scholarly journals Development of an environmental DNA method for monitoring fish communities: ground truthing in diverse lakes with characterised fish faunas

2018 ◽  
Author(s):  
Jianlong Li ◽  
Tristan W. Hatton-Ellis ◽  
Lori-Jayne Lawson Handley ◽  
Helen S. Kimbell ◽  
Marco Benucci ◽  
...  
Keyword(s):  
Water Samples ◽  
Fish Communities ◽  
Environmental Dna ◽  
Quantitative Information ◽  
12S Rrna ◽  
Similar Species ◽  
List Type ◽  
Large Lakes ◽  
Non Invasive ◽  
Wide Range

AbstractAccurate, cost-effective monitoring of fish is required to assess the quality of lakes under the European Water Framework Directive (WFD). Recent studies have shown that environmental DNA (eDNA) metabarcoding is an effective and non-invasive method, which can provide semi-quantitative information on fish communities in large lakes.This study further investigated the potential of eDNA metabarcoding as a tool for WFD status assessment by collecting and analysing water samples from eight Welsh lakes and six meres in Cheshire, England, with well described fish faunas. Water samples (N = 252) were assayed using two mitochondrial DNA regions (Cytb and 12S rRNA).eDNA sampling indicated the presence of very similar species in the lakes compared to those expected on the basis of existing and historical information. In total, 24 species were detected with a total of 111 species occurrences in the lakes studied using eDNA. Secondly, there was a significant positive correlation between expected faunas and eDNA data in terms of confidence of species occurrence (Spearman’s r = 0.74, df = 109, p <; 0.001). Thirdly, eDNA data can estimate relative abundance with the standard five-level classification scale (“DAFOR”). Lastly, four ecological fish communities were characterised using eDNA data which agrees with the pre-defined lake types according to environmental characteristics.Synthesis and applications. This study provides further evidence that eDNA metabarcoding could be a powerful and non-invasive monitoring tool for WFD purpose in a wide range of lake types, considerably outperforming other methods for community level analysis.

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 Utilizing environmental DNA for wide-range distributions of reproductive area of an invasive terrestrial toad in Ishikari river basin in Japan

2021 ◽  
Author(s):  
Hiroki Mizumoto ◽  
Osamu Kishida ◽  
Kotaro Takai ◽  
Naru Matsuura ◽  
Hitoshi Araki
Keyword(s):  
Invasive Species ◽  
River Basin ◽  
Water Samples ◽  
Environmental Dna ◽  
Watershed Scale ◽  
Efficient Tool ◽  
Occupancy Model ◽  
Wide Range ◽  
Powerful Means ◽  
In The Wild

AbstractUnderstanding the distribution of invasive species and their reproductive area is crucial for their managements after invasion. While catch and observation surveys are still embraced, environmental DNA (eDNA) has been increasingly utilized as an efficient tool for identifying these species in the wild. In this study, we developed a Bufo-specific eDNA assay for detecting an invasive, toxic, and terrestrial toad species Bufo japonicus formosus in Hokkaido, Japan, and applied it to their reproductive area at watershed scale. The eDNA assay was field-validated in ponds where B. japonicus were observed, as well as in rivers downstream of the reproductive ponds. Thus, the assay provided us an opportunity to screen watersheds that include their reproductive area by collecting downstream water samples. Applying it to the Ishikari river basin, the largest river basin in Hokkaido (c.a., 14,330 km2), we detected toad eDNA at 32 out of 73 sampling sites. They are composed of eleven sites with species observation records nearby (all the sites with observation records within a 500 m radius) and 21 sites without such records. And those eDNA detections were from twelve out of 31 river systems in the entire river basin. A Bayesian, multiscale occupancy model supported high eDNA detectability among those sites. These results suggest that the eDNA assay can efficiently estimate the presence of reproductive area of the terrestrial toad even from a distant downstream of the watershed, and that it provides a powerful means of detecting new reproductive area and monitoring further spread of invasive species.

