Evaluation of a filtration-based method for detecting Batrachochytrium dendrobatidis in natural bodies of water

Centrifugation is an effective and inexpensive way to determine Batrachochytrium dendrobatidis quantity in water samples with low turbidity

Batrachochytrium dendrobatidis (Bd) is a pathogenic chytrid fungus that is particularly lethal for amphibians. Bd can extirpate amphibian populations within a few weeks and remain in water in the absence of amphibian hosts. Most efforts to determine Bd presence and quantity in the field have focused on sampling hosts, but these data do not give us a direct reflection of the amount of Bd in the water, which are useful for parameterizing disease models, and are not effective when hosts are absent or difficult to sample. Current methods for screening Bd presence and quantity in water are time, resource, and money intensive. Here, we developed a streamlined method for detecting Bd in water with low turbidity (e.g., water samples from laboratory experiments and relatively clear pond water from a natural lentic system). We centrifuged water samples with known amounts of Bd to form a pellet and extracted the DNA from that pellet. This method was highly effective and the resulting concentrations across all tested treatments presented a highly linear relationship with the expected values. While the experimentally derived values were lower than the inoculation doses, the values were highly correlated and a conversion factor allows us to extrapolate the actual Bd concentration. This centrifuge-based method is effective, repeatable, and would greatly expand the domain of tractable questions to be explored in the field of Bd ecology. Importantly, this method increases equity in the field, because it is time- and cost-efficient and requires few resources.

Rapid detection of amphibian chytrid fungus Batrachochytrium dendrobatidis using in situ DNA extraction and a handheld mobile thermocycler

The amphibian chytrid fungus (Bd) has caused declines and some extinctions of amphibian populations worldwide. Early and accurate Bd detection is essential for management of susceptible anurans. We analyzed the effectiveness of in situ DNA extraction with a handheld mobile quantitative PCR (qPCR) thermocycler to detect Bd on frog skin swabs and in water samples using environmental DNA (eDNA). We collected duplicate eDNA samples and skin swabs from 3 Bd-positive Rana sierrae populations. We processed one set of samples using a field protocol (a handheld thermocycler) and the other half using a standard lab protocol. We detected Bd DNA in all R. sierrae swabbed using both the field and lab protocols. We also detected Bd DNA in eDNA samples at all sites, although the field and lab protocols failed to detect Bd eDNA at separate singular sites; results from the field and lab eDNA protocol did not match. The probability of detecting Bd DNA in the technical replicates was lower for the field protocol than the lab protocol, suggesting the field protocol has lower sensitivity and may not detect low quantities of DNA. Our results suggest that the field extraction protocol using a handheld qPCR platform is a promising tool for rapid detection of Bd in susceptible amphibian populations, yielding accurate results in less than 60 min. However, the applied field protocol may be prone to false negatives when analyzing low-quantity DNA samples such as eDNA water samples or frog swabs with low pathogen loads.

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

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.

Reliable eDNA detection and quantification of the European weather loach (Misgurnus fossilis)

The European weather loach (Misgurnus fossilis) is a cryptic and poorly known fish species of high conservation concern. The species is experiencing dramatic population collapses across its native range to the point of regional extinction. Although environmental DNA (eDNA)-based approaches offer clear advantages over conventional field methods for monitoring rare and endangered species, accurate detection and quantification remain difficult and quality assessment is often poorly incorporated. In this study, we developed and validated a novel digital droplet PCR (ddPCR) eDNA-based method for reliable detection and quantification, which allows accurate monitoring of M. fossilis across a number of habitat types. A dilution experiment under laboratory conditions allowed the definition of the limit of detection (LOD) and the limit of quantification (LOQ), which were set at concentrations of 0.07 and 0.14 copies μl^-1 , respectively. A series of aquarium experiments revealed a significant and positive relationship between the number of individuals and the eDNA concentration measured. During a 3 year survey (2017-2019), we assessed 96 locations for the presence of M. fossilis in Flanders (Belgium). eDNA analyses on these samples highlighted 45% positive detections of the species. On the basis of the eDNA concentration per litre of water, only 12 sites appeared to harbour relatively dense populations. The other 31 sites gave a relatively weak positive signal that was typically situated below the LOQ. Combining sample-specific estimates of effective DNA quantity (Q_e ) and conventional field sampling, we concluded that each of these weak positive sites still likely harboured the species and therefore they do not represent false positives. Further, only seven of the classified negative samples warrant additional sampling as our analyses identified a substantial risk of false-negative detections (i.e., type II errors) at these locations. Finally, we illustrated that ddPCR outcompetes conventional qPCR analyses, especially when target DNA concentrations are critically low, which could be attributed to a reduced sensitivity of ddPCR to inhibition effects, higher sample concentrations being accommodated and higher sensitivity obtained.

