Skin microbiome disturbance linked to drought-associated amphibian disease.

The onset of global climate change has led to abnormal rainfall patterns, disrupting associations between wildlife and their symbiotic microorganisms. We monitored a population of pumpkin toadlets and their skin bacteria in the Brazilian Atlantic Forest during a drought. Given the recognized ability of some amphibian skin bacteria to inhibit the widespread fungal pathogen Batrachochytrium dendrobatidis (Bd), we investigated links between skin microbiome health, susceptibility to Bd and host mortality during a die-off event. We found that rainfall deficit was an indirect predictor of Bd loads through microbiome disruption, while its direct effect on Bd was weak. The microbiome was characterized by fewer putative Bd-inhibitory bacteria following the drought, which points to a one-month lagged effect of drought on the microbiome that may have increased toadlet susceptibility to Bd. Our study underscores the capacity of rainfall variability to disturb complex host-microbiome interactions and alter wildlife disease dynamics.

Host immune responses to enzootic and invasive pathogen lineages vary in magnitude, timing, and efficacy.

Infectious diseases of wildlife continue to pose a threat to biodiversity worldwide, yet pathogens are far from uniform in virulence or host disease outcome. Within the same pathogen species, virulence can vary considerably depending on strain or lineage, in turn eliciting variable host responses. One pathogen that has caused extensive biodiversity loss is the amphibian-killing fungus, Batrachochytrium dendrobatidis (Bd), which is comprised of a globally widespread hypervirulent lineage (Bd-GPL), and multiple geographically restricted, enzootic lineages. Whereas host immunogenomic responses to Bd-GPL have been characterized in a number of amphibian species, immunogenomic responses to geographically restricted, enzootic Bd lineages are less clear. To examine lineage-specific host immune responses to Bd, we exposed a species of pumpkin toadlet, Brachycephalus pitanga, which is endemic to Brazil's Southern Atlantic Forest, to either the Bd-GPL or the enzootic Bd-Asia-2/Brazil (hereafter Bd-Brazil) lineage. Using temporal samples from early, mid, and late infection stages, we quantified functional immunogenomic responses over the course of infection using differential gene expression tests and coexpression network analyses. Host immune responses varied significantly with Bd lineage. Relative to controls, toadlet responses to Bd-Brazil were weak at early infection (25 genes significantly differentially expressed), peaked by mid-stage infection (414 genes), and were nearly fully resolved by late-stage infection (nine genes). In contrast, responses to Bd-GPL were magnified and delayed; toadlets significantly differentially expressed 111 genes early, 87 genes at mid-stage infection, and 726 genes by late-stage infection relative to controls. Given that infection intensity did not vary between mid- and late-stage disease in either Bd-Brazil or Bd-GPL treatments, this suggests that pumpkin toadlets may be at least partially tolerant to the enzootic Bd-Brazil lineage. In contrast, late-stage immune activation against Bd-GPL was consistent with immune dysregulation previously observed in other species. Our results demonstrate that both the timing of immune response and the particular immune pathways activated are specific to Bd lineage. Within regions where multiple Bd lineages co-occur, and given continued global Bd movement, these differential host responses may influence not only individual disease outcome, but transmission dynamics at the population and community levels.

Habitat fragmentation in the Brazilian Atlantic Forest is associated with erosion of frog immunogenetic diversity and increased fungal infections.

