On the way for detecting and quantifying elusive species in the sea: The Octopus vulgaris case study

Mauvisseau, Quentin; Parrondo, Marina; Fernández, Marc; García, Luis Pericot; Martínez, José Luis; García‐Vázquez, Eva; Borrell, Yaisel J.

doi:10.1016/j.fishres.2017.02.023

Cited by 37 publications

(27 citation statements)

References 57 publications

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“…The eDNA concentrations measured in the field corresponded well to the observed occurrence of CoTS over [ 500 km of the GBR investigated here. Outbreaks usually start in the 'initiation box' between Cairns and Cooktown, and probably at the Northern End of this box (Pratchett et al 2014;2017), corresponding to the Cooktown region reefs sampled in this study. No water sample collected from that region contained CoTS eDNA above the limit of quantification (LOQ).…”

Section: Discussionmentioning

confidence: 86%

“…However, several recent studies have successfully used eDNA to quantify fish or describe fish diversity in the marine environment (Thomsen et al 2012;Yamamoto et al 2016) using both specific primers or metabarcoding approaches. Methods for monitoring groups that are not well described such as harmful algae and faecal indicators (Yamahara et al 2015) or Octopus vulgaris (Mauvisseau 2017) have also recently been developed. A study on a coral reef used universal barcoding primers to describe Eukaryote diversity across several major taxa (Stat et al 2017).…”

Section: Introductionmentioning

confidence: 99%

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eDNA detection of corallivorous seastar (Acanthaster cf. solaris) outbreaks on the Great Barrier Reef using digital droplet PCR

2018

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Coral loss through consumption by corallivorous crown-of-thorns seastars (CoTS, Acanthaster spp.) is a major contributor to the coral reef crisis in the Indo-Pacific region. The fourth wave of Acanthaster cf. solaris outbreaks since the 1960s started around 2010 on Australia's Great Barrier Reef. Ecological monitoring failed to detect early outbreak stages, thus preventing timely intervention. Here, we develop a digital droplet PCR (ddPCR)-based method to detect environmental DNA (eDNA) of CoTS in 2-l water samples that can be compared with abundances of the species recorded by divers along 200-m 2 transects. Aquarium tests demonstrated that eDNA was readily detectable and increases proportional to the biomass of CoTS (R 2 = 0.99, p \ 0.0001). Adaptation from a quantitative PCR technique developed for CoTS larvae (Doyle et al. in Marine Biology 164:176, 2017) to ddPCR improved the limit of quantification (LOQ) by a factor of 45. During field verification on 11 reefs, CoTS eDNA was detectable on all reefs suffering outbreaks. In contrast, CoTS eDNA was absent from 'post-outbreak' reefs after populations collapsed and from 'pre-outbreak' reefs. In linear models, CoTS densities explained a high amount of variance of eDNA concentrations, both for water samples taken at the depth of transects (R 2 = 0.60, p \ 0.0001) and on the sea surface (R 2 = 0.46, p = 0.0004). The proportion of samples above LOQ was also correlated with CoTS densities, with a similar amount of variance explained as for the concentration (underwater R 2 = 0.68, p \ 0.0001; surface R 2 = 0.49, p = 0.0004). We conclude that, after consideration of sampling locations and times, this method is promising for CoTS population monitoring and early detection of outbreaks and might supplement or replace traditional monitoring. Development of automated samplers and possibly on board PCR in the future will further improve early detection. Keywords Coral reef crisis Á Nuisance species Á Population outbreaks Á eDNA CoTS. This includes reefs in French Polynesia (Kayal et al.

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Section: Discussionmentioning

confidence: 86%

Section: Introductionmentioning

confidence: 99%

eDNA detection of corallivorous seastar (Acanthaster cf. solaris) outbreaks on the Great Barrier Reef using digital droplet PCR

2018

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“…All aquatic organisms shed DNA traces in their environment 17 , and it is now possible to detect a specific species (barcoding) or assess an entire community (metabarcoding) by sampling an aquatic system and amplifying the existing DNA traces using PCR (Polymerase Chain Reaction) based techniques 17 . Since the implementation of eDNA techniques in environmental studies last decade, it has been proven to be successful for the monitoring of invasive 18–22 , endangered 23,24 and/or economically important species from a wide range of taxa 25–27 . However, few studies have used eDNA for monitoring rare or indicator macroinvertebrate species 28–30 .…”

Section: Introductionmentioning

confidence: 99%

Improving detection capabilities of a critically endangered freshwater invertebrate with environmental DNA using digital droplet PCR