Monitoring post-release survival of the northern corroboree frog, Pseudophryne pengilleyi, using environmental DNA

2018 ◽  
Vol 45 (7) ◽  
pp. 620 ◽  
Author(s):  
Jack Rojahn ◽  
Dianne Gleeson ◽  
Elise M. Furlan
Keyword(s):  
Water Samples ◽  
Survey Methods ◽  
Quantitative Polymerase Chain Reaction ◽  
Environmental Dna ◽  
Life Stages ◽  
Breeding Programs ◽  
Non Invasive ◽  
Naturally Occurring ◽  
Cause Of Failure

Context Translocations are becoming an increasingly important conservation tool to combat rising levels of species extinction. Unfortunately, many translocation efforts fail; yet, the timing and cause of failure often remain unknown. Monitoring individuals in the days and weeks following release can provide valuable information on their capacity to survive this initial hurdle. In Australia, breeding programs have been established for the endangered northern corroboree frog, Pseudophryne pengilleyi, to enable reintroduction to the wild via captive-reared individuals, typically, early life stages such as eggs or juvenile frogs that cannot be monitored via traditional survey methods that target adult frogs (e.g. shout–response). Environmental DNA (eDNA) detects trace amounts of DNA that organisms release into their environment and could provide a means to infer population persistence for wildlife releases and translocations. Aims In the present study, we aim to develop an eDNA assay capable of detecting both sexes of P. pengilleyi across multiple life stages, and use it to monitor their survival. Methods An eDNA assay was developed to target the two corroboree frog species (P. pengilleyi and P. corroboree, the southern corroboree frog) and was tested for its sensitivity and specificity in silico and in vitro. Pseudophryne pengilleyi eggs were released into three naturally occurring ponds and water samples were, subsequently, collected from each pond on several occasions over a period of 78 days. Quantitative polymerase chain reaction was used to detect P. pengilleyi eDNA from water samples. Key Results The developed assay was shown to be sensitive and specific to corroboree frogs. eDNA monitoring of reintroduced P. pengilleyi detected the species’ DNA at three of three release ponds and DNA remained detectable until at least 78 days post-release at two of three ponds. Conclusions We show how the development of a corroboree frog-specific assay allowed us to monitor the post-release survival of P. pengilleyi in naturally occurring pools. Implications eDNA surveys may provide a useful tool to monitor post-release survival of translocated populations in a non-invasive manner, with the potential to identify the timing and causes of failure. Such knowledge can be used to inform the management of translocated populations and future release strategies.

scholarly journals In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River

2015 ◽  
Author(s):  
M.V. Cannon ◽  
J. Hester ◽  
A. Shalkhauser ◽  
E.R. Chan ◽  
K. Logue ◽  
...  
Keyword(s):  
High Throughput ◽  
Dna Sequences ◽  
Water Samples ◽  
High Throughput Sequencing ◽  
Biological Diversity ◽  
Pcr Amplification ◽  
Environmental Dna ◽  
Asian Carp ◽  
Broad Perspective ◽  
Wide Range

Analysis of environmental DNA (eDNA) enables the detection of species of interest from water and soil samples, typically using species-specific PCR. Here, we describe a method to characterize the biodiversity of a given environment by amplifying eDNA using primer pairs targeting a wide range of taxa and high-throughput sequencing for species identification. We tested this approach on 91 water samples of 40 mL collected along the Cuyahoga River (Ohio, USA). We amplified eDNA using 12 primer pairs targeting mammals, fish, amphibians, birds, bryophytes, arthropods, copepods, plants and several microorganism taxa and sequenced all PCR products simultaneously by high-throughput sequencing. Overall, we identified DNA sequences from 15 species of fish, 17 species of mammals, 8 species of birds, 15 species of arthropods, one turtle and one salamander. Interestingly, in addition to aquatic and semiaquatic animals, we identified DNA from terrestrial species that live near the Cuyahoga River. We also identified DNA from one Asian carp species invasive to the Great Lakes but that had not been previously reported in the Cuyahoga River. Our study shows that analysis of eDNA extracted from small water samples using wide-range PCR amplification combined with high-throughput sequencing can provide a broad perspective on biological diversity.

