Multi-year dynamics of ranavirus, chytridiomycosis, and co-infections in a temperate host assemblage of amphibians

Relationship between two pathogens in an amphibian community that experienced mass mortalities

Because host species tend to harbor multiple parasitic species, coinfection in a host is common. The chytrid fungus Batrachochytrium dendrobatidis (Bd) and the viruses in the genus Ranavirus (Rv) are responsible for the decline of amphibians worldwide. Despite wide geographical co-occurrence and the serious conservation problem that coinfection with these pathogens could represent, little is known about their possible synergistic interactions and effects in a host community. We investigated the occurrence and associations between these two pathogens in an amphibian community after Rv-driven disease outbreaks were detected in four populations of the Iberian ribbed newt (Pleurodeles waltl) in northwestern Spain. We collected tissue samples from amphibians and fish and estimated Bd and Rv infection loads by qPCR. A few months after the most recent mass mortality event, Rv infection parameters at the affected sites decreased significantly or were lower than such registered at the sites where no outbreaks were recorded. Both pathogens were simultaneously present in almost all sites, but coinfection in a single host was rare. Our findings suggest that the co-occurrence of Bd and Rv does not predict adverse outcomes (e.g., enhanced susceptibility of hosts to one pathogen due to the presence or infection intensity of the other) following an outbreak. Other variables (such as species identity or site) were more important than infection with a pathogen in predicting the infection status and severity of infection with the other pathogen. Our results highlight the importance of host-specific and environmental characteristics in the dynamics of infections, coinfection patterns, and their impacts.

The Binding, Infection, and Promoted Growth of Batrachochytrium dendrobatidis by the Ranavirus FV3

Increasing reports suggest the occurrence of co-infection between Ranaviruses such as Frog Virus 3 (FV3) and the chytrid fungus Batrachochytrium dendrobatidis (Bd) in various amphibian species. However, the potential direct interaction of these two pathogens has not been examined to date. In this study, we investigated whether FV3 can interact with Bd in vitro using qPCR, conventional microscopy, and immunofluorescent microscopy. Our results reveal the unexpected ability of FV3 to bind, promote aggregation, productively infect, and significantly increase Bd growth in vitro. To extend these results in vivo, we assessed the impact of FV3 on Xenopus tropicalis frogs previously infected with Bd. Consistent with in vitro results, FV3 exposure to previously Bd-infected X. tropicalis significantly increased Bd loads and decreased the host's survival.

Ontogeny drives shifts in skin bacterial communities in facultatively paedomorphic salamanders

Microbiomes are major determinants of host growth, development and survival. In amphibians, host-associated bacteria in the skin can inhibit pathogen infection, but many processes can influence the structure and composition of the community. Here we quantified the shifts in skin-associated bacteria across developmental stages in the striped newt (Notophthalmus perstriatus), a threatened salamander species with a complex life history and vulnerable to infection by the amphibian chytrid fungus Batrachochytrium dendrobatidis and ranavirus. Our analyses show that pre-metamorphic larval and paedomorphic stages share similar bacterial compositions, and that the changes in the microbiome coincided with physiological restructuring during metamorphosis. Newts undergoing metamorphosis exhibited microbiome compositions that were intermediate between paedomorphic and post-metamorphic stages, further supporting the idea that metamorphosis is a major driver of host-associated microbes in amphibians. We did not find support for infection-related disruption of the microbiome, though infection replicates were small for each respective life stage.

Widespread amphibian Perkinsea infections associated with Ranidae hosts, cooler months and Ranavirus co-infection

Amphibians suffer from large-scale population declines globally, and emerging infectious diseases contribute heavily to these declines. Amphibian Perkinsea (Pr) is a worldwide anuran pathogen associated with mass mortality events, yet little is known about its epidemiological patterns, especially in comparison to the body of literature on amphibian chytridiomycosis and ranavirosis. Here, we establish Pr infection patterns in natural anuran populations and identify important covariates including climate, host attributes and co-infection with Ranavirus (Rv). We used quantitative (q)PCR to determine the presence and intensity of Pr and Rv across 1234 individuals sampled throughout central Florida in 2017-2019. We then implemented random forest ensemble learning models to predict infection with both pathogens based on physiological and environmental characteristics. Perkinsea infected 32% of all sampled anurans, and Pr prevalence was significantly elevated in Ranidae frogs, cooler months, metamorphosed individuals and frogs co-infected with Rv, while Pr intensity was significantly higher in ranid frogs and individuals collected dead. Ranavirus prevalence was 17% overall and was significantly higher in Ranidae frogs, metamorphosed individuals, locations with higher average temperatures, and individuals co-infected with Pr. Perkinsea prevalence was significantly higher than Rv prevalence across months, regions, life stages and species. Among locations, Pr prevalence was negatively associated with crayfish prevalence and positively associated with relative abundance of microhylids, but Rv prevalence did not associate with any tested co-variates. Co-infections were significantly more common than single infections for both pathogens, and we propose that Pr infections may propel Rv infections because seasonal Rv infection peaks followed Pr infection peaks and random forest models found Pr intensity was a leading factor explaining Rv infections. Our study elucidates epidemiological patterns of Pr in Florida and suggests that Pr may be under-recognized as a cause of anuran declines, especially in the context of pathogen co-infection.

