Development of a sensitive detection method to survey pelagic biodiversity using eDNA and quantitative PCR: a case study of devil ray at seamounts

  title={Development of a sensitive detection method to survey pelagic biodiversity using eDNA and quantitative PCR: a case study of devil ray at seamounts},
  author={Laura M. Gargan and Telmo Morato and Christopher Kim Pham and John A. Finarelli and Jeanette E. L. Carlsson and Jens Carlsson},
  journal={Marine Biology},
Environmental DNA (eDNA) is increasingly being used in aquatic environments for monitoring species, particularly those that are of conservation concern and/or are difficult to visually observe. Quantitative PCR (qPCR) has been employed to detect low abundance species occurring in environmental water samples. However, the qPCR technique has principally been applied to freshwater habitats, with less application to pelagic marine environments. We developed a species-specific eDNA assay for the… 

Using environmental DNA methods to improve detectability in an endangered sturgeon (Acipenser sinensis) monitoring program

The results prove the efficacy of eDNA for monitoring reproductive stock of the Chinese sturgeon and the e decreased eDNA concentration reflect that ChineseSturgeon may survive with an extremely small number of reproductive stock in the Yangtze River.

A workflow for the relative quantification of multiple fish species from oceanic water samples using environmental DNA (eDNA) to support large-scale fishery surveys

A complete workflow for the simultaneous detection and quantification of multiple marine fish species using eDNA is presented and the multiplex qPCR assay is shown to be sensitive and specific for the purposes of simultaneously monitoring the relative abundance of multiple targeted fish species.

e(lasmo)DNA : the role of environmental DNA (eDNA) analysis in marine fish biodiversity assessment, with special focus on elasmobranchs

This novel eDNA approach was developed to investigate elasmobranch diversity in order to assess species richness in areas of special conservation concern while simultaneously examining the influence of interacting factors such as habitat type and conservation regime in determining diversity and abundance.

Validation of eDNA as a viable method of detection for dangerous cubozoan jellyfish

Stings from certain species of cubozoan jellyfish are dangerous to humans and their seasonal presence in tropical marine waters poses a significant risk to coastal communities. The detection of

Environmental DNA (eDNA) From the Wake of the Whales: Droplet Digital PCR for Detection and Species Identification

Droplet digital (dd)PCR technology for detection and species identification of cetaceans using environmental (e)DNA collected from seawater is adopted, with a focus on identification of known killer whale ecotypes.

Use of Environmental DNA to Determine Fantail Darter (Etheostoma flabellare) Density in a Laboratory Setting: Effects of Biomass and Filtration Method

Estimating fish abundance/biomass holds great importance for freshwater ecology and fisheries management, but current techniques can be expensive, time-consuming, and potentially harmful to target

A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (Chrysemys picta) eDNA Under Field Conditions

The “shedding hypothesis”—the possibility that animals with hard, keratinized integument do not shed as much DNA as mucus-covered organisms—is presented as a potential challenge for eDNA studies, and it is remained hopeful that eDNA can be used to detect freshwater turtles in the field.

Correction to: An environmental DNA tool for monitoring the status of the Critically Endangered Smalltooth Sawfish, Pristis pectinata, in the western Atlantic

An eDNA tool: a species-specific Droplet Digital™ PCR (ddPCR) assay targeting a 100-base pair portion of the mitochondrial NADH dehydrogenase subunit 2 gene in P. pectinata, with the ability to reliably detect as little as 0.25 pg of target DNA.

Development of highly sensitive environmental DNA methods for the detection of Bull Sharks, Carcharhinus leucas (Müller and Henle, 1839), using Droplet Digital™ PCR

Background: As apex and mesopredators, elasmobranchs play a crucial role in main‐ taining ecosystem function and balance in marine systems. Elasmobranch populations worldwide are in decline as a

Environmental DNA detection tracks established seasonal occurrence of blacktip sharks (Carcharhinus limbatus) in a semi-enclosed subtropical bay

The results show that C. limbatus eDNA detection follows known seasonal residency patterns consistently over 2 years of monitoring, and species-specific eDNA analysis using real-time PCR could represent a cost-effective, scalable sampling tool to facilitate improved shark population monitoring in semi-enclosed marine habitats.



Using Environmental DNA to Estimate the Distribution of an Invasive Fish Species in Ponds

The eDNA method simply and rapidly detects the presence of the invasive bluegill sunfish with less disturbance to the environment during field surveys than traditional methods.

Detecting an elusive invasive species: a diagnostic PCR to detect Burmese python in Florida waters and an assessment of persistence of environmental DNA

This study shows P. bivittatus eDNA can be isolated from water samples; thus, this method is a new and promising technique for the management of invasive reptiles.

Species detection using environmental DNA from water samples

A novel approach, based on the limited persistence of DNA in the environment, to detect the presence of a species in fresh water, using specific primers that amplify short mitochondrial DNA sequences to track the existence of a frog in controlled environments and natural wetlands.

Environmental DNA detects Critically Endangered largetooth sawfish in the wild

It is demonstrated that an eDNA approach to detecting largetooth sawfish can produce reliable outcomes and can be used as a survey tool to help with conservation efforts for this and other threatened elasmobranchs.

Transport Distance of Invertebrate Environmental DNA in a Natural River

The results indicate that there may be species' specific transport distances for eDNA and demonstrate for the first time that invertebrate eDNA can persist over relatively large distances in a natural river system.

Improving the containment of a freshwater invader using environmental DNA (eDNA) based monitoring

This study used conventional monitoring methods and eDNA-based monitoring using real-time PCR to determine the spread of the invasive redfin perch in an intermittent river system and found that eDNA detection rates were high in the study system, when redfinPerch presence was confirmed by conventional monitoring, compared to previously published works.

Critical considerations for the application of environmental DNA methods to detect aquatic species

A synthesis of knowledge is presented at this stage for application of this new and powerful detection method, which can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species.

Investigating the Potential Use of Environmental DNA (eDNA) for Genetic Monitoring of Marine Mammals

To determine the potential use of eDNA for genetic monitoring, specific primers that amplify short mitochondrial DNA sequences were used to detect the presence of a marine mammal, the harbor porpoise, in a controlled environment and in natural marine locations.

Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples

It is demonstrated that even small samples of seawater contain eDNA from a wide range of local fish species, which indicates the potential of using metabarcoding of environmental DNA (eDNA) obtained directly from seawater samples to account for marine fish biodiversity.