scholarly journals Noninvasive Method for a Statewide Survey of Eastern HellbendersCryptobranchus alleganiensisUsing Environmental DNA

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Amy J. Santas ◽  
Tyler Persaud ◽  
Barbara A. Wolfe ◽  
Jenise M. Bauman
Keyword(s):  
Population Density ◽  
Survey Methods ◽  
Aquatic Organisms ◽  
Environmental Dna ◽  
Specific Primers ◽  
Filtration Time ◽  
Sampling Protocols ◽  
Welfare Implications ◽  
Historical Accounts ◽  
Eastern Hellbender

Traditional survey methods of aquatic organisms may be difficult, lengthy, and destructive to the habitat. Some methods are invasive and can be harmful to the target species. The use of environmental DNA (eDNA) has proven to be effective at detecting low population density aquatic macroorganisms. This study refined the technique to support statewide surveys. Hellbender presence was identified by using hellbender specific primers (cytochrome b gene) to detect eDNA in water samples collected at rivers, streams and creeks in Ohio and Kentucky with historical accounts of the imperiled eastern hellbender (Cryptobranchus a. alleganiensis). Two sampling protocols are described; both significantly reduced the amount of water required for collection from the previously described 6 L collection. Two-liter samples were adequate to detect hellbender presence in natural waterways where hellbenders have been previously surveyed in both Ohio and Kentucky—1 L samples were not reliable. DNA extracted from 3 L of water collected onto multiple filters (1 L/filter) could be combined and concentrated through ethanol precipitation, supporting amplification of hellbender DNA and dramatically reducing the filtration time. This method improves the efficiency and welfare implications of sampling methods for reclusive aquatic species of low population density for statewide surveys that involve collecting from multiple watersheds.

scholarly journals Environmental DNA and Specific Primers for Detecting the Invasive Species Ectopleura crocea (Hydrozoa: Anthoathecata) in Seawater Samples

2020 ◽  
Vol 12 (6) ◽  
pp. 2360 ◽  
Author(s):  
Philjae Kim ◽  
Tae Joong Yoon ◽  
Sook Shin
Keyword(s):  
Invasive Species ◽  
Survey Methods ◽  
Environmental Dna ◽  
Visual Assessment ◽  
Molecular Techniques ◽  
Mitochondrial Cytochrome ◽  
Specific Primer ◽  
Specific Primers ◽  
Seawater Samples ◽  
Species Specific

In marine environments, environmental DNA (eDNA) can be effectively detected and possibly quantified when combined with molecular techniques, as demonstrated by several recent studies. In this study, we developed a species-specific primer set and a probe to detect the distribution and biomass of an invasive hydrozoan in South Korea, Ectopleura crocea. These molecular markers were designed to amplify a 187 bp region based on mitochondrial cytochrome c oxidase subunit I (COI) of E. crocea and were tested on seawater samples from 35 Korean harbors in 2017. Of the 35 sites we investigated, only nine harbors returned positive detections when using traditional survey methods, while surveys based on the use of eDNA techniques detected E. crocea DNA in all seawater samples. These results suggest that eDNA surveys based on molecular techniques are more effective at identifying species distribution and estimating biomass than traditional surveys based on visual assessment of morphology.

scholarly journals Refining sampling protocols for cavefishes and cave crayfishes to account for environmental variation

2021 ◽  
Vol 39 ◽  
pp. 79-105
Author(s):  
Joshua B. Mouser ◽  
Shannon K. Brewer ◽  
Matthew L. Niemiller ◽  
Robert Mollenhauer ◽  
Ronald A. Van Den Bussche
Keyword(s):  
Environmental Conditions ◽  
Detection Probability ◽  
Survey Methods ◽  
Environmental Dna ◽  
Sampling Bias ◽  
Water Velocity ◽  
Conservation Strategies ◽  
Water Volume ◽  
Factors Affecting ◽  
Sampling Protocols