Habitat fragmentation and infectious diseases threaten wildlife globally, but the interactions of these threats are poorly understood. For instance, while habitat fragmentation can impact genetic diversity at neutral loci, the impacts on disease-relevant loci are less well-studied. We examined the effects of habitat fragmentation in Brazil's Atlantic Forest on amphibian genetic diversity at an immune locus related to antigen presentation and detection (MHC IIB Exon 2). We used a custom high-throughput assay to sequence a fragment of MHC IIB and quantified Batrachochytrium dendrobatidis (Bd) infections in six frog species in two Atlantic Forest regions. Habitat fragmentation was associated with genetic erosion at MHC IIB Exon 2. This erosion was most severe in forest specialists. Significant Bd infections were detected only in one Atlantic Forest region, potentially due to relatively higher elevation. In this region, forest specialists showed an increase in both Bd prevalence and infection loads in fragmented habitats. Reduced population-level MHC IIB diversity was associated with increased Bd infection risk. On the individual level, MHC IIB heterozygotes exhibited a trend toward reduced Bd infection risk, although this was marginally non-significant. Our results suggest that habitat fragmentation increases Bd infection susceptibility in amphibians, mediated at least in part through erosion of immunogenetic diversity. Our findings have implications for management of fragmented populations in the face of emerging infectious diseases.

Habitat Disturbance Linked with Host Microbiome Dispersion and Bd Dynamics in Temperate Amphibians.

Anthropogenic habitat disturbances can dramatically alter ecological community interactions, including host-pathogen dynamics. Recent work has highlighted the potential for habitat disturbances to alter host-associated microbial communities, but the associations between anthropogenic disturbance, host microbiomes, and pathogens are unresolved. Amphibian skin microbial communities are particularly responsive to factors like temperature, physiochemistry, pathogen infection, and environmental microbial reservoirs. Through a field survey on wild populations of Acris crepitans (Hylidae) and Lithobates catesbeianus (Ranidae), we assessed the effects of habitat disturbance and connectivity on environmental bacterial reservoirs, Batrachochytrium dendrobatidis (Bd) infection, and skin microbiome composition. We found higher measures of microbiome dispersion (a measure of community variability) in A. crepitans from more disturbed ponds, supporting the hypothesis that disturbance increases stochasticity in biological communities. We also found that habitat disturbance limited microbiome similarity between locations for both species, suggesting greater isolation of bacterial assemblages in more disturbed areas. Higher disturbance was associated with lower Bd prevalence for A. crepitans, which could signify suboptimal microclimates for Bd in disturbed habitats. Combined, our findings show that reduced microbiome stability stemming from habitat disturbance could compromise population health, even in the absence of pathogenic infection.

Presence of invasive American bullfrogs may reduce infectious disease in a native frog species.

Amphibians breeding in aquatic environments may encounter a myriad of threats during their life cycle. One species known to prey on native amphibians in aquatic habitats is the invasive North American bullfrog Lithobates catesbeianus, which, besides being a voracious predator and competitor, often acts as a pathogen carrier and disease superspreader because it tolerates high infection loads of the frog-killing fungus Batrachochytrium dendrobatidis (Bd). Here, we hypothesized that the presence of the bullfrogs in microcosms should either (1) decrease Bd disease severity in native frog species by discouraging them from using the aquatic environment, or (2) increase the mortality of the native species. We tested these 2 mutually exclusive hypotheses by co-housing the snouted treefrog Scinax x-signatus (native to our study area) with L. catesbeianus in the laboratory, exposing them to Bd, and using qPCR analysis to quantify the resulting Bd infection loads in the native frogs. Our experiment had the following replicated treatments: (1) native-only treatment (3 individuals of S. x-signatus), (2) native-predominant treatment (2 S. x-signatus + 1 L. catesbeianus), and (3) exotic-predominant treatment (1 S. x-signatus + 2 L. catesbeianus). We found that Bd infection loads in the native S. x-signatus were highest in the native-only treatment, and lowest in the exotic-predominant treatment, indicating that bullfrogs may discourage native frogs from occupying the aquatic habitat, thus reducing encounter rates between native frogs and the waterborne pathogen. This effect could be driven by the bullfrogs' predatory behavior and their high philopatry to aquatic habitats. Our results highlight that predation risk adds to the complexity of host-species interactions in Bd epidemiology.

Spatiotemporal adaptive evolution of an MHC immune gene in a frog-fungus disease system.