scholarly journals Utilizing environmental DNA for wide-range distributions of reproductive area of an invasive terrestrial toad in Ishikari river basin in Japan

2021 ◽  
Author(s):  
Hiroki Mizumoto ◽  
Osamu Kishida ◽  
Kotaro Takai ◽  
Hitoshi Araki
Keyword(s):  
Invasive Species ◽  
River Basin ◽  
Water Samples ◽  
Detection System ◽  
Environmental Dna ◽  
Watershed Scale ◽  
Efficient Tool ◽  
Wide Range ◽  
Powerful Means ◽  
In The Wild

Abstract Understanding the distribution of invasive species and their reproductive area is crucial for their managements after invasion. While catch and observation surveys are still embraced, environmental DNA (eDNA) has been increasingly utilized as an efficient tool for identifying these species in the wild. In this study, we developed an eDNA detection system for an invasive, toxic, and terrestrial toad species Bufo japonicus in Hokkaido, Japan, and applied it to their reproductive area at watershed scale. We found that our system successfully detected their eDNA not only in ponds where their larvae were observed, but also in rivers downstream of the reproductive ponds. Thus, the system provided us an opportunity to estimate watersheds that include their reproductive area by collecting downstream water samples. Applying it to the Ishikari river basin, the largest river basin in Hokkaido (c.a., 14,330 km2), we detected their eDNA at 32 out of 73 river sampling sites. They are composed of eleven sites with species observation records nearby (all the sites with observation records within a 500 m radius) and21 sites without such records. And those eDNA detections were from 14 out of 31 river systems, and they were widespread across the river basin. These results suggest that the eDNA detection system can efficiently estimate the presence of reproductive area of the terrestrial toad even from a distant downstream of the watershed, and that it provides a powerful means of detecting new reproductive area and monitoring further spread of invasive species.

scholarly journals Aquatic biofilms can act as natural environmental DNA samplers

2021 ◽  
Vol 4 ◽  
Author(s):  
Sinziana Rivera ◽  
Valentin Vasselon ◽  
Frederic Rimet ◽  
Agnès Bouchez
Keyword(s):  
Water Samples ◽  
Ecological Status ◽  
Fish Communities ◽  
Morphological Characteristics ◽  
Environmental Dna ◽  
Reference Database ◽  
Macroinvertebrate Communities ◽  
Taxonomic Assignment ◽  
Novel Approach ◽  
Single Matrix

Diatoms, macroinvertebrates and fish communities are widely used for the assessment of the ecological status of rivers and lakes. Metabarcoding studies of these communities are usually performed from “bulk” samples in the case of diatoms and macroinvertebrates; and from water samples in the case of fish. Recent studies, suggest that aquatic biofilms can physically act as environmental catchers of environmental DNA (eDNA) (e.g. Mariani et al. 2019). Thus, we propose an alternative metabarcoding approach to study macroinvertebrates and fishes directly from this matrix. The capacity of aquatic biofilms to catch macroinvertebrate eDNA was tested from a previous study in Mayotte Island were both biofilm samples and macroinvertebrate morphological inventories were available at same river sites (Rivera et al. 2021). First, macroinvertebrate specimens were identified based on their morphological characteristics. Second, DNA was extracted from biofilms, and macroinvertebrate communities were targeted using a standard COI barcode. The resulting morphological and molecular inventories were compared. Our results showed that both methods provided comparable structures and diversities for macroinvertebrate communities when using unassigned OTUs suggesting that macroinvertebrate DNA is present in biofilms and representative of the communities. However, after taxonomic assignment of OTUs, diversity and richness were no longer correlated. Indeed, many constraints were observed as the need for: a) more specific primers to avoid co-amplification of untargeted taxa inhabiting biofilms, b) primers targeting shorter barcodes to sequence more easily degraded eDNA that may be captured in biofilms, and c) a reference database well adapted to our tropical study sites. Finally, even if the results of this first study were encouraging, we wanted to test the biofilm approach on organisms that do not inhabit this environmental matrix in order to be able to distinguish between intra or extra-cellular DNA. Based on these observations, a second study looking for a fish eDNA signal in aquatic biofilms was performed. Environmental biofilm and water samples were collected in parallel at littoral sites at Lake Geneva. DNA was extracted from these samples, and fish communities were targeted using a standard 12S barcode. The molecular inventories derived from the biofilm and the water samples were compared. Both methods provide comparable floristic lists, providing a novel approach for ecological studies related to fish phenology using eDNA in biofilms. Our results open the door to the study of diatoms, macroinvertebrates and fish communities through metabarcoding from a single matrix reducing sampling efforts and costs.

