Using environmental DNA for detection of <i>Batrachochytrium salamandrivorans</i> in natural water

Sluijs, Annemarieke Spitzen‐van der; Déjean, Tony; Verbrugghe, Elin; Herder, Jelger; Gilbert, Maarten J.; Janse, Jöran; Martel, An; Pasmans, Frank; Valentini, Alice

doi:10.1002/edn3.86

Cited by 22 publications

(31 citation statements)

References 28 publications

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“…Surveys targeting eDNA involve the collection of environmental samples from a location which usually comprises water, soil or sediments (Turner et al, 2015;Buxton et al, 2018;Spitzen-van der Sluijs et al, 2020;Valentin et al, 2020). These samples are then processed following forensic protocols for the extraction of DNA that has been released by organisms into the environment.…”

Section: Introductionmentioning

confidence: 99%

Comparison of eDNA and visual surveys for rare and cryptic bromeliad-dwelling frogs

Barata¹

2021

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Surveys of rare or cryptic species may miss individuals or populations that are actually present. Despite the increasing use of environmental DNA (eDNA) analysis to survey species in ponds, rivers, and lakes, very few studies have attempted to use eDNA for the detection of species using very small water bodies such as those accumulated within plants. Our aim was to investigate the feasibility of an eDNA sampling method for detecting Crossodactylodes itambe, an endemic bromeliad-dwelling frog from a remote location in Brazil. We collected water samples from 19 bromeliads for which we had observational data from direct visual surveys. We compared occupancy estimated from direct observations with the results from quantitative real-time PCR based eDNA assays. For observational surveys, we used a single season occupancy model. We applied a novel Bayesian occupancy model to estimate occupancy from eDNA samples, as well as false positives and false negatives at different stages of the workflow. eDNA from bromeliad tanks provided reliable estimates, with very low error levels and improved detection when compared to detectability from direct observation. Estimated occupancies using eDNA and visual survey methods were similar. The method is feasible for species restricted to small water bodies and exposed to direct UV radiation, and particularly useful to survey remote locations and confirm species presence. eDNA analysis provides a viable alternative to destructive sampling of bromeliads or direct observation methods that require logistically challenging repeated observations. Therefore, eDNA methods may be widely applicable to sampling programmes of other amphibians that live in plants.

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Section: Introductionmentioning

confidence: 99%

Comparison of eDNA and visual surveys for rare and cryptic bromeliad-dwelling frogs

Barata¹

2021

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“…In addition, some samples were sent to Trier University in order to confirm our results. A subset of samples from field and laboratory experiments were retested with a recently-developed assay for Bsal eDNA testing [ 19 ].…”

Section: Methodsmentioning

confidence: 99%

“…We used a Bsal gBlock 213 bp in length that overlaps with the Bsal primers [ 21 ] target sequence by 26 bases on both sides. The same gBlock is also applicable with recently published eDNA qPCR [ 19 ]. Positions 96 and 97 contain two adenine nucleotides in the position of thymine in the reference sequences, in order to identify possible contamination by the gBlock in the event of equivocal results suspected to have been caused by laboratory cross-contamination.…”

Section: Methodsmentioning

confidence: 99%

“…Amphibian chytrid fungi are potentially good targets for the application of eDNA detection, owing to their microscopic size, the large quantities of actively dispersing zoospores that are usually produced, occupation of an aquatic environment, and the ready availability of established detection assays. Attempts to use eDNA detection in the case of Bd [ 15 , 16 , 17 , 18 ] or Bsal [ 19 ] are still surprisingly sparse, although qPCR [ 20 , 21 ], nested PCR [ 22 ], and standard PCR [ 14 ] assays are sensitive enough to detect the DNA equivalents of individual cells. The reasons limiting the broader use of eDNA in the detection of both chytrid fungi include the perceived difficulty of the procedure, inconsistent results in comparison with standard individual sampling protocols [ 15 ], and the potentially high cost of sample collection and processing [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