Genetic diversity of major histocompatibility complex (MHC) genes is linked to reduced pathogen susceptibility in amphibians, but few studies also examine broad spatial and temporal patterns of MHC and neutral genetic diversity. Here, we characterized range-wide MHC diversity in the Northern leopard frog, Rana pipiens, a species found throughout North America that is experiencing disease-related declines. We used previously sequenced neutral markers (mitochondrial DNA and microsatellites), sequenced an expressed MHC class IIß gene fragment, and measured infection prevalence and intensity of the global fungal pathogen Batrachochytrium dendrobatidis (Bd) across 14 populations. Four populations were sampled across two decades, enabling temporal comparisons of selection and demography. We recovered 37 unique MHC alleles, including 17 that were shared across populations. Phylogenetic and population genetic patterns between MHC and neutral markers were incongruent, and five MHC codon positions associated with peptide binding were under positive selection. MHC heterozygosity, but not neutral marker heterozygosity, was a significant factor explaining spatial patterns of Bd prevalence, whereas only environmental variables predicted Bd intensity. MHC allelic richness (AR) decreased significantly over time but microsatellite-based AR did not, highlighting a loss of functional immunogenetic diversity that may be associated with Bd selective pressures. MHC supertype 4 was significantly associated with an elevated risk of Bd infection, whereas one supertype 2 allele was associated with a nearly significant reduced risk of Bd. Taken together, these results provide evidence that positive selection contributes to MHC class IIß evolution in R. pipiens and suggest that functional MHC differences across populations may contribute to disease adaptation.

Widespread Pig Farming Practice Linked to Shifts in Skin Microbiomes and Disease in Pond-Breeding Amphibians.

Farming practices may reshape the structure of watersheds, water quality, and the health of aquatic organisms. Nutrient enrichment from agricultural pollution increases disease pressure in many host-pathogen systems, but the mechanisms underlying this pattern are not always resolved. For example, nutrient enrichment should strongly influence pools of aquatic environmental bacteria, which has the potential to alter microbiome composition of aquatic animals and their vulnerability to disease. However, shifts in the host microbiome have received little attention as a link between nutrient enrichment and diseases of aquatic organisms. We examined nutrient enrichment through the widespread practice of integrated pig-fish farming and its effects on microbiome composition of Brazilian amphibians and prevalence of the globally distributed amphibian skin pathogen Batrachochytrium dendrobatidis (Bd). This farming system drove surges in fecal coliform bacteria, disturbing amphibian skin bacterial communities such that hosts recruited higher proportions of Bd-facilitative bacteria and carried higher Bd prevalence. Our results highlight previously overlooked connections between global trends in land use change, microbiome dysbiosis, and wildlife disease. These interactions may be particularly important for disease management in the tropics, a region with both high biodiversity and continually intensifying anthropogenic pressures on aquatic wildlife habitats.

Assessing amphibian disease risk across tropical streams while accounting for imperfect pathogen detection.

Ecologists studying emerging wildlife diseases need to confront the realism of imperfect pathogen detection across heterogeneous habitats to aid in conservation decisions. For example, spatial risk assessments of amphibian disease caused by Batrachochytrium dendrobatidis (Bd) has largely ignored imperfect pathogen detection across sampling sites. Because changes in pathogenicity and host susceptibility could trigger recurrent population declines, it is imperative to understand how pathogen prevalence and occupancy vary across environmental gradients. Here, we assessed how Bd occurrence, prevalence, and infection intensity in a diverse Neotropical landscape vary across streams in relation to abiotic and biotic predictors using a hierarchical Bayesian model that accounts for imperfect Bd detection caused by qPCR error. Our model indicated that the number of streams harboring Bd-infected frogs is higher than observed, with Bd likely being present at ~ 43% more streams than it was detected. We found that terrestrial-breeders captured along streams had higher Bd prevalence, but lower infection intensity, than aquatic-breeding species. We found a positive relationship between Bd occupancy probability and stream density, and a negative relationship between Bd occupancy probability and amphibian local richness. Forest cover was a weak predictor of Bd occurrence and infection intensity. Finally, we provide estimates for the minimum number of amphibian captures needed to determine the presence of Bd at a given site where Bd occurs, thus, providing guidence for cost-effective disease risk monitoring programs.

