Environmental DNA Detection of the Golden Tree Frog (Phytotriades auratus) in Bromeliads

Using eDNA to survey amphibians: Methods, applications, and challenges

In recent years, environmental DNA (eDNA) has received attention from biologists due to its sensitivity, convenience, labor and material efficiency, and lack of damage to organisms. The extensive application of eDNA has opened avenues for the monitoring and biodiversity assessment of amphibians, which are frequently small and difficult to observe in the field, in areas such as biodiversity survey assessment and detection of specific, rare and threatened, or alien invasive species. However, the accuracy of eDNA can be influenced by factors such as ambient temperature, pH, and false positives or false negatives, which makes eDNA an adjunctive tool rather than a replacement for traditional surveys. This review provides a concise overview of the eDNA method and its workflow, summarizes the differences between applying eDNA for detecting amphibians and other organisms, reviews the research progress in eDNA technology for amphibian monitoring, identifies factors influencing detection efficiency, and discusses the challenges and prospects of eDNA. It aims to serve as a reference for future research on the application of eDNA in amphibian detection.

Current status and topical issues on the use of eDNA-based targeted detection of rare animal species

Animal detection through DNA present in environmental samples (eDNA) is a valuable tool for detecting rare species, that are difficult to observe and monitor. eDNA-based tools are underpinned by molecular evolutionary principles, key to devising tools to efficiently single out a targeted species from an environmental sample. Here, we present a comprehensive review of the use of eDNA-based methods for the detection of targeted animal species, such as rare, endangered, or invasive species, through the analysis of 549 publications (2008-2022). Aquatic ecosystems have been the most surveyed, in particular, freshwaters (74 %), and to a less extent marine (14 %) and terrestrial systems (10 %). Vertebrates, in particular, fish (38 %), and endangered species, have been the focus of most of these studies, and Cytb and COI are the most employed markers. Among invertebrates, assays have been mainly designed for Mollusca and Crustacea species (21 %), in particular, to target invasive species, and COI the most employed marker. Targeted molecular approaches, in particular qPCR, have been the most adopted (75 %), while eDNA metabarcoding has been rarely used to target single or few species (approx. 6 %). However, less attention has been given in these studies to the effects of environmental factors on the amount of shed DNA, the differential amount of shed DNA among species, or the sensitivity of the markers developed, which may impact the design of the assays, particularly to warrant the required detection level and avoid false negatives and positives. The accuracy of the assays will also depend on the availability of genetic data and vouchered tissue or DNA samples from closely related species to assess both marker and primers' specificity. In addition, eDNA-based assays developed for a particular species may have to be refined for use in a new geographic area taking into account site-specific populations, as well as any intraspecific variation.

Environmental DNA Assay for the Detection of the American Bullfrog (Lithobates catesbeianus) in the Early Stages of the Invasion in the Ebre Delta

The American bullfrog (Lithobates catesbeianus) is considered to be one of the most harmful invasive species. In the Iberian Peninsula, this species had been cited occasionally until the year 2018, when L. catesbeianus appeared in the Ebre Delta, and, for the first time, it started breeding in a territory of the Peninsula. Using environmental DNA (eDNA) analysis and visual surveys, the American bullfrog invasion in the Ebre Delta was monitored across two consecutive years (2019-2020). No specimens were observed in 2019, and results for the eDNA survey also failed to detect this species in the Delta. In 2020, two individuals were captured and, under the most conservative criteria to constrain the number of positive detections, eDNA analyses detected the presence of the American bullfrog in at least five locations. Performing an eDNA assay yielded a higher sensitivity with a lower sampling effort than traditional methods. Although the American bullfrog does not appear to still be well-established in the Ebre Delta, only a few bullfrog individuals could be enough for their establishment in suitable habitats. In this context, eDNA assays are essential tools to facilitate the detection, control, and eradication of this species in the first stage of the invasion process.

