Implications of microhabitat selection and patterns of activity on the thermal ecology of high elevation neotropical anurans

This paper focuses on whether microhabitat selection reduces exposure to cold temperatures in highelevation tropical amphibians. I studied the microhabitat associations and thermal ecology of four anurans (Colostethus subpunctatus, Atelopus sp. nov., Eleutherodactylus bogotensis, and Hyla labialis) that live in the Andes of central Colombia. I compared two populations (3500 m and 2900 m) to evaluate the impact of a change in elevation on microhabitat thermal regimes and frog behavior. Ambient temperatures of frequently used microhabitats (soil surface, retreat sites, bogs, and ponds) were significantly lower at 3500 m. However, for each species the microhabitat associations and general patterns of activity were similar at both elevations. Body temperatures of active frogs were mainly determined by the interaction between microhabitat selection and time of the day, therefore frogs at 3500 m had lower activity temperatures than conspecifics at 2900 m. Terrestrial and diurnal anurans (Atelopus sp. nov.) experienced highly variable activity temperatures. Frogs associated with water bodies (C. subpunctatus, and H. labialis) experienced more moderate and less variable temperatures. Terrestrial, nocturnal frogs (E. bogotensis) exhibited the lowest activity temperatures, and their thermal ecology was strongly affected by increase in altitude. The physical nature of high tropical elevations limits the opportunities for behavioral thermoregulation in amphibians, and increases the importance of physiological adjustments to tolerate a wide thermal range. This may partially explain why only a small number of amphibian species, representing genera that are much more diverse at lower elevations, have been able to exploit these environments.     

Temporal Variation in Infection Prevalence by the Amphibian Chytrid Fungus in Three Species of Frogs at La Selva,Costa Rica

The emerging infectious disease chytridiomycosis, caused by the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd), is implicated in widespread population declines, extirpations, and extinctions of amphibians throughout the world. In the Neotropics, most amphibian declines have occurred in cool mid‐ to high‐elevation sites (> 400 m asl), and it is hypothesized that high temperatures limit the growth of Bd in lowland tropical sites, despite few data available on the distribution of Bd in lowland forests. Here, we report the results of a 12‐mo pathogen surveillance program for three common species of frogs at a warm lowland site in northeastern Costa Rica. We combine standard non‐invasive skin swabbing techniques with a quantitative polymerase chain reaction assay to analyze the infection prevalence and Bd load across a 1‐yr period. Our data indicate an overall Bd infection rate of 6.1 percent, but prevalence varies from < 5 percent in warmer months to a peak of 34.7 percent in the coolest months of the year. Despite very little seasonal variation in temperature (< 4°C), our data indicate strong seasonal variation in the prevalence of Bd, with highest prevalence of infection in months with coolest air temperatures. While it has been suggested that Bd is primarily a riparian fungus, we find no difference in prevalence of infection among our species despite considerable differences in affiliation of these species with water. Our study provides further evidence that infection by Bd is regulated by temperature and shows that warm temperatures in lowland forests may restrict, but not prevent, infection by Bd.     

Seasonality of Batrachochytrium dendrobatidis infection in direct-developing frogs suggests a mechanism for persistence

Batrachochytrium dendrobatidis (Bd), a disease-causing amphibian-specific fungus, is widely distributed in Puerto Rico, but is restricted to elevations above 600 m. The effect of this pathogen in the wild was studied by monitoring Eleutherodactylus coqui and E. portoricensis in 2 upland forests at El Yunque, a site characterized by historic population declines in the presence of chytridiomycosis. We tested a potential synergistic interaction between climate and Bd by measuring prevalence of infection and level of infection per individual sampled (number of zoospores), across the dry and wet seasons for 2 yr (between 2005 and 2007). Infection levels in adult frogs were significantly higher during the dry season in both species studied, suggesting a cyclic pattern of dry/ cool-wet/warm climate-driven synergistic interaction. These results are consistent with ex situ experiments in which E. coqui infected with Bd were more susceptible to chytridiomycosis when subjected to limited water treatments resembling drought. Long-term data on the prevalence of Bd in the populations studied versus intensity of infection in individual frogs provided contradictory information. However, the conflicting nature of these data was essential to understand the status of Bd in the species and geographical area studied. We conclude that in Puerto Rico, Bd is enzootic, and vulnerability of eleutherodactylid frogs to this pathogen is related to seasonal climatic variables. Our data suggest a mechanism by which this disease can persist in tropical frog communities without decimation of its hosts, but that complex interactions during severe droughts may lead to population crashes.     

