boaters. Hence, we conducted experiments addressing this knowledge gap using AIS present in Ontario, namely zebra mussels (Dreissena polymorpha), banded mystery snails (Viviparus georgianus), spiny waterfleas (Bythotrephes cederstroemi), Eurasian watermilfoil (Myriophyllum spicatum), Carolina fanwort (Cabomba caroliniana), and European frogbit (Hydrocharis morsus-ranae). Washing at high pressures of 900-1200 psi removed the most biological material (90%) from surfaces. Brief (<10s) exposure to water at ≥60°C caused nearly 100% mortality among all species tested, except snails. Acclimation to temperatures from 15°C to 30°C before hot water exposure had little effect on the minimum temperature required for no survival. Air-drying durations producing complete mortality were ≥60h for zebra mussels and spiny waterfleas, and ≥6 days among plants, whereas survival remained high among snails after a week of air-drying. Hot water exposure followed by air-drying was more effective than either method separately against all species tested, reducing either the minimum water temperature or air-drying duration necessary. These findings can inform best management strategies against AIS spread.

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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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Environmental DNA biomonitoring revealed species diversity of Cnidarian and Poriferan across Jakarta Bay and Seribu Islands National Park

10.21203/rs.3.rs-1167046/v1 ◽

2021 ◽

Author(s):

Ismail Maqbul ◽

Farrahdiba Yossan Fahrezi ◽

Ersya Nurul A Bakhri ◽

Indri Verawati ◽

Lalu M Iqbal Sani ◽

...

Keyword(s):

Invasive Species ◽

Introduced Species ◽

National Park ◽

High Throughput Sequencing ◽

Environmental Dna ◽

Ecological Research ◽

Negative Consequences ◽

Approach Method ◽

Broad Approach ◽

Conservation Method

Abstract Indonesia, as a country having a unique sea lane known as the Indonesian Archipelagic Sea Lanes (ASLs), has become one of the busiest countries in the world with varied shipping activities. These actions have the ability to facilitate the transmission of species (bio-invasion). Until recently, the number of global introduced species has increased, with negative consequences for environment and the economy. Environmental DNA (eDNA) approaches for detecting the presence of invasive species are currently receiving a lot of interest as a broad approach method in ecological research. As a result, the study used the eDNA technique to compare the quantity and variety of introduced species from the Cnidaria and Porifera Phyla, as well as to characterize their invasiveness status and possible presence in the waters of Jakarta Bay. Based on data from the inside Zone of National Park (ZI) and Outside Zone of National Park (ZO), the biological community composition, richness, and diversity were assessed (ZO). The mBrave workflow generated a total of 14,275 reads from high-throughput sequencing of amplicons from two zones, with 8,917 reads in ZI and 5,358 reads in ZO. Blackfordia virginica , Cordylophora caspia , and Ectopleura crocea were among the imported species included in the invasive category, with E. crocea having the highest abundance and being detected in both zones, with a total of 1300 reads, consisting of 1253 reads in ZI and 47 reads in ZO. Based on the findings, the eDNA methodology can be used as a biomonitoring and conservation method for invasive species.

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Detecting aquatic invasive species in bait and pond stores with targeted environmental (e)DNA high-throughput sequencing metabarcode assays: Angler, retailer, and manager implications

Biological Conservation ◽

10.1016/j.biocon.2020.108430 ◽

2020 ◽

Vol 245 ◽

pp. 108430 ◽

Cited By ~ 1

Author(s):

Matthew R. Snyder ◽

Carol A. Stepien ◽

Nathaniel T. Marshall ◽

Hannah B. Scheppler ◽

Christopher L. Black ◽

...

Keyword(s):

Invasive Species ◽

High Throughput ◽

High Throughput Sequencing ◽

Aquatic Invasive Species

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Active and passive environmental DNA surveillance of aquatic invasive species

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/cjfas-2015-0262 ◽

2016 ◽

Vol 73 (1) ◽

pp. 76-83 ◽

Cited By ~ 53

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.

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Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, Dreissena rostriformis bugensis in flowing water

10.1101/2020.01.07.890731 ◽

2020 ◽

Author(s):

Rosetta C Blackman ◽

Kar Keun Sean Ling ◽

Lynsey R Harper ◽

Peter Shum ◽

Bernd Hänfling ◽

...

Keyword(s):

Native Species ◽

Environmental Dna ◽

Quagga Mussel ◽

Source Population ◽

List Type ◽

Flowing Water ◽

Monitoring Methods ◽

Dreissena Rostriformis Bugensis ◽

Management Actions ◽

Molecular Approaches

AbstractThe early detection of invasive non-native species (INNS) is important for informing management actions. Established monitoring methods require the collection or observation of specimens, which is unlikely at the beginning of an invasion when densities are likely to be low. Environmental DNA (eDNA) analysis is a highly promising technique for the detection of INNS – particularly during the early stages of an invasion.Here, we compared the use of traditional kick-net sampling with two eDNA approaches (targeted detection using both conventional and quantitative PCR, and passive detection via metabarcoding with conserved primers) for detection of quagga mussel, Dreissena rostriformis bugensis; a high priority INNS, along a density gradient on the River Wraysbury, UK.All three molecular tools outperformed traditional sampling in terms of detection. Conventional PCR and qPCR both had 100% detection rate in all samples, and outperformed metabarcoding when the target species was at low densities. Additionally, quagga mussel DNA copy number (qPCR) and relative read count (metabarcoding) were significantly influenced by both mussel density and distance from source population, with distance being the most significant predictor.Synthesis and application. All three molecular approaches were more sensitive than traditional kick-net sampling for the detection of the quagga mussel in flowing water, and both qPCR and metabarcoding enabled estimates of relative abundance. Targeted approaches were more sensitive than metabarcoding, but metabarcoding has the advantage of providing information on the wider community, and consequently impacts of INNS.

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