Evaluating environmental DNA as a tool for detecting an amphibian pathogen using an optimized extraction method

Environmental DNA (eDNA) detection is a valuable conservation tool that can be used to identify and monitor imperiled or invasive species and wildlife pathogens. Batrachochytrium pathogens are of global conservation concern because they are a leading cause of amphibian decline. While eDNA techniques have been used to detect Batrachochytrium DNA in the environment, a systematic comparison of extraction methods across environmental samples is lacking. In this study, we first compared eDNA extraction methods and found that a soil extraction kit (Qiagen PowerSoil) was the most effective for detecting Batrachochytrium dendrobatidis in water samples. The PowerSoil extraction had a minimum detection level of 100 zoospores and had a two- to four-fold higher detection probability than other commonly used extraction methods (e.g., QIAamp extraction, DNeasy+Qiashredder extraction method, respectively). Next, we used this extraction method on field-collected water and sediment samples and were able to detect pathogen DNA in both. While field-collected water filters were equivalent to amphibian skin swab samples in detecting the presence of pathogen DNA, the seasonal patterns in pathogen quantity were different between skin swabs and water samples. Detection rate was lowest in sediment samples. We also found that detection probability increases with the volume of water filtered. Our results indicate that water filter eDNA samples can be accurate in detecting pathogen presence at the habitat scale but their utility for quantifying pathogen loads in the environment appears limited. We suggest that eDNA techniques be used for early warning detection to guide animal sampling efforts.

Pooled samples and eDNA-based detection can facilitate the "clean trade" of aquatic animals

The regional and international trade of live animals facilitates the movement, spillover, and emergence of zoonotic and epizootic pathogens around the world. Detecting pathogens in trade is critical for preventing their continued movement and introduction, but screening a sufficient fraction to ensure rare infections are detected is simply infeasible for many taxa and settings because of the vast numbers of animals involved—hundreds of millions of live animals are imported into the U.S.A. alone every year. Batch processing pools of individual samples or using environmental DNA (eDNA)—the genetic material shed into an organism’s environment—collected from whole consignments of animals may substantially reduce the time and cost associated with pathogen surveillance. Both approaches, however, lack a framework with which to determine sampling requirements and interpret results. Here I present formulae for pooled individual samples (e.g,. swabs) and eDNA samples collected from finite populations and discuss key assumptions and considerations for their use with a focus on detecting Batrachochytrium salamandrivorans, an emerging pathogen that threatens global salamander diversity. While empirical validation is key, these formulae illustrate the potential for eDNA-based detection in particular to reduce sample sizes and help bring clean trade into reach for a greater number of taxa, places, and contexts.

eDNA Increases the Detectability of Ranavirus Infection in an Alpine Amphibian Population

The early detection and identification of pathogenic microorganisms is essential in order to deploy appropriate mitigation measures. Viruses in the Iridoviridae family, such as those in the Ranavirus genus, can infect amphibian species without resulting in mortality or clinical signs, and they can also infect other hosts than amphibian species. Diagnostic techniques allowing the detection of the pathogen outside the period of host die-off would thus be of particular use. In this study, we tested a method using environmental DNA (eDNA) on a population of common frogs (Rana temporaria) known to be affected by a Ranavirus in the southern Alps in France. In six sampling sessions between June and September (the species' activity period), we collected tissue samples from dead and live frogs (adults and tadpoles), as well as insects (aquatic and terrestrial), sediment, and water. At the beginning of the breeding season in June, one adult was found dead; at the end of July, a mass mortality of tadpoles was observed. The viral DNA was detected in both adults and tadpoles (dead or alive) and in water samples, but it was not detected in insects or sediment. In live frog specimens, the virus was detected from June to September and in water samples from August to September. Dead tadpoles that tested positive for Ranavirus were observed only on one date (at the end of July). Our results indicate that eDNA can be an effective alternative to tissue/specimen sampling and can detect Ranavirus presence outside die-offs. Another advantage is that the collection of water samples can be performed by most field technicians. This study confirms that the use of eDNA can increase the performance and accuracy of wildlife health status monitoring and thus contribute to more effective surveillance programs.