Development and validation of an eDNA protocol for monitoring endemic Asian spiny frogs in the Himalayan region of Pakistan

Wildlife monitoring programs are instrumental for the assessment of species, habitat status, and for the management of factors affecting them. This is particularly important for species found in freshwater ecosystems, such as amphibians, as they have higher estimated extinction rates than terrestrial species. We developed and validated two species-specific environmental DNA (eDNA) protocols and applied them in the field to detect the Hazara Torrent Frog (Allopaa hazarensis) and Murree Hills Frog (Nanorana vicina). Additionally, we compared eDNA surveys with visual encounter surveys and estimated site occupancy. eDNA surveys resulted in higher occurrence probabilities for both A. hazarensis and N. vicina than for visual encounter surveys. Detection probability using eDNA was greater for both species, particularly for A. hazarensis. The top-ranked detection model for visual encounter surveys included effects of both year and temperature on both species, and the top-ranked occupancy model included effects of elevation and year. The top-ranked detection model for eDNA data was the null model, and the top-ranked occupancy model included effects of elevation, year, and wetland type. To our knowledge, this is the first time an eDNA survey has been used to monitor amphibian species in the Himalayan region.

First extraction of eDNA from tree hole water to detect tree frogs: a simple field method piloted in Madagascar

Environmental DNA (eDNA) is becoming an increasingly used tool for monitoring cryptic species within terrestrial and aquatic systems. We present the first method for extracting water from tree holes for eDNA studies of tree-dwelling frogs, and the first use of eDNA for amphibian monitoring in Madagascar. This pilot study expands on a previously developed method and aims to provide a simple field protocol for DNA extraction from very small water samples, using a relatively inexpensive kit compared to other collection methods. We collected 20 ml of water from tree holes in Ambohitantely Special Reserve in Madagascar, with the aim to survey for the Critically Endangered tree frog Anodonthyla vallani, and we developed species specific cytochrome c oxidase 1 primers for this species. While our two samples did not detect A. vallani, we successfully extracted up to 16.6 ng/µl of eDNA from the samples and using 16S rRNA primers barcoded the tree frog Plethodontohyla mihanika in one of the samples. Despite just two samples being collected, we highlight the future potential of eDNA from tree holes for investigating cryptic habitat specialist amphibians given we extracted frog eDNA from just 20 ml of water. The method provides a rapid, simple, and cost-effective method which can assist cryptic species monitoring in challenging and time-consuming field conditions and should be developed further for frog surveying in Madagascar and beyond. The newly developed primers can be used for further work using this eDNA method to survey threatened Anodonthyla frog species.

Reinforcement of Environmental DNA Based Methods (Sensu Stricto) in Biodiversity Monitoring and Conservation: A Review

Simple Summary

Worldwide biodiversity loss points to a necessity of upgrading to a fast and effective monitoring method that can provide quick conservation action. Newly developed environmental DNA (eDNA) based method found to be more cost-effective, non-invasive, quick, and accurate than traditional monitoring (spot identification, camera trapping). Although the eDNA based methods are proliferating rapidly, as a newly developed branch, it needs more standardization and practitioner adaptation. The present study aims to evaluate the eDNA based methods, and their potential achievements in biodiversity monitoring, and conservation for quick practitioners’ adaption. The investigation shows that the eDNA technique is applicable largely in (i) early detection of invasive species, (ii) species detection for conservation, (iii) community-level biodiversity monitoring, (iv) ecosystem health monitoring, (v) study on trophic interactions, etc. Thus, the eDNA technique shows a great promise with its high accuracy and authenticity, and will be applicable alone or alongside other methods in the near future.