“…Critical considerations to ensure quality assurance and minimum requirements stated in [ 23 ] should be followed, and the current lack of unified criteria for procedures makes comparison of results challenging. As an example, various types of filters are used—polycarbonate track-etched [ 17 ], polyethersulfone [ 18 ], nitrate cellulose [ 15 ], or VigiDNA ® (Spygen, Le Bourget du Lac Cedex, France), unspecified material [ 19 ]. At the same time, the current rapid spread of the pathogens requires simple, fast, robust, and cost-effective surveillance methods.…”

Section: Introductionmentioning

confidence: 99%

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Dual Detection of the Chytrid Fungi Batrachochytrium spp. with an Enhanced Environmental DNA Approach

González

Baláž

Vojar

et al. 2021

JoF

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Environmental DNA (eDNA) is becoming an indispensable tool in biodiversity monitoring, including the monitoring of invasive species and pathogens. Aquatic chytrid fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal) are major threats to amphibians. However, the use of eDNA for detecting these pathogens has not yet become widespread, due to technological and economic obstacles. Using the enhanced eDNA approach (a simple and cheap sampling protocol) and the universally accepted qPCR assay, we confirmed the presence of Bsal and Bd in previously identified sites in Spain, including four sites that were new for Bsal. The new approach was successfully tested in laboratory conditions using manufactured gene fragments (gBlocks) of the targeted DNA sequence. A comparison of storage methods showed that samples kept in ethanol had the best DNA yield. Our results showed that the number of DNA copies in the Internal Transcribed Spacer region was 120 copies per Bsal cell. Eradication of emerging diseases requires quick and cost-effective solutions. We therefore performed cost-efficiency analyses of standard animal swabbing, a previous eDNA approach, and our own approach. The procedure presented here was evaluated as the most cost-efficient. Our findings will help to disseminate information about efforts to prevent the spread of chytrid fungi.

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Landscape epidemiology of Batrachochytrium salamandrivorans: reconciling data limitations and conservation urgency

Beukema

Erens

Schulz

et al. 2021

Ecological Applications

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Starting in 2010, rapid-fire salamander (Salamandra salamandra) population declines in northwestern Europe heralded the emergence of Batrachochytrium salamandrivorans (Bsal), a salamander-pathogenic chytrid fungus. Bsal poses an imminent threat to global salamander diversity owing to its wide host range, high pathogenicity, and long-term persistence in ecosystems. While there is a pressing need to develop further research and conservation actions, data limitations inherent to recent pathogen emergence obscure necessary insights into Bsal disease ecology. Here, we use a hierarchical modeling framework to describe Bsal landscape epidemiology of outbreak sites in light of these methodological challenges. Using model selection and machine learning, we find that Bsal presence is associated with humid and relatively cool, stable climates. Outbreaks are generally located in areas characterized by low landscape heterogeneity and low steepness of slope. We further find an association between Bsal presence and high trail density, suggesting that human-mediated spread may increase risk for spillover between populations. We then use distribution modeling to show that favorable conditions occur in lowlands influenced by the North Sea, where increased survey effort is needed to determine how Bsal impacts local newt populations, but also in hill-and mountain ranges in northeastern France and the lower half of Germany. Finally, connectivity analyses suggest that these hill-and mountain ranges may act as stepping stones for further spread southward. Our results provide initial insight into regional environmental conditions underlying Bsal epizootics, present updated invasibility predictions for northwestern Europe, and lead us to discuss a wide variety of potential survey and research actions needed to advance future conservation and mitigation efforts.

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Using environmental DNA for detection of Batrachochytrium salamandrivorans in natural water

Cited by 22 publications

References 28 publications

Comparison of eDNA and visual surveys for rare and cryptic bromeliad-dwelling frogs

Comparison of eDNA and visual surveys for rare and cryptic bromeliad-dwelling frogs

Dual Detection of the Chytrid Fungi Batrachochytrium spp. with an Enhanced Environmental DNA Approach

Landscape epidemiology of Batrachochytrium salamandrivorans: reconciling data limitations and conservation urgency

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