Concurrent visual encounter sampling validates eDNA selectivity and sensitivity for the endangered wood turtle (Glyptemys insculpta)

Environmental DNA (eDNA) has been used to record the presence of many different organisms in several different aquatic and terrestrial environments. Although eDNA has been demonstrated as a useful tool for the detection of invasive and/or cryptic and declining species, this approach is subject to the same considerations that limit the interpretation of results from traditional survey techniques (e.g. imperfect detection). The wood turtle is a cryptic semi-aquatic species that is declining across its range and, like so many chelonian species, is in-need of a rapid and effective method for monitoring distribution and abundance. To meet this need, we used an eDNA approach to sample for wood turtle presence in northern Virginia streams. At the same time, we used repeat visual encounter surveys in an occupancy-modelling framework to validate our eDNA results and reveal the relationship of detection and occupancy for both methods. We sampled 37 stream reaches of varying size within and beyond the known distribution of the wood turtle across northern Virginia. Wood turtle occupancy probability was 0.54 (0.31, 0.76) and while detection probability for wood turtle occupancy was high (0.88; 0.58, 0.98), our detection of turtle abundance was markedly lower (0.28; 0.21, 0.37). We detected eDNA at 76% of sites confirmed occupied by VES and at an additional three sites where turtles were not detected but were known to occur. Environmental DNA occupancy probability was 0.55 (0.29, 0.78); directly comparable to the VES occupancy estimate. Higher probabilities of detecting wood turtle eDNA were associated with higher turtle densities, an increasing number of days since the last rainfall, lower water temperatures, and lower relative discharges. Our results suggest that eDNA technology holds promise for sampling aquatic chelonians in some systems, even when discharge is high and biomass is relatively low, when the approach is validated and sampling error is quantified.

Evaluating observer bias and seasonal detection rates in amphibian pathogen eDNA collections by citizen scientists

We trained volunteers from conservation organizations to collect environmental DNA (eDNA) from 21 ponds with amphibian communities that had a history of Batrachochytrium dendrobatidis (Bd) and ranavirus (Rv) infections. Volunteers were given sampling kits to filter pond water and preserve eDNA on filter paper, as were the principal investigators (PIs), who made independent collections within 48 h of volunteer collections. Using multi-scale occupancy modeling, we found no evidence to suggest the observer who collected the water sample (volunteer or PI) influenced either the probability of capturing eDNA on a filter or the probability of detecting extracted eDNA in a quantitative PCR (qPCR) reaction. The cumulative detection probability of Bd eDNA at a pond decreased from May through July 2017 because there was a decrease in the probability of detecting eDNA in qPCR reactions. In contrast, cumulative detection probability increased from May to July for Rv due to a higher probability of capturing eDNA on filters later in the year. Our models estimate that both pathogens could be detected with 95% confidence in as few as 5 water samples taken in June or July tested with either 4 or 3 qPCR reactions, respectively. Our eDNA protocols appeared to detect pathogens with 95% confidence using considerably fewer samples than protocols which typically recommend sampling ≥30 individual animals. In addition, eDNA sampling could reduce some biosecurity concerns, jurisdictional and institutional permitting, and stress to biota at ponds.

Odds, challenges and new approaches in the control of helminthiasis, an Asian study

The time is passing, and the worms are still a major struggle for local people in Asian countries, especially the less empowered and in a situation of social vulnerability. We are working in the field in Laos, Thailand, and the Philippines where the usual control programs based only on human treatment are partially effective. Areas with mass drug administration could diminish, but not eliminate STHs of endemic areas. The persistence of helminthic NTDs in the environment and animal hosts makes the eradication a very difficult task. Great changes in the landscapes of endemic areas, such as construction of dams, can change the fauna and the lifestyle of local people. Those changes can improve infrastructure, but it can also lead to social vulnerability. The challenge, then, is to conceive new and directed control programs for helminthiasis based on multi- and transdisciplinary approaches diminishing the health gap in a globalized world. In this short review, we summarize the actual scenario concerning the main helminths in Southeast Asia and how an environmental DNA approach and the use of GIS could contribute to surveillance and control programs.