Low-load pathogen spillover predicts shifts in skin microbiome and survival of a terrestrial-breeding amphibian.

Wildlife disease dynamics are strongly influenced by the structure of host communities and their symbiotic microbiota. Conspicuous amphibian declines associated with the waterborne fungal pathogen Batrachochytrium dendrobatidis (Bd) have been observed in aquatic-breeding frogs globally. However, less attention has been given to cryptic terrestrial-breeding amphibians that have also been declining in tropical regions. By experimentally manipulating multiple tropical amphibian assemblages harbouring natural microbial communities, we tested whether Bd spillover from naturally infected aquatic-breeding frogs could lead to Bd amplification and mortality in our focal terrestrial-breeding host: the pumpkin toadlet Brachycephalus pitanga. We also tested whether the strength of spillover could vary depending on skin bacterial transmission within host assemblages. Terrestrial-breeding toadlets acquired lethal spillover infections from neighbouring aquatic hosts and experienced dramatic but generally non-protective shifts in skin bacterial composition primarily attributable to their Bd infections. By contrast, aquatic-breeding amphibians maintained mild Bd infections and higher survival, with shifts in bacterial microbiomes that were unrelated to Bd infections. Our results indicate that Bd spillover from even mildly infected aquatic-breeding hosts may lead to dysbiosis and mortality in terrestrial-breeding species, underscoring the need to further investigate recent population declines of terrestrial-breeding amphibians in the tropics.

Arthropod-bacteria interactions influence assembly of aquatic host microbiome and pathogen defense.

The host-associated microbiome is vital to host immunity and pathogen defense. In aquatic ecosystems, organisms may interact with environmental bacteria to influence the pool of potential symbionts, but the effects of these interactions on host microbiome assembly and pathogen resistance are unresolved. We used replicated bromeliad microecosystems to test for indirect effects of arthropod-bacteria interactions on host microbiome assembly and pathogen burden, using tadpoles and the fungal amphibian pathogen Batrachochytrium dendrobatidis as a model host-pathogen system. Arthropods influenced host microbiome assembly by altering the pool of environmental bacteria, with arthropod-bacteria interactions specifically reducing host colonization by transient bacteria and promoting antimicrobial components of aquatic bacterial communities. Arthropods also reduced fungal zoospores in the environment, but fungal infection burdens in tadpoles corresponded most closely with arthropod-mediated patterns in microbiome assembly. This result indicates that the cascading effects of arthropods on the maintenance of a protective host microbiome may be more strongly linked to host health than negative effects of arthropods on pools of pathogenic zoospores. Our work reveals tight links between healthy ecosystem dynamics and the functioning of host microbiomes, suggesting that ecosystem disturbances such as loss of arthropods may have downstream effects on host-associated microbial pathogen defenses and host fitness.

Historical amphibian declines and extinctions in Brazil linked to chytridiomycosis.