Mauvisseau

Davy‐Bowker

Bulling

et al. 2019

Preprint

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21Isogenus nubecula is a critically endangered Plecoptera species. Considered extinct in the UK, the 22 species was recently rediscovered in one location of the river Dee in Wales after 22 years of absence. As 23 many species belonging to the Perlodidae, this species can be a bio-indicator, utilised for assessing 24 water quality and health status of a given freshwater system. However, conventional monitoring of 25 invertebrates via kick-sampling for example, is an invasive and expensive (time consuming). Further, 26 such methods require a high level of taxonomic expertise. Here, we compared the traditional kick-27 sampling method with the use of eDNA detection using qPCR and ddPCR-analyses. In spring 2018, we 28 sampled eDNA from twelve locations on the river Dee. I. nubecula was detected using kick-sampling in 29 five of these locations, three locations using both eDNA detection and kick-sampling and one location 30 using eDNA detection alone -resulting in a total of six known and distinct populations of this critically 31 endangered species. Interestingly, despite the eDNA assay being validated in vitro and in silico, and 32 results indicating high sensitivity, qPCR analysis of the eDNA samples proved to be ineffective. In 33 contrast, ddPCR analyses resulted in a clear detection of I. nubecula at four locations suggesting that 34 inhibition most likely explains the big discrepancy between the obtained qPCR and ddPCR results. It is 35 therefore important to explore inhibition effects on any new eDNA assay. We also highlight that ddPCR 36 may well be the best option for the detection of aquatic organisms which are either rare or likely to shed 37 low levels of eDNA into their environment. 38

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“…The results of our study provide a validated approach for using eDNA to assess the presence of C. mydas. However, further study is required to optimise the assay for C. mydas eDNA detection and investigate the potential for relative abundance/biomass estimation as has been demonstrated for other assays targeting taxa from freshwater (Takahara et al, 2012;Thomsen et al, 2012;Pilliod et al, 2013;Doi et al, 2015;Buxton et al, 2017;Levi et al, 2018) and marine water (Mauvisseau et al, 2017;Nichols and Marko, 2019). Our results suggest that the primer pair producing the shorter amplicon (LCMint2/H950g, 253 bp) would be a better candidate to further develop eDNA methodologies for C. mydas than LTCM2/HDCM2, which produces a longer amplicon (488 bp).…”

Section: Discussionmentioning

confidence: 99%

Finding Crush: Environmental DNA Analysis as a Tool for Tracking the Green Sea Turtle Chelonia mydas in a Marine Estuary

et al. 2020

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Environmental DNA (eDNA) analysis is a rapid, non-invasive method for species detection and distribution assessment using DNA released into the surrounding environment by an organism. eDNA analysis is recognised as a powerful tool for detecting endangered or rare species in a range of ecosystems. Although the number of studies using eDNA analysis in marine systems is continually increasing, there appears to be no published studies investigating the use of eDNA analysis to detect sea turtles in natural conditions. We tested the efficacy of two primer pairs known to amplify DNA fragments of differing lengths (488 and 253 bp) from Chelonia mydas tissues for detecting C. mydas eDNA in water samples. The capture, extraction, and amplification of C. mydas eDNA from aquaria (Sea World, San Diego, CA, United States) and natural water (San Diego Bay, CA, United States) were successful using either primer set. The primer pair providing the shorter amplicon, LCMint2/H950g, demonstrated the ability to distinguish cross-reactive species by melt curve analysis and provided superior amplification metrics compared to the other primer set (LTCM2/HDCM2); although primer dimer was observed, warranting future design refinement. Results indicated that water samples taken from deeper depths might improve detection frequency, consistent with C. mydas behaviour. Overall, this pilot study suggests that with refinement of sampling methodology and further assay optimisation, eDNA analysis represents a promising tool to monitor C. mydas. Potential applications include rapid assessment across broad geographical areas to pinpoint promising locations for further evaluation with traditional methods.

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On the way for detecting and quantifying elusive species in the sea: The Octopus vulgaris case study

Cited by 37 publications

References 57 publications

eDNA detection of corallivorous seastar (Acanthaster cf. solaris) outbreaks on the Great Barrier Reef using digital droplet PCR

eDNA detection of corallivorous seastar (Acanthaster cf. solaris) outbreaks on the Great Barrier Reef using digital droplet PCR

Improving detection capabilities of a critically endangered freshwater invertebrate with environmental DNA using digital droplet PCR

Finding Crush: Environmental DNA Analysis as a Tool for Tracking the Green Sea Turtle Chelonia mydas in a Marine Estuary

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