scholarly journals Towards a simple way to collect eDNA using a 3D-printed passive sampler

2021 ◽  
Vol 4 ◽  
Author(s):  
Héloïse Verdier ◽  
Lara Konecny ◽  
Christophe Marquette ◽  
Tristan Lefebure
Keyword(s):  
Field Experiments ◽  
High Efficiency ◽  
Environmental Dna ◽  
Aquatic Biodiversity ◽  
Non Invasive ◽  
Physico Chemical ◽  
Wide Range ◽  
3D Printed ◽  
Promising Solution ◽  
High Binding Affinity

Environmental DNA has emerged as a revolutionary approach to monitor aquatic biodiversity. The study of the DNA released by macro-organisms in their habitat offers a fast, non-invasive and sensitive approach to monitor their presence. Despite its many advantages, methodological challenges limit the widespread use of eDNA. Among them, eDNA sampling represents one of the most challenging step. Often based on the filtration of a large volume of water, this process can be long and tedious, requiring human intervention and special care, and which is not applicable to a wide range of habitats. As an alternative to filtration, passive eDNA sampling using natural substrates appears to be a promising solution. This approach uses the natural properties of some minerals (eg. silica), organisms (eg. sponges) or even communities (e.g. biofilms) to collect and preserved eDNA. Yet, such approaches are difficult to standardize and may not be applicable in many habitats. To circumvent that problem, we have designed 3D-printed samplers made of hydroxyapatite (HAp samplers), a mineral known for its high binding affinity with DNA. The shape of the samplers has been designed to facilitate their handling in laboratory and field experiments. Here we describe and test the ability of HAp samplers to recover freshwater eDNA. We show that HAp samplers recover DNA with high efficiency and are effective even on small amounts of waterlouse eDNA. However, the eDNA recovery is also highly variable across experiments. We show that by understanding the physico-chemical interactions between DNA and the HAp sampler surface, we could improve the replicability of the process and provide a robust alternative to filtration.

scholarly journals The composition of northeast pacific fishes in a fish tank examined by eDNA metabarcoding

2020 ◽  
Author(s):  
Sergei V. Turanov ◽  
Olesia A. Rutenko
Keyword(s):  
Fish Species ◽  
Molecular Genetic ◽  
Environmental Dna ◽  
12S Rrna ◽  
Taxonomic Identification ◽  
Reference Library ◽  
Operational Taxonomic Units ◽  
Non Invasive ◽  
Northeast Pacific ◽  
Fish Tank

AbstractThe taxonomy of fish in the northeast Pacific area has been recently revised using molecular genetic methods, including the development of a reference library of DNA fragments for species identification. Such libraries are the basis for the development of non-invasive, high-throughput methods for monitoring biodiversity using environmental DNA (eDNA). In order to validate this approach, we used a water eDNA metabarcoding technique based on 12S rRNA and COI mitochondrial fragments and assessed the composition of the twenty northeast Pacific fish species held in a fish tank at the Primorsky Aquarium (Vladivostok, Russia). Only the 12S fragment revealed data on fish-related operational taxonomic units (OTUs). Approximately 68% of the reads were classified into two species of the genus Oncorhynchus, whose shredded fillet is used for feeding. According to the taxonomic identification for the rest of the reads, 8 out of 20 fish species in the tank (40%) were identified unambiguously, while two species could not be identified. Ten taxa can be considered conditionally identifiable since they might be concealed behind a conflicting taxonomic identification at the genus or family level. In this case, an improvement of the reference library would provide resolution. We detected contamination, which may be related to both intra-laboratory contaminants occurring during DNA extraction and water intake supplying the fish tank.