Factors at multiple scales drive parasite community structure

Understanding how ecological communities are assembled remains a key goal of ecosystem ecology. Because communities are hierarchical, factors acting at multiple scales can contribute to patterns of community structure. Parasites provide a natural system to explore this idea, as they exist as discrete communities within host individuals, which are themselves part of a community and metacommunity. We aimed to understand the relative contribution of multi-scale drivers in parasite community assembly and assess how patterns at one level may mask those occurring at another. Specifically, we wanted to disentangle patterns caused by passive sampling from those determined by ecological drivers, and how these vary with scale. We applied a Markov Random Fields model and assessed measures of β-diversity and nestedness for 420 replicate parasite infracommunities (parasite assemblages in host individuals) across two freshwater mussel host species, three sites and two time periods, comparing our results to simulations from four different ecologically relevant null models. We showed that β-diversity between sites (explaining 25% of variation in parasite distribution) and host species (41%) is greater than expected, and β-diversity between individual hosts is smaller than expected, even after accounting for parasite prevalence and characteristics of host individuals. Furthermore, parasite communities were significantly less nested than expected once parasite prevalence and host characteristics were both accounted for, but more nested than expected otherwise, suggesting a degree of modularity at the within-host level that is masked if underlying host and parasite characteristics are not taken into account. The Markov Random Fields model provided evidence for possible competitive within-host parasite interactions, providing a mechanism for the observed infracommunity modularity. An integrative approach that examines factors at multiple scales is necessary to understand the composition of ecological communities. Furthermore, patterns at one level can alter the interpretation of ecologically important drivers at another if variation at higher scales is not accounted for.

Infection with Batrachochytrium dendrobatidis reduces salamander capacity to mount a cell-mediated immune response

The vertebrate immune system is a costly defense system that is responsible for preventing and eliminating parasites and pathogens. Theory predicts that hosts experience tradeoffs associated with immune deployment and other physiological functions. Although empirical evidence for immune-physiology tradeoffs are well documented in the literature, fewer studies have examined tradeoffs within the immune system in wild vertebrates. We explored the topic of concomitant immune challenges in amphibians by exposing salamanders (Plethodon cinereus) to a fungal pathogen Batrachochytrium dendrobatidis (hereafter "Bd") and then to phytohemagglutinin (hereafter "PHA"). We measured Bd infection using quantitative PCR and used measurements of the tail thickness at the PHA injection site as an estimate of skin swelling. We tested whether Bd reduced the salamander's capacity to mount an immune response towards PHA or whether Bd would stimulate immune activity and thereby increase the response towards PHA. Salamanders that were infected with Bd had a reduced skin-swelling when injected with PHA compared to noninfected salamanders, a result that is consistent with the hypothesis that Bd-infected salamanders have lower immunocompetence than noninfected salamanders. We also found that PHA-induced swelling response was negatively associated with Bd infection abundance (i.e., the infection burden of all exposed salamanders, including those that were exposed but not infected), indicating that salamanders with a higher infection abundance had the lowest swelling response to PHA. Our results suggest that individuals of P. cinereus might experience an energetic tradeoff between successfully fighting off Bd and mounting an immune response towards PHA.