Distribution and risk factors for spread of amphibian chytrid fungus Batrachochytrium dendrobatidis in the Tasmanian Wilderness World Heritage Area, Australia

Chytridiomycosis is an emerging infectious disease caused by the pathogen Batrachochytrium dendrobatidis (Bd) and is the cause of the decline and extinction of amphibian species throughout the world. We surveyed the distribution of Bd within and around the Tasmanian Wilderness World Heritage Area (TWWHA), a 1.38 million ha area of significant fauna conservation value, which provides the majority of habitat for Tasmania's 3 endemic frog species (Litoria burrowsae, Bryobatrachus nimbus and Crinia tasmaniensis). Bd was detected at only 1 (3%) of the 33 sites surveyed within the TWWHA and at 15 (52%) of the 29 sites surveyed surrounding the TWWHA. The relatively low incidence of the disease within the TWWHA suggests that the majority of the TWWHA is currently free of the pathogen despite the fact that the region provides what appears to be optimal conditions for the persistence of Bd. For all survey sites within and around the TWWHA, the presence of Bd was strongly associated with the presence of gravel roads, forest and < 1000 m altitude--factors that in this study were associated with human-disturbed landscapes around the TWWHA. Conversely, the presence of walking tracks was strongly associated with the absence of Bd, suggesting an association of absence with relatively remote locations. The wide distribution of Bd in areas of Tasmania with high levels of human disturbance and its very limited occurrence in remote wilderness areas suggests that anthropogenic activities may facilitate the dissemination of the pathogen on a landscape scale in Tasmania. Because the majority of the TWWHA is not readily accessible and appears to be largely free of Bd, and because Tasmanian frogs reproduce in ponds rather than streams, it may be feasible to control the spread of the disease in the TWWHA.     

Investigating Differences across Host Species and Scales to Explain the Distribution of the Amphibian Pathogen Batrachochytrium dendrobatidis

Many pathogens infect more than one host species, and clarifying how these different hosts contribute to pathogen dynamics can facilitate the management of pathogens and can lend insight into the functioning of pathogens in ecosystems. In this study, we investigated a suite of native and non-native amphibian hosts of the pathogen Batrachochytrium dendrobatidis (Bd) across multiple scales to identify potential mechanisms that may drive infection patterns in the Colorado study system. Specifically, we aimed to determine if: 1) amphibian populations vary in Bd infection across the landscape, 2) amphibian community composition predicts infection (e.g., does the presence or abundance of any particular species influence infection in others?), 3) amphibian species vary in their ability to produce infectious zoospores in a laboratory infection, 4) heterogeneity in host ability observed in the laboratory scales to predict patterns of Bd prevalence in the landscape. We found that non-native North American bullfrogs (Lithobates catesbeianus) are widespread and have the highest prevalence of Bd infection relative to the other native species in the landscape. Additionally, infection in some native species appears to be related to the density of sympatric L. catesbeianus populations. At the smaller host scale, we found that L. catesbeianus produces more of the infective zoospore stage relative to some native species, but that this zoospore output does not scale to predict infection in sympatric wild populations of native species. Rather, landscape level infection relates most strongly to density of hosts at a wetland as well as abiotic factors. While non-native L. catesbeianus have high levels of Bd infection in the Colorado Front Range system, we also identified Bd infection in a number of native amphibian populations allopatric with L. catesbeianus, suggesting that multiple host species are important contributors to the dynamics of the Bd pathogen in this landscape.     

Composition of symbiotic bacteria predicts survival in Panamanian golden frogs infected with a lethal fungus

Symbiotic microbes can dramatically impact host health and fitness, and recent research in a diversity of systems suggests that different symbiont community structures may result in distinct outcomes for the host. In amphibians, some symbiotic skin bacteria produce metabolites that inhibit the growth of Batrachochytrium dendrobatidis (Bd), a cutaneous fungal pathogen that has caused many amphibian population declines and extinctions. Treatment with beneficial bacteria (probiotics) prevents Bd infection in some amphibian species and creates optimism for conservation of species that are highly susceptible to chytridiomycosis, the disease caused by Bd. In a laboratory experiment, we used Bd-inhibitory bacteria from Bd-tolerant Panamanian amphibians in a probiotic development trial with Panamanian golden frogs, Atelopus zeteki, a species currently surviving only in captive assurance colonies. Approximately 30% of infected golden frogs survived Bd exposure by either clearing infection or maintaining low Bd loads, but this was not associated with probiotic treatment. Survival was instead related to initial composition of the skin bacterial community and metabolites present on the skin. These results suggest a strong link between the structure of these symbiotic microbial communities and amphibian host health in the face of Bd exposure and also suggest a new approach for developing amphibian probiotics.     