Beyond the swab: ecosystem sampling to understand the persistence of an amphibian pathogen

Understanding the ecosystem-level persistence of pathogens is essential for predicting and measuring host-pathogen dynamics. However, this process is often masked, in part due to a reliance on host-based pathogen detection methods. The amphibian pathogens Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal) are pathogens of global conservation concern. Despite having free-living life stages, little is known about the distribution and persistence of these pathogens outside of their amphibian hosts. We combine historic amphibian monitoring data with contemporary host- and environment-based pathogen detection data to obtain estimates of Bd occurrence independent of amphibian host distributions. We also evaluate differences in filter- and swab-based detection probability and assess inferential differences arising from using different decision criteria used to classify samples as positive or negative. Water filtration-based detection probabilities were lower than those from swabs but were > 10%, and swab-based detection probabilities varied seasonally, declining in the early fall. The decision criterion used to classify samples as positive or negative was important; using a more liberal criterion yielded higher estimates of Bd occurrence than when a conservative criterion was used. Different covariates were important when using the liberal or conservative criterion in modeling Bd detection. We found evidence of long-term Bd persistence for several years after an amphibian host species of conservation concern, the boreal toad (Anaxyrus boreas boreas), was last detected. Our work provides evidence of long-term Bd persistence in the ecosystem, and underscores the importance of environmental samples for understanding and mitigating disease-related threats to amphibian biodiversity.

Using environmental DNA for early detection of amphibian chytrid fungus Batrachochytrium dendrobatidis prior to a ranid die-off

Amphibian chytridiomycosis caused by the fungus Batrachochytrium dendrobatidis (Bd) is an emerging infectious disease that has been associated with mass mortality and extinctions of amphibians worldwide. Environmental DNA (eDNA) techniques have been used to detect the presence of Bd in the environment, but not to detect Bd prior to an amphibian die-off. We collected eDNA using filtered water samples from 13 lakes across Sequoia Kings Canyon National Park. Seven of those sites had populations of mountain yellow-legged frogs, an amphibian highly susceptible to chytridiomycosis, and 3 of those populations experienced a Bd related die-off 1 mo post-eDNA sampling. We detected Bd in eDNA samples that were collected 1 mo prior to the observed Bd-caused die-off at all 3 sites affected by Bd, and we did not detect Bd at the other sites where no die-off was observed. Our study indicates the potential to use eDNA techniques for early detection of Bd in the environment.

ednaoccupancy: An r package for multiscale occupancy modelling of environmental DNA data

In this article, we describe ednaoccupancy, an r package for fitting Bayesian, multiscale occupancy models. These models are appropriate for occupancy surveys that include three nested levels of sampling: primary sample units within a study area, secondary sample units collected from each primary unit and replicates of each secondary sample unit. This design is commonly used in occupancy surveys of environmental DNA (eDNA). ednaoccupancy allows users to specify and fit multiscale occupancy models with or without covariates, to estimate posterior summaries of occurrence and detection probabilities, and to compare different models using Bayesian model-selection criteria. We illustrate these features by analysing two published data sets: eDNA surveys of a fungal pathogen of amphibians and eDNA surveys of an endangered fish species.

Detection of amphibian chytrid fungus on waterfowl integument in natural settings

The chytrid fungus Batrachochytrium dendrobatidis (Bd), the causal agent of the amphibian disease chytridiomycosis, has spread at an alarming rate since its discovery. Bd was initially thought to only infect keratinizing epithelial cells in amphibians, a core component of amphibian skin. However, recent studies have detected Bd on the integument of non-amphibian hosts. We conducted a survey of 3 duck species (gadwalls, green-winged teals, and mallards) to determine whether Bd DNA could be found on their feet. Bd was found on the feet, by quantitative PCR, of individuals from all 3 species (5/11 gadwalls, 4/8 green-winged teals, and 13/21 mallards), though there were no significant differences in zoospore presence or load between species. We conclude that these waterfowl species may act as vector hosts for Bd, adding to the growing list of potential waterfowl vectors. Future studies are needed to determine whether Bd on waterfowl feet is viable and infectious to amphibian hosts.