Host-multiparasite interactions in amphibians: a review

Parasites, including viruses, bacteria, fungi, protists, helminths, and arthropods, are ubiquitous in the animal kingdom. Consequently, hosts are frequently infected with more than one parasite species simultaneously. The assessment of such co-infections is of fundamental importance for disease ecology, but relevant studies involving non-domesticated animals have remained scarce. Many amphibians are in decline, and they generally have a highly diverse parasitic fauna. Here we review the literature reporting on field surveys, veterinary case studies, and laboratory experiments on co-infections in amphibians, and we summarize what is known about within-host interactions among parasites, which environmental and intrinsic factors influence the outcomes of these interactions, and what effects co-infections have on hosts. The available literature is piecemeal, and patterns are highly diverse, so that identifying general trends that would fit most host–multiparasite systems in amphibians is difficult. Several examples of additive, antagonistic, neutral, and synergistic effects among different parasites are known, but whether members of some higher taxa usually outcompete and override the effects of others remains unclear. The arrival order of different parasites and the time lag between exposures appear in many cases to fundamentally shape competition and disease progression. The first parasite to arrive can gain a marked reproductive advantage or induce cross-reaction immunity, but by disrupting the skin and associated defences (i.e., skin secretions, skin microbiome) and by immunosuppression, it can also pave the way for subsequent infections. Although there are exceptions, detrimental effects to the host are generally aggravated with increasing numbers of co-infecting parasite species. Finally, because amphibians are ectothermic animals, temperature appears to be the most critical environmental factor that affects co-infections, partly via its influence on amphibian immune function, partly due to its direct effect on the survival and growth of parasites. Besides their importance for our understanding of ecological patterns and processes, detailed knowledge about co-infections is also crucial for the design and implementation of effective wildlife disease management, so that studies concentrating on the identified gaps in our understanding represent rewarding research avenues.

The application of community ecology theory to co-infections in wildlife hosts

Priority effect theory, a foundational concept from community ecology, states that the order and timing of species arrival during species assembly can affect species composition. Although this theory has been applied to co-infecting parasite species, it has almost always been with a single time lag between co-infecting parasites. Thus, how the timing of parasite species arrival affects co-infections and disease remains poorly understood. To address this gap in the literature, we exposed postmetamorphic Cuban tree frogs (Osteopilus septentrionalis) to Ranavirus, the fungus Batrachochytrium dendrobatidis (Bd), a nematode Aplectana hamatospicula, or pairs of these parasites either simultaneously or sequentially at a range of time lags and quantified load of the secondary parasite and host growth, survival, and parasite tolerance. Prior exposure to Bd or A. hamatospicula significantly increased viral loads relative to hosts singly infected with Ranavirus, whereas A. hamatospicula loads in hosts were higher when coexposed to Bd than when coexposed to Ranavirus. There was a significant positive relationship between time since Ranavirus infection and Bd load, and prior exposure to A. hamatospicula decreased Bd loads compared to simultaneous co-infection with these parasites. Infections with Bd and Ranavirus either singly or in co-infections decreased host growth and survival. This research reveals that time lags between co-infections can affect parasite loads, in line with priority effects theory. As co-infections in the field are unlikely to be simultaneous, an understanding of when co-infections are impacted by time lags between parasite exposures may play a major role in controlling problematic co-infections.

Single infection with Batrachochytrium dendrobatidis or Ranavirus does not increase probability of co-infection in a montane community of amphibians

Understanding the occurrence and consequence of co-infections can be useful in designing disease management interventions. Amphibians are the most highly threatened vertebrates, and emerging pathogens are a serious threat to their conservation. The amphibian chytrid fungus and the viruses of the Ranavirus genus are already widely distributed, causing disease outbreaks and population declines worldwide. However, we lack information about the occurrence and consequences of coinfection with these pathogens across age-classes of amphibian hosts. Here, we analyze the occurrence of infection of the amphibian chytrid fungus and ranaviruses during one season in two susceptible amphibian species at two different locations at which outbreaks have occurred. We found that the co-occurrence of both pathogens in a particular host is not common except in highly susceptible life-stages, and that single infections are the most common situation. Moreover, we found that the occurrence of one pathogen in a particular host did not predict the occurrence of the other. We attribute these results to the niches in which both pathogens proliferate in amphibian hosts.