Subterranean habitats represent focal habitats in many conservation strategies; however, these environments are some of the most difficult to sample. New sampling methods, such as environmental DNA (eDNA), show promise to improve stygobiont detection, but sources of sampling bias are poorly understood. Therefore, we determined the factors affecting detection probability using traditional visual surveys and eDNA surveys for both cavefishes and cave crayfishes and demonstrated how detection affects survey efforts for these taxa. We sampled 40 sites (179 visual and 183 eDNA surveys) across the Ozark Highlands ecoregion. We estimated the detection probability of cave crayfishes and cavefishes using both survey methods under varying environmental conditions. The effectiveness of eDNA or visual surveys varied by environmental conditions (i.e., water volume, prevailing substrate, and water velocity) and the target taxa. When sampling in areas with average water velocity, no flow, and coarse substrate, eDNA surveys had a higher detection probability (0.49) than visual surveys (0.35) for cavefishes and visual surveys (0.67) had a higher detection probability than eDNA surveys (0.40) for cave crayfishes. Under the same sampling conditions, 5 visual surveys compared to 10 eDNA surveys would be needed to confidently detect cave crayfishes and 9 visual surveys compared to 4 eDNA surveys for cavefishes. Environmental DNA is a complementary tool to traditional visual surveys; however, the limitations we identified indicate eDNA currently cannot replace visual surveys in subterranean environments. Although sampling designs that account for imperfect sampling are particularly useful, they may not be practical; thus, increasing sampling efforts to offset known detection bias would benefit conservation strategies.

Using environmental DNA and occupancy modelling to identify drivers of eastern hellbender (Cryptobranchus alleganiensis alleganiensis) extirpation

2018 ◽  
Vol 64 (1) ◽  
pp. 208-221 ◽  
Author(s):  
Sean M. Wineland ◽  
Shane M. Welch ◽  
Thomas K. Pauley ◽  
Joseph J. Apodaca ◽  
Max Olszack ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Occupancy Modelling ◽  
Cryptobranchus Alleganiensis ◽  
Eastern Hellbender

scholarly journals An experimental assessment of the distribution of environmental DNA along the water column

2020 ◽  
Author(s):  
André O. Agostinis ◽  
Giorgi Dal Pont ◽  
Alexandre Borio ◽  
Aline Horodesky ◽  
Ana Paula da Silva Bertão ◽  
...  
Keyword(s):  
Water Column ◽  
Environmental Dna ◽  
Aquatic Communities ◽  
Natural Conditions ◽  
Sampling Protocol ◽  
Experimental Assessment ◽  
Qpcr Analysis ◽  
Time Period ◽  
Sampling Protocols ◽  
Different Depths

AbstractThe study of environmental DNA (eDNA) is increasingly becoming a valuable tool to survey and monitor aquatic communities. However, there are important gaps in our understanding of the dynamics governing the distribution of eDNA under natural conditions. In this report we carry out controlled experiments to assess the extent and timing of eDNA distribution along the water column. A sample of known eDNA concentration was placed at the bottom of a 5-m high tube (20 cm in diameter and total volume of 160 L), and water samples were obtained at different depths over an 8 h-period. The presence of the target eDNA was assessed by qPCR analysis. This sampling protocol allowed for assessing the timescale for the diffusion of eDNA while minimizing the influence of turbulence. We demonstrate that, after a time-period of as little as 30 min, the eDNA had spread across the entire container. The implications of these results for eDNA sampling protocols in the field are discussed.

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.

scholarly journals A comparison of density estimation methods in plateau pika populations in an alpine meadow ecosystem

2020 ◽  
Vol 101 (4) ◽  
pp. 1091-1096
Author(s):  
Wanrong Wei ◽  
Jundong He ◽  
Qiaoyan Zheng ◽  
Yuli He ◽  
Maria K Oosthuizen
Keyword(s):  
Population Density ◽  
Relative Density ◽  
Alpine Meadow ◽  
Survey Methods ◽  
Estimation Methods ◽  
Plateau Pika ◽  
Relative Population ◽  
Burrow Density ◽  
The Absolute ◽  
Absolute Population