scholarly journals eDNA in a bottleneck: obstacles to fish metabarcoding studies in megadiverse freshwater systems

2021 ◽  
Author(s):  
Jake M Jackman ◽  
Chiara Benvenuto ◽  
Ilaria Coscia ◽  
Cintia O Carvalho ◽  
Jonathan S Ready ◽  
...  
Keyword(s):  
Water Samples ◽  
Gap Analysis ◽  
Environmental Dna ◽  
Threshold Value ◽  
Taxonomic Resolution ◽  
12S Rrna ◽  
Rrna Gene ◽  
Neotropical Fish ◽  
Β Diversity ◽  
Α Diversity

The current capacity of environmental DNA (eDNA) to provide accurate insights into the biodiversity of megadiverse regions (e.g., the Neotropics) requires further evaluation to ensure its reliability for long-term monitoring. In this study, we first evaluated the taxonomic resolution capabilities of a short fragment from the 12S rRNA gene widely used in fish eDNA metabarcoding studies, and then compared eDNA metabarcoding data from water samples with traditional sampling using nets. For the taxonomic discriminatory power analysis, we used a specifically curated reference dataset consisting of 373 sequences from 264 neotropical fish species (including 47 newly generated sequences) to perform a genetic distance-based analysis of the amplicons targeted by the MiFish primer set. We obtained an optimum delimitation threshold value of 0.5% due to lowest cumulative errors. The barcoding gap analysis revealed only a 50.38% success rate in species recovery (133/264), highlighting a poor taxonomic resolution from the targeted amplicon. To evaluate the empirical performance of this amplicon for biomonitoring, we assessed fish biodiversity using eDNA metabarcoding from water samples collected from the Amazon (Adolpho Ducke Forest Reserve and two additional locations outside the Reserve). From a total of 84 identified Molecular Operational Taxonomic Units (MOTUs), only four could be assigned to species level using a fixed threshold. Measures of α-diversity analyses within the Reserve showed similar patterns in each site between the number of MOTUs (eDNA dataset) and species (netting data) found. However, β-diversity revealed contrasting patterns between the methods. We therefore suggest that a new approach is needed, underpinned by sound taxonomic knowledge, and a more thorough evaluation of better molecular identification procedures such as multi-marker metabarcoding approaches and tailor-made (i.e., order-specific) taxonomic delimitation thresholds.

scholarly journals Passive sampling of environmental DNA in aquatic environments using 3D-printed hydroxyapatite samplers

2021 ◽  
Author(s):  
Heloise Verdier ◽  
Lara Konecny-Dupre ◽  
Christophe Marquette ◽  
Helen Reveron ◽  
Solene Tadier ◽  
...  
Keyword(s):  
Aquatic Organisms ◽  
Environmental Dna ◽  
Aquatic Environments ◽  
Non Invasive ◽  
Turbid Waters ◽  
Physico Chemical ◽  
Wide Range ◽  
Artificial Dna ◽  
3D Printed ◽  
High Binding Affinity

1. The study of environmental DNA released by aquatic organisms in their habitat offers a fast, non-invasive and sensitive approach to monitor their presence. Common eDNA sampling methods such as filtration and precipitation are time consuming, require human intervention and are not applicable to a wide range of habitats such as turbid waters and poorly-accessible environments. To circumvent these limitations, we propose to use the binding properties of minerals to create a passive eDNA sampler. 2. We have designed 3D-printed samplers made of hydroxyapatite (HAp samplers), a mineral known for its high binding affinity with DNA. The shape and the geometry of the samplers have been designed to facilitate their handling in laboratory and field. Here we describe and test the ability of HAp samplers to recover artificial DNA and eDNA. 3. We show that HAp samplers efficiently recover DNA and are effective even on small amounts of eDNA (<1 ng). However, we also observed large variations in the amount of DNA recovered even under controlled conditions. 4. By better understanding the physico-chemical interactions between DNA and the HAp sampler surface, one could improve the repeatability of the sampling process and provide an easy-to-use eDNA sampling tool for aquatic environments.

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