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

2020 ◽  
Vol 2020 ◽  
pp. 1-7
Author(s):  
Ramon A. Guivas ◽  
Ben F. Brammell
Keyword(s):  
Environmental Dna ◽  
Filter Method ◽  
Laboratory Setting ◽  
Widespread Application ◽  
Filtration Method ◽  
Etheostoma Flabellare ◽  
Real Time Quantitative Pcr ◽  
Species Specific ◽  
Filter Clogging ◽  
Fantail Darter

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 organisms. Environmental DNA (eDNA) has proven an effective and efficient technique for presence/absence detection of freshwater vertebrates. Additionally, recent studies report correlations between target organism density/biomass and eDNA levels, although widespread application of this technique is limited by the number of studies examining this relationship in various species and settings. Additionally, filter clogging is a commonly encountered issue in eDNA studies in environments with significant sediment and/or phytoplankton algae. Frequently, a sample must be split into multiple aliquots and filtered separately in order to process the entire sample. The present study examines both the relationship between biomass and eDNA and the effects of single versus multiple filter sampling on eDNA concentrations of fantail darters (Etheostoma flabellare) in a laboratory setting. Tank tests were performed in quadruplicate at four environmentally relevant fantail biomass levels. eDNA samples were collected and processed in parallel (one as a whole through a single filter and one in parts through multiple filters). Species-specific primers and a probe were developed for E. flabellare from cytochrome b sequences obtained from locally collected specimens, and real-time quantitative PCR was used to analyze eDNA levels at each biomass. Significant correlations were observed with increasing biomass for both methods, although this relationship was stronger for samples processed by the multiple filter method. These data should be useful in eDNA studies in which turbidity necessitates the use of multiple filters per sample as well as in the use of eDNA to estimate darter populations.

scholarly journals Comparing conservation monitoring approaches: traditional and environmental DNA tools for a critically endangered mammal

2017 ◽  
Author(s):  
Chanjuan Qu ◽  
Kathryn A Stewart
Keyword(s):  
Data Collection ◽  
Environmental Dna ◽  
Critically Endangered ◽  
Conventional Pcr ◽  
Aquatic Mammal ◽  
Real Time Quantitative Pcr ◽  
Trade Offs ◽  
Sampling Protocols ◽  
Species Specific ◽  
The Cost

While conservation management has made tremendous strides in the last few decades, the decision of knowing where and how to invest (often) small surveying budgets for biodiversity data collection remains a central hurdle for impactful conservation decision making. New analytical tools, such as environmental DNA (eDNA), are now facilitating broader biodiversity monitoring to take place at unprecedented scales, in part due to its time-efficient, and presumably cost-efficient, premise. eDNA approaches vary from conventional PCR (detecting presence/absence of species), metabarcoding (community structure), to qPCR (relative DNA abundance), and knowing when to employ these techniques over traditional sampling protocols could enable conservation practitioners to make informed trade-offs between cost, accuracy, and speed of data collection. Using 12 species-specific primers designed for conventional PCR use in eDNA analysis of the Yangtze Finless Porpoise (Neophocaena asiaeorientalis asiaeorientalis), a critically endangered aquatic mammal within the Yangtze River, we validated and optimized these same primers for use in real-time Quantitative PCR (qPCR). We tested the repeatability and sensitivity of primer each to detect YFP eDNA and subsequently compared the cost of traditional visual sampling to both conventional PCR and qPCR eDNA tools. Our results suggest qPCR to be substantially more sensitive than conventional PCR eDNA analysis, although the later remains the least-expensive sampling option. Still, due to a lack of sensitivity causing an increased probability of false negatives, conventional PCR may not be the most robust sampling method for this taxa and should only be employed as a supplementary tool or when large populations are expected to be present. Alternatively, utilizing qPCR for eDNA protocols is still less-expensive than visual surveying and represents a highly repeatable and sensitive method for this behaviorally elusive species. Presenting a cost assessment of eDNA to traditional surveying practices has scarcely been discussed, while contrasting deliverables to the cost of different eDNA methods has, to date, been ignored. Yet given budgetary constraints, particularly for developing countries where low-governance and high endemism are present, we encourage managers to carefully consider the trade-offs among data accuracy, cost, coverage and speed for biodiversity collections.

scholarly journals Comparing conservation monitoring approaches: traditional and environmental DNA tools for a critically endangered mammal

2017 ◽  
Author(s):  
Chanjuan Qu ◽  
Kathryn A Stewart
Keyword(s):  
Data Collection ◽  
Environmental Dna ◽  
Critically Endangered ◽  
Conventional Pcr ◽  
Aquatic Mammal ◽  
Real Time Quantitative Pcr ◽  
Trade Offs ◽  
Sampling Protocols ◽  
Species Specific ◽  
The Cost

