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PeerJ
2023 Jan 01;11:e15455. doi: 10.7717/peerj.15455.
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Environmental DNA and visual encounter surveys for amphibian biomonitoring in aquatic environments of the Ecuadorian Amazon.
Quilumbaquin W
,
Carrera-Gonzalez A
,
Van der Heyden C
,
Ortega-Andrade HM
.
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BACKGROUND: The development of anthropogenic activities has generated a decline in aquatic fauna populations, and amphibians have been the most affected. The decline of batrachofauna is concerning, as 41% of all species worldwide are endangered. For this reason, rapid, efficient, and non-invasive biodiversity monitoring techniques are needed, and environmental DNA (eDNA) is one such tool that has been sparsely applied in Ecuador. This technique has allowed scientists generates information on species diversity and amphibian community composition from a water sample. This study applied eDNA-based biomonitoring analyses and visual encounter surveys (VES) as inventory techniques to identify the diversity of aquatic amphibians in the Tena River micro-basin (TRMB).
METHODS: The experimental design was divided into three components: (1) fieldwork: all amphibians were recorded by the VES technique and water samples were collected; (2) laboratory work: DNA isolation from amphibian tissue samples and eDNA-containing filters, amplification, electrophoresis, and sequencing were performed; (3) Data analysis: a local DNA reference database was constructed, and eDNA sequence data were processed for classification, taxonomic assignment, and ecological interpretation.
RESULTS: Using both eDNA and VES, we detected 33 amphibian species (13 with eDNA only, five with VES only, and 15 with both methods). These species belonged to six amphibian families: Hylidae being the richest with 14 species (three eDNA, one VES, and 10 with both methods), followed by Strabomantidae with nine species (six eDNA, one VES, and two with both methods). All families were detected with both methods, except for the Aromobatidae, having one single record (Allobates aff. insperatus) by VES. Individually, eDNA detected 28 species and had a detection probability (DP) of 0.42 CI [0.40-0.45], while VES recorded 20 species with a DP of 0.17 CI [0.14-0.20]. Similarly, using VES, Cochranella resplendens was detected for the first time in TRMB, while with eDNA, four mountain frogs Pristimantis acerus, Pristimantis eriphus, Pristimantis mallii, and Pristimantis sp. (INABIO 15591) previously recorded at 1,518 m.a.s.l. at altitudes below 600 m.a.s.l. were detected.
CONCLUSIONS: Results obtained in this study showed that eDNA-based detection had a greater capacity to detect amphibians in aquatic environments compared to VES. The combination of VES and eDNA improves the sensitivity of species detection and provides more reliable, robust, and detailed information. The latter is essential for developing conservation strategies in the Ecuadorian Amazon.
Apothéloz-Perret-Gentil,
Monitoring the ecological status of rivers with diatom eDNA metabarcoding: A comparison of taxonomic markers and analytical approaches for the inference of a molecular diatom index.
2021, Pubmed
Apothéloz-Perret-Gentil,
Monitoring the ecological status of rivers with diatom eDNA metabarcoding: A comparison of taxonomic markers and analytical approaches for the inference of a molecular diatom index.
2021,
Pubmed
Apothéloz-Perret-Gentil,
Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring.
2017,
Pubmed
Barata,
The power of monitoring: optimizing survey designs to detect occupancy changes in a rare amphibian population.
2017,
Pubmed
Bohmann,
Environmental DNA for wildlife biology and biodiversity monitoring.
2014,
Pubmed
Bonin,
Optimal sequence similarity thresholds for clustering of molecular operational taxonomic units in DNA metabarcoding studies.
2023,
Pubmed
Borst,
False-positive results and contamination in nucleic acid amplification assays: suggestions for a prevent and destroy strategy.
2004,
Pubmed
Brozio,
Development and Application of an eDNA Method to Detect the Critically Endangered Trinidad Golden Tree Frog (Phytotriades auratus) in Bromeliad Phytotelmata.
2017,
Pubmed
Bálint,
Accuracy, limitations and cost efficiency of eDNA-based community survey in tropical frogs.
2018,
Pubmed
Deiner,
Environmental DNA reveals that rivers are conveyer belts of biodiversity information.
2016,
Pubmed
Dowden,
Host genotype and exercise exhibit species-level selection for members of the gut bacterial communities in the mouse digestive system.
2020,
Pubmed
Fediajevaite,
Meta-analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards.
2021,
Pubmed
Ficetola,
An in silico approach for the evaluation of DNA barcodes.
2010,
Pubmed
Furlan,
A framework for estimating the sensitivity of eDNA surveys.
2016,
Pubmed
Gwak,
Data-Driven Modeling for Species-Level Taxonomic Assignment From 16S rRNA: Application to Human Microbiomes.
2020,
Pubmed
Keck,
Meta-analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment.
2022,
Pubmed
Lacoursière-Roussel,
Improving herpetological surveys in eastern North America using the environmental DNA method.
2016,
Pubmed
Lopes,
eDNA metabarcoding: a promising method for anuran surveys in highly diverse tropical forests.
2017,
Pubmed
Maestri,
A Rapid and Accurate MinION-Based Workflow for Tracking Species Biodiversity in the Field.
2019,
Pubmed
Nevers,
Influence of sediment and stream transport on detecting a source of environmental DNA.
2020,
Pubmed
Ortega-Andrade,
Red List assessment of amphibian species of Ecuador: A multidimensional approach for their conservation.
2021,
Pubmed
Pawlowski,
Environmental DNA for biomonitoring.
2021,
Pubmed
Pedersen,
Ancient and modern environmental DNA.
2015,
Pubmed
Pentinsaari,
BOLD and GenBank revisited - Do identification errors arise in the lab or in the sequence libraries?
2020,
Pubmed
Petitot,
Optimizing occupancy surveys by maximizing detection probability: application to amphibian monitoring in the Mediterranean region.
2014,
Pubmed
Roh,
Comparative study of methods for extraction and purification of environmental DNA from soil and sludge samples.
2006,
Pubmed
Schultz,
Modeling the Sensitivity of Field Surveys for Detection of Environmental DNA (eDNA).
2015,
Pubmed
Shaw,
Comparison of the effects of sterilisation techniques on subsequent DNA profiling.
2008,
Pubmed
Shogren,
Controls on eDNA movement in streams: Transport, Retention, and Resuspension.
2017,
Pubmed
Stuart,
Status and trends of amphibian declines and extinctions worldwide.
2004,
Pubmed
Takahashi,
Comparing the efficiency of open and enclosed filtration systems in environmental DNA quantification for fish and jellyfish.
2020,
Pubmed
Valentini,
Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding.
2016,
Pubmed
Vences,
Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians.
2005,
Pubmed
Vierstraete,
Amplicon_sorter: A tool for reference-free amplicon sorting based on sequence similarity and for building consensus sequences.
2022,
Pubmed
Wang,
Development of an eDNA metabarcoding tool for surveying the world's largest amphibian.
2022,
Pubmed
Wang,
Methodology of fish eDNA and its applications in ecology and environment.
2021,
Pubmed
Weigand,
DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work.
2019,
Pubmed
Willette,
Characterizing Industrial and Artisanal Fishing Vessel Catch Composition Using Environmental DNA and Satellite-Based Tracking Data.
2021,
Pubmed
Zavala,
Quantifying and reducing cross-contamination in single- and multiplex hybridization capture of ancient DNA.
2022,
Pubmed