Abstract

Recently developed non-invasive environmental DNA-based (eDNA) techniques have enlightened modern conservation biology, propelling the monitoring/management of natural populations to a more effective and efficient approach, compared to traditional surveys. However, due to rapid-expansion of eDNA, confusion in terminology and collection/analytical pipelines can potentially jeopardize research progression, methodological standardization, and practitioner adoption in several ways. Present investigation reflects the developmental progress of eDNA (sensu stricto) including highlighting the successful case studies in conservation management. The eDNA technique is successfully relevant in several areas of conservation research (invasive/conserve species detection) with a high accuracy and authentication, which gradually upgrading modern conservation approaches. The eDNA technique related bioinformatics (e.g., taxon-specific-primers MiFish, MiBird, etc.), sample-dependent methodology, and advancement of sequencing technology (e.g., oxford-nanopore-sequencing) are helping in research progress. The investigation shows that the eDNA technique is applicable largely in (i) early detection of invasive species, (ii) species detection for conservation, (iii) community level biodiversity monitoring, (iv) ecosystem health monitoring, (v) study on trophic interactions, etc. Thus, the eDNA technique with a high accuracy and authentication can be applicable alone or coupled with traditional surveys in conservation biology. However, a comprehensive eDNA-based monitoring program (ecosystem modeling and function) is essential on a global scale for future management decisions.

Heterodissemination: precision insecticide delivery to mosquito larval habitats by cohabiting vertebrates

Conventional larvicide delivery strategies originally developed for permanent and floodwater mosquitoes have proved suboptimal in the small, scattered, and cryptic larval habitats preferred by container-inhabiting Aedes mosquitoes. New methods such as autodissemination, wherein adult mosquitoes spread insecticides to their own larval habitats, have been under study. Another novel delivery method termed heterodissemination, i.e. larvicide delivery by other species sharing the same habitats, has also been proposed. We conducted a proof-of-concept study with four independent experiments using American bullfrogs (Lithobates catesbeianus) and green frogs Lithobates clamitans as carriers of pyriproxyfen, an insect growth regulator, under semi-field conditions in three different locations, two in New Jersey, and one in Utah. Frogs with attached slow-release pyriproxyfen tablets were introduced into outdoor enclosures with water containers. Water samples from the containers were periodically tested using larval Aedes albopictus and Culex pipiens mosquitoes to assess mortality and percent eclosure inhibition. Overall pupal mortality [95% credible intervals] estimated by Bayesian analysis for the treatment group was 73.4% [71.3–75.2] compared to 4.1% [2.9–5.5] for the control group. Mortality within treatment groups in four different experiments ranged from 41 to 100%, whereas control mortalities ranged from 0.5% to 11%. We conclude that heterodissemination is a promising and effective approach deserving of further study.

Development and validation of a quantitative qPCR assay for detecting Natterjack toad (Epidalea calamita) eDNA samples

The Natterjack toad (Epidalea calamita) is the rarest amphibian species in Ireland, regionally Red-Listed as Endangered. We applied an eDNA approach to detect species presence in breeding pond water samples. We developed a species-specific qPCR assay targeting the cytochrome c oxidase subunit I (COI). The assay was tested in silico, in vitro (DNA extracted from tissue) and in vivo (DNA extracted from water samples). Water samples were collected from five ponds with known Natterjack toad presence or absence to validate the sensitivity and specificity of the assay. The assay was shown to be highly specific to the Natterjack toad and tested positive only against toad tissue samples and eDNA samples from ponds with known species presence. We believe this method can be used for rapid assessment of species occurrence.

Ecosystem services provided by bromeliad plants: A systematic review

The unprecedented loss of biological diversity has negative impacts on ecosystems and the associated benefits which they provide to humans. Bromeliads have high diversity throughout the Neotropics, but they have been negatively affected by habitat loss and fragmentation, climate change, invasive species, and commercialization for ornamental purpose. These plants provide direct benefits to the human society, and they also form microecosystems in which accumulated water and nutrients support the communities of aquatic and terrestrial species, thus maintaining local diversity. We performed a systematic review of the contribution of bromeliads to ecosystem services across their native geographical distribution. We showed that bromeliads provide a range of ecosystem services such as maintenance of biodiversity, community structure, nutrient cycling, and the provisioning of food and water. Moreover, bromeliads can regulate the spread of diseases, and water and carbon cycling, and they have the potential to become important sources of chemical and pharmaceutical products. The majority of this research was performed in Brazil, but future research from other Neotropical countries with a high diversity of bromeliads would fill the current knowledge gaps and increase the generality of these findings. This systematic review identified that future research should focus on provisioning, regulating, and cultural services that have been currently overlooked. This would enhance our understanding of how bromeliad diversity contributes to human welfare, and the negative consequences that loss of bromeliad plants can have on communities of other species and the healthy functioning of the entire ecosystems.