While conservation management has made tremendous strides in the last few decades, the decision of knowing where and how to invest (often) small surveying budgets for biodiversity data collection remains a central hurdle for impactful conservation decision making. New analytical tools, such as environmental DNA (eDNA), are now facilitating broader biodiversity monitoring to take place at unprecedented scales, in part due to its time-efficient, and presumably cost-efficient, premise. eDNA approaches vary from conventional PCR (detecting presence/absence of species), metabarcoding (community structure), to qPCR (relative DNA abundance), and knowing when to employ these techniques over traditional sampling protocols could enable conservation practitioners to make informed trade-offs between cost, accuracy, and speed of data collection. Using 12 species-specific primers designed for conventional PCR use in eDNA analysis of the Yangtze Finless Porpoise (Neophocaena asiaeorientalis asiaeorientalis), a critically endangered aquatic mammal within the Yangtze River, we validated and optimized these same primers for use in real-time Quantitative PCR (qPCR). We tested the repeatability and sensitivity of primer each to detect YFP eDNA and subsequently compared the cost of traditional visual sampling to both conventional PCR and qPCR eDNA tools. Our results suggest qPCR to be substantially more sensitive than conventional PCR eDNA analysis, although the later remains the least-expensive sampling option. Still, due to a lack of sensitivity causing an increased probability of false negatives, conventional PCR may not be the most robust sampling method for this taxa and should only be employed as a supplementary tool or when large populations are expected to be present. Alternatively, utilizing qPCR for eDNA protocols is still less-expensive than visual surveying and represents a highly repeatable and sensitive method for this behaviorally elusive species. Presenting a cost assessment of eDNA to traditional surveying practices has scarcely been discussed, while contrasting deliverables to the cost of different eDNA methods has, to date, been ignored. Yet given budgetary constraints, particularly for developing countries where low-governance and high endemism are present, we encourage managers to carefully consider the trade-offs among data accuracy, cost, coverage and speed for biodiversity collections.

scholarly journals Water pre-filtration methods to improve environmental DNA detection by real-time PCR and metabarcoding

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0250162
Author(s):  
Kazuto Takasaki ◽  
Hiroki Aihara ◽  
Takanobu Imanaka ◽  
Takahiro Matsudaira ◽  
Keita Tsukahara ◽  
...  
Keyword(s):  
Fish Species ◽  
Environmental Samples ◽  
Pcr Amplification ◽  
Environmental Dna ◽  
12S Rrna ◽  
Filtration Method ◽  
Pcr Inhibitors ◽  
Novel Approach ◽  
Pale Chub ◽  
Filter Clogging

Environmental DNA (eDNA) analysis is a novel approach for biomonitoring and has been mostly used in clear water. It is difficult to detect eDNA in turbid water as filter clogging occurs, and environmental samples contain various substances that inhibit the polymerase chain reaction (PCR) and affect the accuracy of eDNA analysis. Therefore, we applied a pre-filtration method to better detect the fish species (particularly pale chub, Opsariichthys platypus) present in a water body by measuring eDNA in environmental samples containing PCR inhibitors. Upon conducting 12S rRNA metabarcoding analysis (MiFish), we found that pre-filtration did not affect the number or identities of fish species detected in our samples, but pre-filtration through pore sizes resulted in significantly reduced variance among replicate samples. Additionally, PCR amplification was improved by the pre-filtration of environmental samples containing PCR inhibitors such as humic substances. Although this study may appear to be a conservative and ancillary experiment, pre-filtration is a simple technique that can not only improve the physical properties of water, such as turbidity, but also the quality of eDNA biomonitoring.

scholarly journals Development of species-specific Cichla species eDNA primers for alien invasive species (AIS) monitoring in Malaysia

2021 ◽  
Vol 4 ◽  
Author(s):  
O. Nurul Fizatul Nabilah ◽  
A. R. Ramizah ◽  
A. B. Adibah ◽  
S. Syazwan ◽  
A.G. Intan Faraha ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Environmental Dna ◽  
Coi Gene ◽  
Alien Invasive Species ◽  
Survey Method ◽  
Specific Primers ◽  
Invasive Fishes ◽  
Specific Amplification ◽  
Species Specific ◽  
High Level

Peacock bass or the cichlids are known locally as top predator fishes which are invasive in Malaysia freshwater system. Detection probabilities for these fishes are typically low, especially using conventional capture-survey method due to the fish’s behaviour of hiding beneath the water’s surface. Hence, the environmental DNA (eDNA) monitoring is a relatively new approach that can be used to assess the distribution of these invasive fishes. Here, we report the strategy to develop small fragment (280- 400 bp) specific-specific primers for three selected invasive Cichla species namely, C. ocellaris, C. monoculus, and C. kelberi based on mitochondrial DNA (mtDNA) sequences. Current research showed that the developed species-specific primers from cytochrome oxidase I (COI) gene has high resolution at species level. Species-specific amplification tests also proved the specificity of the developed primers, securing the high- level species identification potential which may help in controlling the spread of alien invasive fish species.