The recent increase in emerging fungal diseases is causing unprecedented threats to biodiversity. The origin of spread of the frog-killing fungus Batrachochytrium dendrobatidis (Bd) is a matter of continued debate. To date, the historical amphibian declines in Brazil could not be attributed to chytridiomycosis; the high diversity of hosts coupled with the presence of several Bd lineages predating the reported declines raised the hypothesis that a hypervirulent Bd genotype spread from Brazil to other continents causing the recent global amphibian crisis. We tested for a spatio-temporal overlap between Bd and areas of historical amphibian population declines and extinctions in Brazil. A spatio-temporal convergence between Bd and declines would support the hypothesis that Brazilian amphibians were not adapted to Bd prior to the reported declines, thus weakening the hypothesis that Brazil was the global origin of Bd emergence. Alternatively, a lack of spatio-temporal association between Bd and frog declines would indicate an evolution of host resistance in Brazilian frogs predating Bd's global emergence, further supporting Brazil as the potential origin of the Bd panzootic. Here, we Bd-screened over 30 000 museum-preserved tadpoles collected in Brazil between 1930 and 2015 and overlaid spatio-temporal Bd data with areas of historical amphibian declines. We detected an increase in the proportion of Bd-infected tadpoles during the peak of amphibian declines (1979-1987). We also found that clusters of Bd-positive samples spatio-temporally overlapped with most records of amphibian declines in Brazil's Atlantic Forest. Our findings indicate that Brazil is post epizootic for chytridiomycosis and provide another piece to the puzzle to explain the origin of Bd globally.

Spatial distribution of Batrachochytrium dendrobatidis in South American caecilians.

The amphibian-killing fungus Batrachochytrium dendrobatidis (Bd) is linked to population declines in anurans and salamanders globally. To date, however, few studies have attempted to screen Bd in live caecilians; Bd-positive caecilians have only been reported in Africa and French Guiana. Here, we performed a retrospective survey of museum preserved specimens to (1) describe spatial patterns of Bd infection in Gymnophiona across South America and (2) test whether areas of low climatic suitability for Bd in anurans predict Bd spatial epidemiology in caecilians. We used quantitative PCR to detect Bd in preserved caecilians collected over a 109 yr period, and performed autologistic regressions to test the effect of bioclimatic metrics of temperature and precipitation, vegetation density, and elevation on the likelihood of Bd occurrence. We detected an overall Bd prevalence of 12.4%, with positive samples spanning the Uruguayan savanna, Brazil's Atlantic Forest, and the Amazon basin. Our autologistic models detected a strong effect of macroclimate, a weaker effect of vegetation density, and no effect of elevation on the likelihood of Bd occurrence. Although most of our Bd-positive records overlapped with reported areas of high climatic suitability for the fungus in the Neotropics, many of our new Bd-positive samples extend far into areas of poor suitability for Bd in anurans. Our results highlight an important gap in the study of amphibian chytridiomycosis: the potential negative impact of Bd on Neotropical caecilians and the hypothetical role of caecilians as Bd reservoirs.

Physiological responses of Brazilian amphibians to an enzootic infection of the chytrid fungus Batrachochytrium dendrobatidis.

Pathophysiological effects of clinical chytridiomycosis in amphibians include disorders of cutaneous osmoregulation and disruption of the ability to rehydrate, which can lead to decreased host fitness or mortality. Less attention has been given to physiological responses of hosts where enzootic infections of Batrachochytrium dendrobatidis (Bd) do not cause apparent population declines in the wild. Here, we experimentally tested whether an enzootic strain of Bd causes significant mortality and alters host water balance (evaporative water loss, EWL; skin resistance, R(s); and water uptake, WU) in individuals of 3 Brazilian amphibian species (Dendropsophus minutus, n = 19; Ischnocnema parva, n = 17; Brachycephalus pitanga, n = 15). Infections with enzootic Bd caused no significant mortality, but we found an increase in R(s) in 1 host species concomitant with a reduction in EWL. These results suggest that enzootic Bd infections can indeed cause sub-lethal effects that could lead to reduction of host fitness in Brazilian frogs and that these effects vary among species. Thus, our findings underscore the need for further assessment of physiological responses to Bd infections in different host species, even in cases of sub-clinical chytridiomycosis and long-term enzootic infections in natural populations.

Partitioning the net effect of host diversity on an emerging amphibian pathogen.