Application of environmental DNA analysis for the detection of Opisthorchis viverrini DNA in water samples

Opisthorchiasis, which can lead to cholangiocarcinoma in cases of chronic infection, is a major public health problem in Southeast Asian countries. The trematode, Opisthorchis viverrini, is the causative agent of the disease. Accurate and rapid monitoring of O. viverrini is crucial for disease prevention and containment. Therefore, in this study we sought to develop a novel species-specific real-time PCR assay for detecting O. viverrini using environmental DNA (eDNA). The diagnostic sensitivity of the newly developed real-time PCR assay was similar to that of the traditional PCR assay for 50 fecal samples collected in Lao PDR (21 and 19 samples were positive by real-time PCR and traditional PCR, respectively). The efficacy of eDNA analysis and its applicability in the field were tested using a total of 94 environmental water samples collected from 44 sites in Savannakhet, Lao PDR during May and October 2015 and February 2016. O. viverrini eDNA was detected in five samples by real-time PCR, indicating the presence of the fluke in the area and the risk of infection for individuals consuming fish from these water sources. The application of eDNA analysis would facilitate the identification of O. viverrini endemic hotspots and contribute to the ecological control of opisthorchiasis, and this strategy can be applied to other eukaryotic water pathogens.

I Environmental DNA sampling is more sensitive than a traditional survey technique for detecting an aquatic invader

Effective management of alien species requires detecting populations in the early stages of invasion. Environmental DNA (eDNA) sampling can detect aquatic species at relatively low densities, but few studies have directly compared detection probabilities of eDNA sampling with those of traditional sampling methods. We compare the ability of a traditional sampling technique (bottle trapping) and eDNA to detect a recently established invader, the smooth newt Lissotriton vulgaris vulgaris, at seven field sites in Melbourne, Australia. Over a four-month period, per-trap detection probabilities ranged from 0.01 to 0.26 among sites where L. v. vulgaris was detected, whereas per-sample eDNA estimates were much higher (0.29-1.0). Detection probabilities of both methods varied temporally (across days and months), but temporal variation appeared to be uncorrelated between methods. Only estimates of spatial variation were strongly correlated across the two sampling techniques. Environmental variables (water depth, rainfall, ambient temperature) were not clearly correlated with detection probabilities estimated via trapping, whereas eDNA detection probabilities were negatively correlated with water depth, possibly reflecting higher eDNA concentrations at lower water levels. Our findings demonstrate that eDNA sampling can be an order of magnitude more sensitive than traditional methods, and illustrate that traditional- and eDNA-based surveys can provide independent information on species distributions when occupancy surveys are conducted over short timescales.

Evaluating environmental DNA-based quantification of ranavirus infection in wood frog populations

A variety of challenges arise when monitoring wildlife populations for disease. Sampling tissues can be invasive to hosts, and obtaining sufficient sample sizes can be expensive and time-consuming, particularly for rare species and when pathogen prevalence is low. Environmental DNA (eDNA)-based detection of pathogens is an alternative approach to surveillance for aquatic communities that circumvents many of these issues. Ranaviruses are emerging pathogens of ectothermic vertebrates linked to die-offs of amphibian populations. Detecting ranavirus infections is critical, but nonlethal methods have the above issues and are prone to false negatives. We report on the feasibility and effectiveness of eDNA-based ranavirus detection in the field. We compared ranavirus titres in eDNA samples collected from pond water to titres in wood frog (Lithobates sylvaticus; n = 5) tadpoles in sites dominated by this one species (n = 20 pond visits). We examined whether ranavirus DNA can be detected in eDNA from pond water when infections are present in the pond and if viral titres detected in eDNA samples correlate with the prevalence or intensity of ranavirus infections in tadpoles. With three 250 mL water samples, we were able to detect the virus in all visits with infected larvae (0.92 diagnostic sensitivity). Also, we found a strong relationship between the viral eDNA titres and titres in larval tissues. eDNA titres increased prior to observed die-offs and declined afterwards, and were two orders of magnitude higher in ponds with a die-off. Our results suggest that eDNA is useful for detecting ranavirus infections in wildlife and aquaculture.

Rapid Response to Evaluate the Presence of Amphibian Chytrid Fungus (Batrachochytrium dendrobatidis) and Ranavirus in Wild Amphibian Populations in Madagascar