Changes in the abundance of small littoral-zone fishes in Lake Mendota, Wisconsin

1989 ◽  
Vol 67 (12) ◽  
pp. 2910-2916 ◽  
Author(s):  
John Lyons
Keyword(s):  
Littoral Zone ◽  
Myriophyllum Spicatum ◽  
Single Species ◽  
Lake Mendota ◽  
Nearshore Area ◽  
Etheostoma Flabellare ◽  
Fundulus Notatus ◽  
Environmentally Sensitive ◽  
Fantail Darter ◽  
Banded Killifish

Since 1900, major changes have occurred in the assemblage of small littoral-zone fishes (maximum total length < 150 mm; usually encountered in the nearshore area) that inhabits Lake Mendota, Wisconsin. A diverse assemblage that included several environmentally sensitive species has been replaced by an assemblage dominated by a single species, the brook silverside (Labidesthes sicculus), whose abundance fluctuates dramatically from year to year. Between 1900 and 1981, eight species, the pugnose shiner (Notropis anogenus), common shiner (Notropis cornutus), blackchin shiner (Notropis heterodon), blacknose shiner (Notropis heterolepis), tadpole madtom (Noturus gyrinus), banded killifish (Fundulus diaphanus), blackstripe topminnow (Fundulus notatus), and fantail darter (Etheostoma flabellare), disappeared from the lake. The blackchin shiner and banded killifish were the most abundant small littoral-zone species in 1914–1916, and remained common until the late 1960's. Their decline was associated with the invasion and explosive increase in abundance of an exotic macrophyte, the Eurasian water milfoil (Myriophyllum spicatum), in the mid-1960's. The decline and disappearance of the blackchin shiner and banded killifish in three other Wisconsin lakes was also associated with the invasion of Eurasian water milfoil. Changes in the assemblage of small littoral-zone fishes in Lake Mendota indicate environmental degradation in the nearshore area, and may have important implications for the entire fish community of the lake.

scholarly journals Improving herpetological surveys in eastern North America using the environmental DNA method

Genome ◽  
2016 ◽  
Vol 59 (11) ◽  
pp. 991-1007 ◽  
Author(s):  
Anaïs Lacoursière-Roussel ◽  
Yohann Dubois ◽  
Eric Normandeau ◽  
Louis Bernatchez
Keyword(s):  
Large Scale ◽  
Habitat Type ◽  
Environmental Dna ◽  
Conservation Strategies ◽  
Natural Environments ◽  
Detection Rates ◽  
Survey Tool ◽  
Declining Species ◽  
Species Specific ◽  
Wood Turtle

Among vertebrates, herpetofauna has the highest proportion of declining species. Detection of environmental DNA (eDNA) is a promising method towards significantly increasing large-scale herpetological conservation efforts. However, the integration of eDNA results within a management framework requires an evaluation of the efficiency of the method in large natural environments and the calibration of eDNA surveys with the quantitative monitoring tools currently used by conservation biologists. Towards this end, we first developed species-specific primers to detect the wood turtle (Glyptemys insculpta) a species at risk in Canada, by quantitative PCR (qPCR). The rate of eDNA detection obtained by qPCR was also compared to the relative abundance of this species in nine rivers obtained by standardized visual surveys in the Province of Québec (Canada). Second, we developed multi-species primers to detect North American amphibian and reptile species using eDNA metabarcoding analysis. An occurrence index based on the distribution range and habitat type was compared with the eDNA metabarcoding dataset from samples collected in seven lakes and five rivers. Our results empirically support the effectiveness of eDNA metabarcoding to characterize herpetological species distributions. Moreover, detection rates provided similar results to standardized visual surveys currently used to develop conservation strategies for the wood turtle. We conclude that eDNA detection rates may provide an effective semiquantitative survey tool, provided that assay calibration and standardization is performed.

Improving reliability in environmental DNA detection surveys through enhanced quality control

2017 ◽  
Vol 68 (2) ◽  
pp. 388 ◽  
Author(s):  
Elise M. Furlan ◽  
Dianne Gleeson
Keyword(s):  
Quality Control ◽  
Native Species ◽  
Conservation Management ◽  
Environmental Dna ◽  
Positive Control ◽  
False Negatives ◽  
Method Error ◽  
Target Dna ◽  
Species Specific ◽  
Australian Freshwater

Species-specific environmental DNA (eDNA) surveys are increasingly being used to infer species presence in an environment. Current inadequacies in quality control increase concern for false negatives, which can have serious ramifications for both the management of invasive species and the conservation of native species. eDNA surveys involve a multi-step process to sample, capture, extract and amplify target DNA from the environment. We outline various positive control options and show that many of the commonly used controls are capable of detecting false negatives arising during the amplification stage only. We suggest a secondary, generic primer, designed to co-amplify endogenous DNA sampled during species-specific eDNA surveys, constitutes a superior positive control to monitor method success throughout all stages of eDNA analysis. We develop a species-specific European carp (Cyprinus carpio) assay and a generic fish assay for use as an endogenous control for eDNA surveys in Australian freshwater systems where fish are known to be abundant. We use these assays in a multiplex on eDNA samples that are simultaneously sampled, captured, extracted and amplified. This positive control allows us to distinguish method error from informative non-amplification results, improving reliability in eDNA surveys, which will ultimately lead to better informed conservation management decisions.

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