Species-level correlates of susceptibility to the pathogenic amphibian fungus Batrachochytrium dendrobatidis in the United States

Disease is often implicated as a factor in population declines of wildlife and plants. Understanding the characteristics that may predispose a species to infection by a particular pathogen can help direct conservation efforts. Recent declines in amphibian populations world-wide are a major conservation issue and may be caused in part by a fungal pathogen, Batrachochytrium dendrobatidis (Bd). We used Random Forest, a machine learning approach, to identify species-level characteristics that may be related to susceptibility to Bd. Our results suggest that body size at maturity, aspects of egg laying behavior, taxonomic order and family, and reliance on water are good predictors of documented infection for species in the continental United States. These results suggest that, whereas local-scale environmental variables are important to the spread of Bd, species-level characteristics may also influence susceptibility to Bd. The relationships identified in this study suggest future experimental tests, and may target species for conservation efforts.     

A reservoir species for the emerging Amphibian pathogen Batrachochytrium dendrobatidis thrives in a landscape decimated by disease

Chytridiomycosis, a disease caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), is driving amphibian declines and extinctions in protected areas globally. The introduction of invasive reservoir species has been implicated in the spread of Bd but does not explain the appearance of the pathogen in remote protected areas. In the high elevation (>1500 m) Sierra Nevada of California, the native Pacific chorus frog, Pseudacris regilla, appears unaffected by chytridiomycosis while sympatric species experience catastrophic declines. We investigated whether P. regilla is a reservoir of Bd by comparing habitat occupancy before and after a major Bd outbreak and measuring infection in P. regilla in the field, monitoring susceptibility of P. regilla to Bd in the laboratory, examining tissues with histology to determine patterns of infection, and using an innovative soak technique to determine individual output of Bd zoospores in water. Pseudacris regilla persists at 100% of sites where a sympatric species has been extirpated from 72% in synchrony with a wave of Bd. In the laboratory, P. regilla carried loads of Bd as much as an order of magnitude higher than loads found lethal to sympatric species. Histology shows heavy Bd infection in patchy areas next to normal skin, a possible mechanism for tolerance. The soak technique was 77.8% effective at detecting Bd in water and showed an average output of 68 zoospores per minute per individual. The results of this study suggest P. regilla should act as a Bd reservoir and provide evidence of a tolerance mechanism in a reservoir species.     

Upslope Range Shifts of Andean Dung Beetles in Response to Deforestation: Compounding and Confounding Effects of Microclimatic Change

Warmer, and sometimes drier, conditions associated with global climate change are driving many species to shift poleward and/or upslope. I hypothesized that microclimatic changes related to deforestation cause similar shifts for forest species persisting within degraded landscapes. This appears to be the first study to examine this novel hypothesis. I examined elevational distributions of dung beetle communities along parallel intact and disturbed elevational gradients from 290 to 3450 m asl in the Andes of southeastern Peru. Deforested sites were consistently warmer and drier than forested sites. To maintain the same ambient temperature as in forest, species in a deforested landscape would need to shift on average 489±59 m upslope. Dung beetle species showed a mean upslope range shift of 132±64 m (maximum=743 m) in the deforested landscape. Eight species occurred farther upslope in the degraded landscape, while none shifted downslope. In addition to upper range limit expansions, six species shifting upslope also showed range contractions or population declines at their lower range boundary. High elevation and disturbance‐tolerant species did not show range shifts. These findings suggest that land‐use change may both confound and compound the influence of global climate change on biodiversity. Synergies between habitat degradation and climate change could more than double previous range shift projections for this century, leading to unexpectedly rapid changes in biodiversity, especially for sensitive organisms such as tropical insects. On the other hand, range shifts caused by habitat degradation may be mistakenly attributed to global climate change. Abstract in Spanish is available in the online version of this article.     

Leaf Litter Inhibits Growth of an Amphibian Fungal Pathogen

Past studies have found a heterogeneous distribution of the amphibian chytrid fungal pathogen, Batrachochytrium dendrobatidis (Bd). Recent studies have accounted for some of this heterogeneity through a positive association between canopy cover and Bd abundance, which is attributed to the cooling effect of canopy cover. We questioned whether leaf litter inputs that are also associated with canopy cover might also alter Bd growth. Leaf litter inputs exhibit tremendous interspecific chemical variation, and we hypothesized that Bd growth varies with leachate chemistry. We also hypothesized that Bd uses leaf litter as a growth substrate. To test these hypotheses, we conducted laboratory trials in which we exposed cultures of Bd to leachate of 12 temperate leaf litter species at varying dilutions. Using a subset of those 12 litter species, we also exposed Bd to pre-leached litter substrate. We found that exposure to litter leachate and substrate reduced Bd spore and sporangia densities, although there was substantial variation among treatments. In particular, Bd densities were inversely correlated with concentrations of phenolic acids. We conducted a field survey of phenolic concentrations in natural wetlands which verified that the leachate concentrations in our lab study are ecologically relevant. Our study reinforces prior indications that positive associations between canopy cover and Bd abundance are likely mediated by water temperature effects, but this phenomenon might be counteracted by changes in aquatic chemistry from leaf litter inputs.     