We performed a rapid response investigation to evaluate the presence and distribution of amphibian pathogens in Madagascar following our identification of amphibian chytrid fungus (Batrachochytrium dendrobatidis, Bd) and ranavirus in commercially exported amphibians. This targeted risk-based field surveillance program was conducted from February to April 2014 encompassing 12 regions and 47 survey sites. We simultaneously collected amphibian and environmental samples to increase survey sensitivity and performed sampling both in wilderness areas and commercial amphibian trade facilities. Bd was not detected in any of 508 amphibian skin swabs or 68 water filter samples, suggesting pathogen prevalence was below 0.8%, with 95% confidence during our visit. Ranavirus was detected in 5 of 97 amphibians, including one adult Mantidactylus cowanii and three unidentified larvae from Ranomafana National Park, and one adult Mantidactylus mocquardi from Ankaratra. Ranavirus was also detected in water samples collected from two commercial amphibian export facilities. We also provide the first report of an amphibian mass-mortality event observed in wild amphibians in Madagascar. Although neither Bd nor ranavirus appeared widespread in Madagascar during this investigation, additional health surveys are required to disentangle potential seasonal variations in pathogen abundance and detectability from actual changes in pathogen distribution and rates of spread. Accordingly, our results should be conservatively interpreted until a comparable survey effort during winter months has been performed. It is imperative that biosecurity practices be immediately adopted to limit the unintentional increased spread of disease through the movement of contaminated equipment or direct disposal of contaminated material from wildlife trade facilities. The presence of potentially introduced strains of ranaviruses suggests that Madagascar's reptile species might also be threatened by disease. Standardized population monitoring of key amphibian and reptile species should be established with urgency to enable early detection of potential impacts of disease emergence in this global biodiversity hotspot.

Pathogenic chytrid fungus Batrachochytrium dendrobatidis, but not B. salamandrivorans, detected on eastern hellbenders

Recent worldwide declines and extinctions of amphibian populations have been attributed to chytridiomycosis, a disease caused by the pathogenic fungus Batrachochytrium dendrobatidis (Bd). Until recently, Bd was thought to be the only Batrachochytrium species that infects amphibians; however a newly described species, Batrachochytrium salamandrivorans (Bs), is linked to die-offs in European fire salamanders (Salamandra salamandra). Little is known about the distribution, host range, or origin of Bs. In this study, we surveyed populations of an aquatic salamander that is declining in the United States, the eastern hellbender (Cryptobranchus alleganiensis alleganiensis), for the presence of Bs and Bd. Skin swabs were collected from a total of 91 individuals in New York, Pennsylvania, Ohio, and Virginia, and tested for both pathogens using duplex qPCR. Bs was not detected in any samples, suggesting it was not present in these hellbender populations (0% prevalence, 95% confidence intervals of 0.0–0.04). Bd was found on 22 hellbenders (24% prevalence, 95% confidence intervals of 0.16 ≤ 0.24 ≤ 0.34), representing all four states. All positive samples had low loads of Bd zoospores (12.7 ± 4.9 S.E.M. genome equivalents) compared to other Bd susceptible species. More research is needed to determine the impact of Batrachochytrium infection on hellbender fitness and population viability. In particular, understanding how hellbenders limit Bd infection intensity in an aquatic environment may yield important insights for amphibian conservation. This study is among the first to evaluate the distribution of Bs in the United States, and is consistent with another, which failed to detect Bs in the U.S. Knowledge about the distribution, host-range, and origin of Bs may help control the spread of this pathogen, especially to regions of high salamander diversity, such as the eastern United States.

Swabbing often fails to detect amphibian Chytridiomycosis under conditions of low infection load

The pathogenic chytrid fungus, Batrachochytrium dendrobatidis (denoted Bd), causes large-scale epizootics in naïve amphibian populations. Intervention strategies to rapidly respond to Bd incursions require sensitive and accurate diagnostic methods. Chytridiomycosis usually is assessed by quantitative polymerase chain reaction (qPCR) amplification of amphibian skin swabs. Results based on this method, however, sometimes yield inconsistent results on infection status and inaccurate scores of infection intensity. In Asia and other regions where amphibians typically bear low Bd loads, swab results are least reliable. We developed a Bd-sampling method that collects zoospores released by infected subjects into an aquatic medium. Bd DNA is extracted by filters and amplified by nested PCR. Using laboratory colonies and field populations of Bombina orientalis, we compare results with those obtained on the same subjects by qPCR of DNA extracted from swabs. Many subjects, despite being diagnosed as Bd-negative by conventional methods, released Bd zoospores into collection containers and thus must be considered infected. Infection loads determined from filtered water were at least 1000 times higher than those estimated from swabs. Subjects significantly varied in infection load, as they intermittently released zoospores, over a 5-day period. Thus, the method might be used to compare the infectivity of individuals and study the periodicity of zoospore release. Sampling methods based on water filtration can dramatically increase the capacity to accurately diagnose chytridiomycosis and contribute to a better understanding of the interactions between Bd and its hosts.

