Environmental DNA as a non-invasive alternative for surveying aquatic communities in tank bromeliads

2021 ◽  
Author(s):  
Carla Martins Lopes ◽  
Marcus Thadeu T. Santos ◽  
Délio Baêta ◽  
Ariadne Fares Sabbag ◽  
Célio Fernando Baptista Haddad
Keyword(s):  
Environmental Dna ◽  
Aquatic Communities ◽  
Non Invasive ◽  
Tank Bromeliads

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 Environmental DNA as a non‐invasive sampling tool to detect the spawning distribution of European anadromous shads ( Alosa  spp.)

2019 ◽  
Vol 29 (1) ◽  
pp. 148-152 ◽  
Author(s):  
Caterina Maria Antognazza ◽  
J. Robert Britton ◽  
Caitlin Potter ◽  
Elizabeth Franklin ◽  
Emilie A. Hardouin ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Non Invasive

scholarly journals Monitoring spawning migrations of potamodromous fish species via eDNA

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Bettina Thalinger ◽  
Elisabeth Wolf ◽  
Michael Traugott ◽  
Josef Wanzenböck
Keyword(s):  
Fish Species ◽  
Anthropogenic Impacts ◽  
Environmental Dna ◽  
Signal Strength ◽  
Digital Pcr ◽  
Freshwater Ecosystems ◽  
Non Invasive ◽  
River Stretch ◽  
Daily Discharge ◽  
Invasive Techniques

Abstract Potamodromous fish are considered important indicators of habitat connectivity in freshwater ecosystems, but they are globally threatened by anthropogenic impacts. Hence, non-invasive techniques are necessary for monitoring during spawning migrations. The use of environmental DNA (eDNA) potentially facilitates these efforts, albeit quantitative examinations of spawning migrations remain so far mostly uncharted. Here, we investigated spawning migrations of Danube bleak, Alburnus mento, and Vimba bream, Vimba vimba, and found a strong correlation between daily visual fish counts and downstream eDNA signals obtained from filtered water samples analysed with digital PCR and end-point PCR coupled with capillary electrophoresis. By accounting for daily discharge fluctuations, it was possible to predict eDNA signal strength from the number of migrating fish: first, the whole spawning reach was taken into account. Second, the model was validated using eDNA signals and fish counts obtained from the upper half of the examined river stretch. Consequently, fish counts and their day-to-day changes could be described via an eDNA-based time series model for the whole migration period. Our findings highlight the capability of eDNA beyond delivering simple presence/absence data towards efficient and informative monitoring of highly dynamic aquatic processes such as spawning migrations of potamodromous fish species.

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

2019 ◽  
Author(s):  
Clare I. M. Adams ◽  
Luke A. Hoekstra ◽  
Morgan R. Muell ◽  
Fredric J. Janzen
Keyword(s):  
Rank Order ◽  
Environmental Dna ◽  
Chrysemys Picta ◽  
Field Conditions ◽  
Painted Turtle ◽  
Freshwater Turtles ◽  
Detection Rates ◽  
Non Invasive ◽  
Painted Turtles ◽  
Current State

Environmental DNA (eDNA) is an increasingly used non-invasive molecular tool for detecting species presence and monitoring populations. In this article, we review the current state of non-avian reptile eDNA work in aquatic systems, as well as present a field experiment on detecting the presence of painted turtle (Chrysemys picta) eDNA. Thus far, turtle and snake eDNA studies have been successful mostly in detecting the presence of these animals in field conditions. However, some instances of low detection rates and non-detection occur for these non-avian reptiles, especially for squamates. We explored this matter by sampling lentic ponds with different densities (0 kg/ha, 6 kg/ha, 9 kg/ha, and 13 kg/ha) of painted turtles over three months, attempting to detect differences in eDNA accumulation using a qPCR assay. Only one sample of the highest density pond readily amplified eDNA. Yet, estimates of eDNA concentration from pond eDNA were rank-order correlated with turtle density. We present a “shedding hypothesis”–the possibility that animals with hard, keratinized integument do not shed as much DNA as mucus-covered organisms–as a potential challenge for turtle eDNA studies. Despite challenges with eDNA inhibition and availability in water samples, we remain hopeful that eDNA can be used to detect freshwater turtles in the field. We provide key recommendations for biologists wishing to use eDNA methods for detecting non-avian reptiles.