The 'dilution effect' (DE) hypothesis predicts that diverse host communities will show reduced disease. The underlying causes of pathogen dilution are complex, because they involve non-additive (driven by host interactions and differential habitat use) and additive (controlled by host species composition) mechanisms. Here, we used measures of complementarity and selection traditionally employed in the field of biodiversity-ecosystem function (BEF) to quantify the net effect of host diversity on disease dynamics of the amphibian-killing fungus Batrachochytrium dendrobatidis (Bd). Complementarity occurs when average infection load in diverse host assemblages departs from that of each component species in uniform populations. Selection measures the disproportionate impact of a particular species in diverse assemblages compared with its performance in uniform populations, and therefore has strong additive and non-additive properties. We experimentally infected tropical amphibian species of varying life histories, in single- and multi-host treatments, and measured individual Bd infection loads. Host diversity reduced Bd infection in amphibians through a mechanism analogous to complementarity (sensu BEF), potentially by reducing shared habitat use and transmission among hosts. Additionally, the selection component indicated that one particular terrestrial species showed reduced infection loads in diverse assemblages at the expense of neighbouring aquatic hosts becoming heavily infected. By partitioning components of diversity, our findings underscore the importance of additive and non-additive mechanisms underlying the DE.

Batrachochytrium dendrobatidis infection dynamics vary seasonally in upstate New York, USA.

The amphibian disease chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), is a major cause of worldwide amphibian declines and extinctions. Although several studies indicate that Bd prevalence and infection intensity vary seasonally, temporal variation of Bd at high-latitude sites, such as the northeastern USA, is still poorly characterized. We screened amphibians for Bd monthly at 2 study sites in New York State from April to October 2011 and used quantitative polymerase chain reaction (qPCR) to detect and quantify temporal variability in Bd infection prevalence and intensity. We found pronounced seasonal variation in both Bd infection prevalence and intensity at the community level, and our data indicate that this pattern is due to a few species (Lithobates catesbeianus, L. clamitans, and Notophthalmus viridescens) that drive temporal variability in disease dynamics. Amphibian body mass and sex were significant predictors of infection intensity but not infection prevalence. Understanding the temporal dynamics of Bd host-pathogen interactions provides important insight into regional, seasonal, and host-specific determinants of disease outbreaks. Further, our study elucidates the most relevant and informative timing for Bd surveys in temperate amphibian assemblages. Seasonal variation of infection dynamics suggests that Bd surveys from different sampling time points are not comparable, and summer surveys to evaluate chytridiomycosis may significantly underestimate Bd prevalence and intensity, leading to false conclusions about the severity of chytridiomycosis-induced amphibian mortality and population decline.

Tropical amphibian populations experience higher disease risk in natural habitats.

Habitat loss and disease are main drivers of global amphibian declines, yet the interaction between them remains largely unexplored. Here we show that paradoxically, habitat loss is negatively associated with occurrence, prevalence, and infection intensity of the chytrid fungus Batrachochytrium dendrobatidis (Bd) in amphibian populations in the tropics. At a large spatial scale, increased habitat loss predicted lower disease risk in amphibian populations across Costa Rica and eastern Australia, even after jointly considering the effect of potential biotic and abiotic correlates. Lower host-species richness and suboptimal microclimates for Bd in disturbed habitats are potential mechanisms underlying this pattern. Furthermore, we found that anthropogenic deforestation practices biased to lowlands and natural vegetation remaining in inaccessible highlands explain increased Bd occurrence at higher elevations. At a smaller spatial scale, holding constant elevation, latitude, and macroclimate, we also found a negative relationship between habitat loss, and both Bd prevalence and infection intensity in frog populations in two landscapes of the Brazilian Atlantic Forest. Our results indicate that amphibians will be disproportionately affected by emerging diseases in pristine environments, and that, paradoxically, disturbed habitats may act as shelters from disease, but only for the very few species that can tolerate deforestation. Thus, tropical amphibian faunas are threatened both by destruction of natural habitats as well as increased disease in pristine forests. To curb further extinctions and develop effective mitigation and restoration programs we must look to interactions between habitat loss and disease, the two main factors at the root of global amphibian declines.