Persistence of an amphibian ranavirus in aquatic communities

Host-parasite dynamics can be strongly influenced by interactions with other members of the biotic community, particularly when the parasite spends some fraction of its life in the environment unprotected by its host. Ranaviruses-often lethal viruses of cold-blooded vertebrate hosts transmitted by direct contact, and via water and fomites-offer an interesting system for understanding these community influences. Previous laboratory studies have shown that ranaviruses can persist for anywhere from days to years, depending on the conditions, with much longer times under sterile conditions. To address the role of the biotic community and particulate matter on ranavirus persistence, we experimentally inoculated filter-sterilized, UV-treated, and unmanipulated pond water with a Frog virus 3 (FV3)-like Ranavirus and took samples over 78 d, quantifying viral titers with real-time quantitative PCR and plaque assays. Viral counts dropped quickly in all treatments, by an order of magnitude in under a day in unmanipulated pond water and in 8 d in filter-sterilized pond water. In a second experiment, we measured viral titers over 24 h in virus-spiked spring water with Daphnia pulex. Presence of D. pulex reduced the concentration of infectious ranavirus, but not viral DNA, by an order of magnitude in 24 h. D. pulex themselves did not accumulate the virus. We conclude that both microbial and zooplanktonic communities can play an important role in ranavirus epidemiology, rapidly inactivating ranavirus in the water and thereby minimizing environmental transmission. We suspect that interactions with the biotic community will be important for most pathogens with environmental resting or transmission stages.

Heterogeneous occupancy and density estimates of the pathogenic fungus Batrachochytrium dendrobatidis in waters of North America

Biodiversity losses are occurring worldwide due to a combination of stressors. For example, by one estimate, 40% of amphibian species are vulnerable to extinction, and disease is one threat to amphibian populations. The emerging infectious disease chytridiomycosis, caused by the aquatic fungus Batrachochytrium dendrobatidis (Bd), is a contributor to amphibian declines worldwide. Bd research has focused on the dynamics of the pathogen in its amphibian hosts, with little emphasis on investigating the dynamics of free-living Bd. Therefore, we investigated patterns of Bd occupancy and density in amphibian habitats using occupancy models, powerful tools for estimating site occupancy and detection probability. Occupancy models have been used to investigate diseases where the focus was on pathogen occurrence in the host. We applied occupancy models to investigate free-living Bd in North American surface waters to determine Bd seasonality, relationships between Bd site occupancy and habitat attributes, and probability of detection from water samples as a function of the number of samples, sample volume, and water quality. We also report on the temporal patterns of Bd density from a 4-year case study of a Bd-positive wetland. We provide evidence that Bd occurs in the environment year-round. Bd exhibited temporal and spatial heterogeneity in density, but did not exhibit seasonality in occupancy. Bd was detected in all months, typically at less than 100 zoospores L(-1). The highest density observed was ∼3 million zoospores L(-1). We detected Bd in 47% of sites sampled, but estimated that Bd occupied 61% of sites, highlighting the importance of accounting for imperfect detection. When Bd was present, there was a 95% chance of detecting it with four samples of 600 ml of water or five samples of 60 mL. Our findings provide important baseline information to advance the study of Bd disease ecology, and advance our understanding of amphibian exposure to free-living Bd in aquatic habitats over time.

Susceptibility to the amphibian chytrid fungus varies with ontogeny in the direct-developing frog, Eleutherodactylus coqui

Age-related differences in susceptibility to infectious disease are known from a wide variety of plant and animal taxonomic groups. For example, the immature immune systems of young vertebrates, along with limited prior exposure to pathogens and behavioral factors, can place juveniles at greater risk of acquiring and succumbing to a pathogen. We studied the ontogenetic susceptibility of terrestrial direct-developing frogs (Eleutherodactylus coqui) to the fungal pathogen, Batrachochytrium dendrobatidis (Bd), which is responsible for the decline of amphibian species worldwide. By exposing juvenile and adult frogs to the same dose and strain of Bd, we uncovered ontogenetic differences in susceptibility. Froglets exposed to the pathogen had significantly lower survival rates compared with control froglets, while adult frogs largely cleared infection and had survival rates indistinguishable from control frogs, even when exposed to a much higher dose of Bd. The high disease-induced mortality rate of juveniles may explain ongoing population declines in eastern Puerto Rico, where Bd is endemic and juveniles experience higher prevalence and infection intensity compared to adults. Our results have important implications for understanding and modeling the decline, possibly to extinction, of amphibian populations and species.

