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

2014 ◽  
Vol 48 (21) ◽  
pp. 12800-12806 ◽  
Author(s):  
Lucas M. Nathan ◽  
Megan Simmons ◽  
Benjamin J. Wegleitner ◽  
Christopher L. Jerde ◽  
Andrew R. Mahon
2020 ◽  
Vol 35 (8) ◽  
pp. 668-678 ◽  
Author(s):  
Adam J. Sepulveda ◽  
Nanette M. Nelson ◽  
Christopher L. Jerde ◽  
Gordon Luikart

2020 ◽  
Vol 11 (2) ◽  
pp. 201-217
Author(s):  
Francis LeBlanc ◽  
Valérie Belliveau ◽  
Erica Watson ◽  
Chantal Coomber ◽  
Nathalie Simard ◽  
...  

NeoBiota ◽  
2021 ◽  
Vol 66 ◽  
pp. 117-159
Author(s):  
Sheena M. Feist ◽  
Richard F. Lance

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.


Author(s):  
Bastian Egeter ◽  
Joana Veríssimo ◽  
Manuel Lopes-Lima ◽  
Cátia Chaves ◽  
Joana Pinto ◽  
...  

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.


Author(s):  
D Yanuarita ◽  
D F Inaku ◽  
N Nurdin ◽  
S W Rahim ◽  
H Kudsiah ◽  
...  

Fisheries ◽  
2010 ◽  
Vol 35 (3) ◽  
pp. 121-132 ◽  
Author(s):  
John D. Rothlisberger ◽  
W. Lindsay Chadderton ◽  
Joanna McNulty ◽  
David M. Lodge

2020 ◽  
Author(s):  
Jacopo Cerri ◽  
Ernesto Azzurro

Aquatic Invasive species (AIS) are a growing driver of change across marine and freshwater ecosystems but spatially-explicit information is seldom available for supporting management actions and decision making. Here we conceived and tested a new participatory method to map the distribution of three invasive species (Callinectes sapidus, Procambarus clarkii and Oreochromis niloticus) in the coastal lagoon of Lesina (Italy). Local fishers were asked to draw the distribution of each species on pre-printed maps, indicating districts of the lagoon characterized by different abundance levels. Then, maps were converted to a lattice grid and a Bayesian hierarchical Generalized Additive Modeling was adopted to model species distribution in the lagoon, calculating the coefficient of variation for model fitted values to map fishers agreement about the distribution of each species.The spatial gradient in the abundance of the three species in the lagoon aligned with their ecological requirements. C. sapidus was abundant throughout the whole lagoon, peaking in correspondence of saltmarsh vegetation, while P. clarkii and O. niloticus, were much less abundant and remained distributed near to freshwater inputs. Experts agreed about the spatial distribution of C. sapidus in the lagoon, with a median coefficient of variation in model fitted values of 3.9%. On the other hand, the coefficient of variation was higher for P.clarkii (19.9%) O. niloticus (18.4%), indicating a higher level of uncertainty about their estimated distribution.With this example, we provided new metrics to evaluate the quality of LEK-based participatory mapping in terms of agreement and consistency among experts. The resulting information provides new insights for spatially informed management across aquatic realms in relation to the increasing ecological and socio-economical pressures posed by biological invaders.


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