Effects of grassland controlled burning on symbiotic skin microbes in Neotropical amphibians.

Climate change has led to an alarming increase in the frequency and severity of wildfires worldwide. While it is known that amphibians have physiological characteristics that make them highly susceptible to fire, the specific impacts of wildfires on their symbiotic skin bacterial communities (i.e., bacteriomes) and infection by the deadly chytrid fungus, Batrachochytrium dendrobatidis, remain poorly understood. Here, we address this research gap by evaluating the effects of fire on the amphibian skin bacteriome and the subsequent risk of chytridiomycosis. We sampled the skin bacteriome of the Neotropical species Scinax squalirostris and Boana leptolineata in fire and control plots before and after experimental burnings. Fire was linked with a marked increase in bacteriome beta dispersion, a proxy for skin microbial dysbiosis, alongside a trend of increased pathogen loads. By shedding light on the effects of fire on amphibian skin bacteriomes, this study contributes to our broader understanding of the impacts of wildfires on vulnerable vertebrate species.

Amphibian tolerance to arsenic: microbiome-mediated insights.

Amphibians are often recognized as bioindicators of healthy ecosystems. The persistence of amphibian populations in heavily contaminated environments provides an excellent opportunity to investigate rapid vertebrate adaptations to harmful contaminants. Using a combination of culture-based challenge assays and a skin permeability assay, we tested whether the skin-associated microbiota may confer adaptive tolerance to tropical amphibians in regions heavily contaminated with arsenic, thus supporting the adaptive microbiome principle and immune interactions of the amphibian mucus. At lower arsenic concentrations (1 and 5 mM As3+), we found a significantly higher number of bacterial isolates tolerant to arsenic from amphibians sampled at an arsenic contaminated region (TES) than from amphibians sampled at an arsenic free region (JN). Strikingly, none of the bacterial isolates from our arsenic free region tolerated high concentrations of arsenic. In our skin permeability experiment, where we tested whether a subset of arsenic-tolerant bacterial isolates could reduce skin permeability to arsenic, we found that isolates known to tolerate high concentrations of arsenic significantly reduced amphibian skin permeability to this metalloid. This pattern did not hold true for bacterial isolates with low arsenic tolerance. Our results describe a pattern of environmental selection of arsenic-tolerant skin bacteria capable of protecting amphibians from intoxication, which helps explain the persistence of amphibian populations in water bodies heavily contaminated with arsenic.

Selection of an anti-pathogen skin microbiome following prophylaxis treatment in an amphibian model system.

With emerging diseases on the rise, there is an urgent need to identify and understand novel mechanisms of prophylactic protection in vertebrate hosts. Inducing resistance against emerging pathogens through prophylaxis is an ideal management strategy that may impact pathogens and their host-associated microbiome. The host microbiome is recognized as a critical component of immunity, but the effects of prophylactic inoculation on the microbiome are unknown. In this study, we investigate the effects of prophylaxis on host microbiome composition, focusing on the selection of anti-pathogenic microbes contributing to host acquired immunity in a model host-fungal disease system, amphibian chytridiomycosis. We inoculated larval Pseudacris regilla against the fungal pathogen Batrachochytrium dendrobatidis (Bd) with a Bd metabolite-based prophylactic. Increased prophylactic concentration and exposure duration were associated with significant increases in proportions of putatively Bd-inhibitory host-associated bacterial taxa, indicating a protective prophylactic-induced shift towards microbiome members that are antagonistic to Bd. Our findings are in accordance with the adaptive microbiome hypothesis, where exposure to a pathogen alters the microbiome to better cope with subsequent pathogen encounters. Our study advances research on the temporal dynamics of microbiome memory and the role of prophylaxis-induced shifts in microbiomes contributing to prophylaxis effectiveness. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.