Conventional versus real-time quantitative PCR for rare species detection

Detection of species in nature at very low abundance requires innovative methods. Conventional PCR (cPCR) and real-time quantitative PCR (qPCR) are two widely used approaches employed in environmental DNA (eDNA) detection, though lack of a comprehensive comparison of them impedes method selection. Here we test detection capacity and false negative rate of both approaches using samples with different expected complexities. We compared cPCR and qPCR to detect invasive, biofouling golden mussels (Limnoperna fortunei), in samples from laboratory aquaria and irrigation channels where this mussel was known to occur in central China. Where applicable, the limit of detection (LoD), limit of quantification (LoQ), detection rate, and false negative rate of each PCR method were tested. Quantitative PCR achieved a lower LoD than cPCR (1 × 10-7 vs. 10-6 ng/μl) and had a higher detection rate for both laboratory (100% vs. 87.9%) and field (68.6% vs. 47.1%) samples. Field water samples could only be quantified at a higher concentration than laboratory aquaria and total genomic DNA, indicating inhibition with environmental samples. The false negative rate was inversely related to the number of sample replicates. Target eDNA concentration was negatively related to distance from sampling sites to the water (and animal) source. Detection capacity difference between cPCR and qPCR for genomic DNA and laboratory aquaria can be translated to field water samples, and the latter should be prioritized in rare species detection. Field environmental samples may involve more complexities-such as inhibitors-than laboratory aquaria samples, requiring more target DNA. Extensive sampling is critical in field applications using either approach to reduce false negatives.

Metabarcoding of Environmental DNA Samples to Explore the Use of Uranium Mine Containment Ponds as a Water Source for Wildlife

Understanding how anthropogenic impacts on the landscape affect wildlife requires a knowledge of community assemblages. Species surveys are the first step in assessing community structure, and recent molecular applications such as metabarcoding and environmental DNA analyses have been proposed as an additional and complementary wildlife survey method. Here, we test eDNA metabarcoding as a survey tool to examine the potential use of uranium mine containment ponds as water sources by wildlife. We tested samples from surface water near mines and from one mine containment pond using two markers, 12S and 16S rRNA gene amplicons, to survey for vertebrate species. We recovered large numbers of sequence reads from taxa expected to be in the area and from less common or hard to observe taxa such as the tiger salamander and gray fox. Detection of these two species is of note because they were not observed in a previous species assessment, and tiger salamander DNA was found in the mine containment pond sample. We also found that sample concentration by centrifugation was a more efficient and more feasible method than filtration in these highly turbid surface waters. Ultimately, the use of eDNA metabarcoding could allow for a better understanding of the area’s overall biodiversity and community composition as well as aid current ecotoxicological risk assessment work.

Development and Application of an eDNA Method to Detect the Critically Endangered Trinidad Golden Tree Frog (Phytotriades auratus) in Bromeliad Phytotelmata

The use of environmental DNA (eDNA) to monitor rare and elusive species has great potential for conservation biology. Traditional surveying methods can be time-consuming, labour-intensive, subject to error or can be invasive and potentially damaging to habitat. The Trinidad golden treefrog (Phytotriades auratus) is one such species that would benefit from such an approach. This species inhabits the giant bromeliad (Glomeropitcairnia erectiflora) on two peaks on the Caribbean island of Trinidad. Traditional survey methods for this species have required the destruction of the giant bromeliad, which is the only known habitat of this frog. Here we described the development of an eDNA PCR-based assay that uses water drawn from the water-filled phytotelmata of the giant bromeliad along with the use of a synthetic DNA positive control that can be easily amplified in the bacterium Escherichia coli. The assay can detect to a DNA concentration of 1.4ng. Sampling of 142 bromeliads using this method revealed 9% were positive for P. auratus DNA. These data suggest that eDNA methods also have great potential for revealing the presence of elusive species in arboreal habitats.