scholarly journals Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modelling

2018 ◽  
Author(s):  
Keiichi Fukaya ◽  
Hiroaki Murakami ◽  
Seokjin Yoon ◽  
Kenji Minami ◽  
Yutaka Osada ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Cost Effective ◽  
Population Monitoring ◽  
Fish Population ◽  
Abundance Estimation ◽  
Population Abundance ◽  
Jack Mackerel ◽  
Non Invasive ◽  
Quantitative Measurements ◽  
Japanese Jack Mackerel

AbstractWe propose a general framework of abundance estimation based on spatially replicated quantitative measurements of environmental DNA in which production, transport, and degradation of DNA are explicitly accounted for. Application to a Japanese jack mackerel (Trachurus japonicus) population in Maizuru Bay revealed that the method gives an estimate of population abundance comparable to that of a quantitative echo sounder method. These findings indicate the ability of environmental DNA to reliably reflect population abundance of aquatic macroorganisms and may offer a new avenue for population monitoring based on the fast, cost-effective, and non-invasive sampling of genetic information.

scholarly journals Environmental DNA for conservation

2021 ◽  
pp. 157-176
Author(s):  
Antoinette J. Piaggio
Keyword(s):  
Wildlife Conservation ◽  
Empirical Studies ◽  
Sampling Site ◽  
Environmental Dna ◽  
Successful Implementation ◽  
Pilot Studies ◽  
Sampling Schemes ◽  
Non Invasive ◽  
Elusive Species ◽  
Negative Impacts

Detection and monitoring of wildlife species of concern is a costly and time-consuming challenge that is critical to the management of such species. Tools such as lures and traps can cause unnecessary stress or other health impacts to sensitive species. Development and refinement of tools that provide means to detect rare and elusive species without requiring contact with them reduce such impacts. Further, the potential of detection after the target species has moved on from a sampling site could allow for higher potential for detection of rare species. The ability to amplify DNA from environmental samples (e.g. water, soil, air, and other substrates) has provided a non-invasive method for detection of rare or elusive species while reducing negative impacts to wildlife. Like other non-invasive methods, such as cameras, there are methodological pitfalls associated with environmental DNA (eDNA) sampling to consider. Each study system will provide unique challenges to adequate eDNA sampling. Thus, pilot studies are critical for successful implementation of a larger-scale detection and monitoring study. This chapter will describe the benefits and challenges of using eDNA, detail types of eDNA sampling, and provide guidance on designing appropriate study design and sampling schemes. Empirical studies using eDNA applied to wildlife conservation efforts will be highlighted and discussed.

scholarly journals Non-invasive surveys of mammalian viruses using environmental DNA

2020 ◽  
Author(s):  
Niccolò Alfano ◽  
Anisha Dayaram ◽  
Jan Axtner ◽  
Kyriakos Tsangaras ◽  
Marie-Louise Kampmann ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Environmental Dna ◽  
List Type ◽  
Dna Viruses ◽  
Remote Areas ◽  
Hybridization Capture ◽  
Non Invasive ◽  
Zoonotic Viruses ◽  
Wildlife Pathogens ◽  
Rna And Dna

ABSTRACTEnvironmental DNA (eDNA) and invertebrate-derived DNA (iDNA) have been used to survey biodiversity non-invasively to mitigate difficulties of obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA have been applied to monitor known wildlife pathogens, however, most wildlife pathogens are unknown and often evolutionarily divergent.To detect and identify known and novel mammalian viruses from eDNA/iDNA sources, we used a curated set of RNA oligonucleotides as viral baits in a hybridization capture system coupled with high throughput sequencing.We detected multiple known and novel mammalian RNA and DNA viruses from multiple viral families from both waterhole eDNA and leech derived iDNA. Congruence was found between detected hosts and viruses identified in leeches and waterholes.Our results demonstrate that eDNA/iDNA samples represent an effective non-invasive resource for studying wildlife viral diversity and for detecting novel potentially zoonotic viruses prior to their emergence.

scholarly journals An assay validation framework to compare and evaluate targeted environmental DNA assays for routine species monitoring

2021 ◽  
Vol 4 ◽  
Author(s):  
Bettina Thalinger ◽  
Kristy Deiner ◽  
Lynsey Harper ◽  
Helen Rees ◽  
Rosetta Blackman ◽  
...  
Keyword(s):  
Meta Analysis ◽  
Environmental Dna ◽  
Single Species ◽  
End Users ◽  
Specific System ◽  
Initial Development ◽  
Assay Validation ◽  
Non Invasive ◽  
Detection Probabilities ◽  
User Friendly