Abstract Plateau pikas are a keystone species and ecosystem engineers in alpine meadow ecosystems. A number of surveying methods have been used to estimate pika density, but the reliability of these methods is not known. In addition, better population density methodologies allow for more reliable density estimates. We therefore compared the relationship among several commonly used methods of estimating pika relative density and the absolute density (AD) of pika populations. This relationship was investigated in summer and winter pastures to determine whether distribution pattern of the pikas (patchy or uniform) would influence this relationship. During August of 2015 and August of 2016, we measured the relative and absolute population density of pikas in an alpine meadow in the County, Gansu province, northwestern China. Relative density was measured with three indirect and direct methods: the total burrow density (TBD), the active burrow density (ABD), and the direct counting density (DCD) at the peak of pika activity. AD was assessed by removal sampling. Our results showed that the relative population density with all three survey methods was significantly related to the absolute population density. In particular, DCD at the peak of the pika activity showed the best correlation with AD. A simple linear model showed the effect of grazing time by livestock had a significant effect on TBD and ABD. These results imply that using DCD as a method to survey at the peak of the pika activity is more reliable than other methods.

scholarly journals Novel Primers Reveal Wider Diversity among Marine Aerobic Anoxygenic Phototrophs

2005 ◽  
Vol 71 (12) ◽  
pp. 8958-8962 ◽  
Author(s):  
Natalya Yutin ◽  
Marcelino T. Suzuki ◽  
Oded Béjà
Keyword(s):  
Reaction Center ◽  
Photosynthetic Reaction Center ◽  
Environmental Dna ◽  
Anoxygenic Phototrophic Bacteria ◽  
Specific Primers ◽  
Genomic Libraries ◽  
Anoxygenic Phototrophs ◽  
Marine Bacterioplankton ◽  
Aerobic Anoxygenic Phototrophic Bacteria ◽  
Ecological Importance

ABSTRACT Aerobic anoxygenic phototrophic bacteria (AAnPs) were previously proposed to account for up to 11% of marine bacterioplankton and to potentially have great ecological importance in the world's oceans. Our data show that previously used primers based on the M subunit of anoxygenic photosynthetic reaction center genes (pufM) do not comprehensively identify the diversity of AAnPs in the ocean. We have designed and tested a new set of pufM-specific primers and revealed several new AAnP variants in environmental DNA samples and genomic libraries.

scholarly journals Environmental DNA sampling in a terrestrial environment: methods to detect a critically endangered frog and a global pathogen

2020 ◽  
Author(s):  
Thomas J. Burns ◽  
Nick Clemann ◽  
Anthony R. van Rooyen ◽  
Ben C. Scheele ◽  
Andrew R. Weeks ◽  
...  
Keyword(s):  
Field Experiments ◽  
Survey Methods ◽  
Environmental Dna ◽  
Wash Water ◽  
Critically Endangered ◽  
Chytrid Fungus ◽  
Amphibian Skin ◽  
Natural Habitats ◽  
Amphibian Species ◽  
Terrestrial Environment

AbstractEnvironmental DNA techniques have become established as a useful tool for biological monitoring and are used extensively to determine species presence in aquatic systems. However, their application in terrestrial systems has been more limited, likely in part due to difficulties in choosing where to sample and ensuring that collected DNA reflects current species presence. We developed methods to sample eDNA in the terrestrial environment and trialled them under controlled and field conditions. We targeted three species, an elusive critically endangered frog, an abundant non-threatened frog, and the globally distributed amphibian skin pathogen chytrid fungus, which has been implicated in the decline of over 500 amphibian species. We used a sandpaper-sampling surface to ‘trap’ DNA. After sampling, we washed the surface and filtered the wash water to gather material for DNA extraction and subsequent qPCR. Our controlled condition experiments demonstrated that frog and chytrid fungus DNA was detectable after as few as five contacts between a frog and the sampling surface. Furthermore, this DNA remained detectable after two weeks in cool, shaded, outdoor conditions. Our field experiments demonstrated that these techniques were transferable to natural habitats, where we detected both the common and rare amphibian target species, as well as chytrid fungus. Field sampling eDNA results were broadly consistent with those derived from conventional survey methods. Our methods have potential application in non-invasive sampling of amphibians and other species in terrestrial systems, broadening the applicability of eDNA techniques for species detection and monitoring.

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.

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