Evolutionary principles guiding amphibian conservation

The Anthropocene has witnessed catastrophic amphibian declines across the globe. A multitude of new, primarily human-induced drivers of decline may lead to extinction, but can also push species onto novel evolutionary trajectories. If these are recognized by amphibian biologists, they can be engaged in conservation actions. Here, we summarize how principles stemming from evolutionary concepts have been applied for conservation purposes, and address emerging ideas at the vanguard of amphibian conservation science. In particular, we examine the consequences of increased drift and inbreeding in small populations and their implications for practical conservation. We then review studies of connectivity between populations at the landscape level, which have emphasized the limiting influence of anthropogenic structures and degraded habitat on genetic cohesion. The rapid pace of environmental changes leads to the central question of whether amphibian populations can cope either by adapting to new conditions or by shifting their ranges. We gloomily conclude that extinction seems far more likely than adaptation or range shifts for most species. That said, conservation strategies employing evolutionary principles, such as selective breeding, introduction of adaptive variants through translocations, ecosystem interventions aimed at decreasing phenotype-environment mismatch, or genetic engineering, may effectively counter amphibian decline in some areas or for some species. The spread of invasive species and infectious diseases has often had disastrous consequences, but has also provided some premier examples of rapid evolution with conservation implications. Much can be done in terms of setting aside valuable amphibian habitat that should encompass both natural and agricultural areas, as well as designing protected areas to maximize the phylogenetic and functional diversity of the amphibian community. We conclude that an explicit consideration and application of evolutionary principles, although certainly not a silver bullet, should increase effectiveness of amphibian conservation in both the short and long term.

Chiggers (Acariformes: Trombiculoidea) do not increase rates of infection by Batrachochytrium dendrobatidis fungus in the endemic Dwarf Mexican Treefrog Tlalocohyla smithii (Anura: Hylidae)

Amphibian populations are globally declining at an alarming rate, and infectious diseases are among the main causes of their decline. Two micro-parasites, the fungus Batrachochytrium dendrobatidis (Bd) and the virus Ranavirus (RV) have caused mass mortality of amphibians and population declines. Other, less understood epizootics are caused by macro-parasites, such as Trombiculoidea chiggers. Infection with chiggers can affect frog behavior and survival. Furthermore, synergistic effects of co-infection with both macro and micro-parasites may lead to higher morbidity. To better understand these potential synergies, we investigated the presence and co-infection by chiggers, Bd and RV in the endemic frog Tlalocohyla smithii (T. smithii). Co-infection of Bd, RV, and/or chiggers is expected in habitats that are suitable for their co-occurrence; and if infection with one parasite facilitates infection with the others. On the other hand, co-infection could decrease if these parasites were to differ in their micro-environmental requirements (i.e. niche apportionment). A total of 116 frogs of T. smithii were studied during 2014 and 2016 in three streams within the Chamela-Cuixmala Biosphere Reserve in Jalisco, Mexico. Our results show that 31% of the frogs were infected with Trombiculoidea chiggers (Hannemania sp. and Eutrombicula alfreddugesi); Hannemania prevalence increased with air temperature and decreased in sites with high canopies and with water pH values above 8.5 and below 6.7. Bd prevalence was 2.6%, RV prevalence was 0%, and none of the frogs infected with chiggers were co-infected with Bd. Together, this study suggests that chiggers do not facilitate infection with Bd, as these are apportioned in different micro-habitats. Nevertheless, the statistical power to assure this is low. We recommend further epidemiological monitoring of multiple parasites in different geographical locations in order to provide insight on the true hazards, risks and conservation options for amphibian populations.

Outbreaks of an Emerging Viral Disease Covary With Differences in the Composition of the Skin Microbiome of a Wild United Kingdom Amphibian

There is growing appreciation of the important role of commensal microbes in ensuring the normal function and health of their hosts, including determining how hosts respond to pathogens. A range of infectious diseases are threatening amphibians worldwide, and evidence is accumulating that the host-associated bacteria that comprise the microbiome may be key in mediating interactions between amphibian hosts and infectious pathogens. We used 16S rRNA amplicon sequencing to quantify the skin microbial community structure of over 200 individual wild adult European common frogs (Rana temporaria), from ten populations with contrasting history of the lethal disease ranavirosis, caused by emerging viral pathogens belonging to the genus Ranavirus. All populations had similar species richness irrespective of disease history, but populations that have experienced historical outbreaks of ranavirosis have a distinct skin microbiome structure (beta diversity) when compared to sites where no outbreaks of the disease have occurred. At the individual level, neither age, body length, nor sex of the frog could predict the structure of the skin microbiota. Our data potentially support the hypothesis that variation among individuals in skin microbiome structure drive differences in susceptibility to infection and lethal outbreaks of disease. More generally, our results suggest that population-level processes are more important for driving differences in microbiome structure than variation among individuals within populations in key life history traits such as age and body size.