Environmental DNA (eDNA) analysis utilises trace DNA released by organisms into their environment for species detection and is revolutionising non ‐ invasive species and biodiversity monitoring. However, this technology requires rigorous validation along the whole workflow – from field sampling to statistical analysis – to ensure appropriate and meaningful interpretation of results. Targeted eDNA assays are often validated within a specific system and with particular aims, but without fulfilling predefined criteria. Consequently, their applicability beyond initial development often remains undetermined. Additionally, there tends to be poor understanding of the uncertainties and limitations associated with already published assays and thus potentially inappropriate interpretation of the results they produce. The lack of a “gold standard” limits the incorporation of targeted eDNA assays into species monitoring and policy making by end-users and is therefore key for the future implementation of eDNA-based surveys. Here, we present a framework (https://edna-validation.com/) and user-friendly criteria for the classification of assays, which is based on previous validation efforts. A 5 ‐ level assay validation scale (“incomplete” to “operational”) was defined by reviewing the current eDNA literature and conducting a meta-analysis on sampling, laboratory practices, detection limits, and detection probabilities. The so far published single species eDNA assays were reviewed for their performance in this new framework and we identified steps within the validation process that often remain untouched. Finally, we provide guidance for end ‐ users as to which criteria are most important for validation and suggest how results obtained from assays at different levels of the validation scale should be interpreted.

scholarly journals A eDNA-qPCR assay to non-invasively detect the presence of the parasiteSchistocephalus solidusinside its threespine stickleback host

2017 ◽  
Author(s):  
Chloé Suzanne Berger ◽  
Nadia Aubin-Horth
Keyword(s):  
Detection Method ◽  
Abdominal Cavity ◽  
Environmental Dna ◽  
Threespine Stickleback ◽  
Complex Life Cycle ◽  
Non Invasive ◽  
Schistocephalus Solidus ◽  
Host Parasite Interactions ◽  
Ventilation Rates ◽  
Host Parasite

ABSTRACTDetecting the presence of a parasite within its host is crucial to the study of host-parasite interactions. TheSchistocephalus solidus- threespine stickleback pair has been studied extensively to investigate host phenotypic alterations associated with a parasite with a complex life cycle. This cestode is localized inside the stickleback’s abdominal cavity and can be visually detected only once it passes a mass threshold. We present a non-invasive quantitative PCR approach based on detection of environmental DNA from the worm(eDNA),sampled in the fish abdominal cavity. Using this approach on two fish populations (n=151), 98% of fish were correctly assigned to theirS. solidusinfection status. There was a significant correlation between eDNA concentration and total parasitic mass. We also assessed ventilation rates as a complimentary mean to detect infection. Our eDNA detection method gives a reliable presence/absence response and its future use for quantitative assessment is promising.

The making of sedimentary DNA: Insights from distribution patterns of DNA in sediments

2020 ◽  
Author(s):  
Laura S. Epp ◽  
Anan Ibrahim ◽  
Yi Wang ◽  
Lisa Gutbrod ◽  
Patrick Bartolin ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Rare Species ◽  
Surface Sediments ◽  
Aquatic Organisms ◽  
Environmental Dna ◽  
Distribution Patterns ◽  
Aquatic Communities ◽  
Biodiversity Change ◽  
Source Of Information ◽  
Initial Results

<p>Sedimentary ancient DNA has by now become a recognized source of information on past biodiversity change, but our understanding of its dynamics and taphonomy is still limited. While for environmental DNA in water, dedicated investigations on its provenance and degradation are being increasingly carried out, we know very little about sedimentary DNA, in particular with respect to aquatic organisms. We are therefore conducting investigations on the distribution of DNA in surface sediments and a short sediment core, with a focus on aquatic communities in the large and heterogeneous Lake Constance. Targeted organisms range from phyto- and zooplankton to fish and waterbirds. Initial results and comparison with sightings of rare species indicate that the DNA is not distributed uniformly or widely across the lake, especially for multicellular animals, but rather linked to the local presence of the organisms. This has implications for our understanding of how DNA enters the sediment and for paleoecological inferences derived from these records.</p>

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