A fungal pathogen of amphibians, Batrachochytrium dendrobatidis, attenuates in pathogenicity with in vitro passages

Laboratory investigations into the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd), have accelerated recently, given the pathogen's role in causing the global decline and extinction of amphibians. Studies in which host animals were exposed to Bd have largely assumed that lab-maintained pathogen cultures retained the infective and pathogenic properties of wild isolates. Attenuated pathogenicity is common in artificially maintained cultures of other pathogenic fungi, but to date, it is unknown whether, and to what degree, Bd might change in culture. We compared zoospore production over time in two samples of a single Bd isolate having different passage histories: one maintained in artificial media for more than six years (JEL427-P39), and one recently thawed from cryopreserved stock (JEL427-P9). In a common garden experiment, we then exposed two different amphibian species, Eleutherodactylus coqui and Atelopus zeteki, to both cultures to test whether Bd attenuates in pathogenicity with in vitro passages. The culture with the shorter passage history, JEL427-P9, had significantly greater zoospore densities over time compared to JEL427-P39. This difference in zoospore production was associated with a difference in pathogenicity for a susceptible amphibian species, indicating that fecundity may be an important virulence factor for Bd. In the 130-day experiment, Atelopus zeteki frogs exposed to the JEL427-P9 culture experienced higher average infection intensity and 100% mortality, compared with 60% mortality for frogs exposed to JEL427-P39. This effect was not observed with Eleutherodactylus coqui, which was able to clear infection. We hypothesize that the differences in phenotypic performance observed with Atelopus zeteki are rooted in changes of the Bd genome. Future investigations enabled by this study will focus on the underlying mechanisms of Bd pathogenicity.

First survey for the amphibian chytrid fungus Batrachochytrium dendrobatidis in Connecticut (USA) finds widespread prevalence

The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) is an emerging infectious fungal pathogen of amphibians and is linked to global population declines. Until now, there has only been 1 survey for the fungus in the northeastern USA, which focused primarily on northern New England. We tested for Bd in a large number of samples (916 individuals from 116 sites) collected throughout the state of Connecticut, representing 18 native amphibian species. In addition, 239 preserved wood frog Lithobates sylvaticus tadpoles from throughout the state were screened for the fungus. Bd presence was assessed in both the fresh field swabs and the preserved samples using a sensitive quantitative PCR assay. Our contemporary survey found widespread Bd prevalence throughout Connecticut, occurring in 14 species and in 28% of all sampled animals. No preserved L. sylvaticus specimens tested positive for the fungus. Two common species, bullfrogs R. catesbeiana and green frogs R. clamitans had particularly high infection rates (0.21-0.39 and 0.33-0.42, respectively), and given their wide distribution throughout the state, we suggest they may serve as sentinels for Bd occurrence in this region. Further analyses found that several other factors increase the likelihood of infection, including life stage, host sex, and host family. Within sites, ponds with ranids, especially green frogs, increased the likelihood of Bd prevalence. By studying Bd in populations not facing mass declines, the results from this study are an important contribution to our understanding of how some amphibian species and populations remain infected yet exhibit no signs of chytridiomycosis even when Bd is widely distributed.

Potential influence of plant chemicals on infectivity of Batrachochytrium dendrobatidis

We explored whether extracts of trees frequently found associated with amphibian habitats in Australia and Arizona, USA, may be inhibitory to the fungal pathogen Batrachochytrium dendrobatidis (Bd), which has been associated with global amphibian declines. We used salamanders Ambystoma tigrinum as the model system. Salamanders acquired significantly lower loads of Bd when exposed on leaves and extracts from the river red gum Eucalyptus camaldulensis, and loads were also low in some animals exposed on extracts of 2 oak species, Quercus emoryi and Q. turbinella. Some previously infected salamanders had their pathogen loads reduced, and some were fully cured, by placing them in leaf extracts, although some animals also self cured when housed in water alone. A significant number of animals cured of Bd infections 6 mo earlier were found to be resistant to reinfection. These results suggest that plants associated with amphibian habitats should be taken into consideration when explaining the prevalence of Bd in these habitats and that some amphibians may acquire resistance to the fungus if previously cured.