Bd on the Beach: High Prevalence of Batrachochytrium dendrobatidis in the Lowland Forests of Gorgona Island (Colombia, South America)

The amphibian chytrid fungus, Batrachochytrium dendrobatidis, Bd, has been implicated in the decimation and extinction of many amphibian populations worldwide, especially at mid and high elevations. Recent studies have demonstrated the presence of the pathogen in the lowlands from Australia and Central America. We extend here its elevational range by demonstrating its presence at the sea level, in the lowland forests of Gorgona Island, off the Pacific coast of Colombia. We conducted two field surveys, separated by four?years, and diagnosed Bd by performing polymerase chain reactions on swab samples from the skin of five amphibian species. All species, including the Critically Endangered Atelopus elegans, tested positive for the pathogen, with prevalences between 3.9?% in A. elegans (in 2010) and 52?% in Pristimantis achatinus. Clinical signs of chytridiomycosis were not detected in any species. To our knowledge, this is the first report of B. dendrobatidis in tropical lowlands at sea level, where temperatures may exceed optimal growth temperatures of this pathogen. This finding highlights the need to understand the mechanisms allowing the interaction between frogs and pathogen in lowland ecosystems.     

Effects of an invasive anuran [the cane toad (Bufo marinus)] on the invertebrate fauna of a tropical Australian floodplain

The ways in which invasive organisms influence native ecosystems remain poorly understood. For example, feral cane toads Bufo marinus have spread extensively through tropical Australia over the last 70 years, but assessments of their ecological impact remain largely anecdotal. We conducted experimental trials to examine the effect of cane toad presence on invertebrate fauna in relatively small (2.4 × 1.2 m) outdoor enclosures on a floodplain near Darwin in the wet–dry tropics. Toads significantly reduced invertebrate abundance and species richness, but only to about the same degree as did an equivalent biomass of native anurans. Thus, if toads simply replaced native anurans, the offtake of invertebrates might not be substantially different from that due to native anurans before toad invasion. However, our field surveys suggest that toads cause a massive (fourfold) increase in total amphibian biomass. The end result is that cane toads act as a massive nutrient sink in the floodplain ecosystem because they consume vast numbers of invertebrates but (unlike native frogs) are largely invulnerable to predation by frog-eating predators.     

Bird diversity along elevational gradients in the Andes of Colombia: area and mass effects

Aim The decrease in species richness with increasing elevation is a widely recognized pattern. However, recent work has shown that there is variation in the shape of the curve, such that both negative monotonic or unimodal patterns occur, influenced by a variety of factors at local and regional scales. Discerning the shape of the curve may provide clues to the underlying causes of the observed pattern. At regional scales, the area of the altitudinal belts and mass effects are important determinants of species richness. This paper explores the relationship between bird species richness, elevation, mass effects and area of altitudinal zones for birds in tropical mountains. Location The three Andean ranges of Colombia and the peripheral mountain ranges of La Macarena and Santa Marta. Methods Lists of bird species were compiled for altitudinal belts in eastern and western slopes of the three Andean Cordilleras and for La Macarena and Santa Marta. The area of the altitudinal belts was computed from digital elevation models. The effect of area was analysed by testing for differences among altitudinal belts in the slopes and intercepts of the species‐area relationships. Mass effects were explored by separately analysing two sets of species: broadly distributed species, i.e. lowland species whose distributions extend into the Andes, and tropical Andean species, i.e., species that evolved in the Andes. Results Plotting total number of species in each altitudinal belt revealed a decline in species richness with elevation. In slopes with a complete elevational gradient from lowlands to mountain peaks, the decrease was monotonic. In internal Andean slopes where the lower elevational belts are truncated, there was a peak at mid elevations. There was a linear relationship between number of species and area of the altitudinal belts. When controlling for area, there were no differences in the number of species among altitudinal belts (500–2600 m), except for the two upper‐elevation zones (2600–3200 and > 3200 m), which had lower species richness. Diversity of widely distributed species declined monotonically with elevation, whereas tropical Andean species exhibited a mid‐elevation peak. Main conclusions A large proportion of the variation in species richness with elevation was explained by area of the altitudinal belts. When controlling for area, species richness remained constant up to 2600 m and then decreased. This pattern contrasts with a previously reported hump‐shaped pattern for Andean birds. Diversity patterns of widely distributed species suggested that immigration of lowland species inflates diversity of lower elevational belts through mass effects. This influence was particularly evident in slopes with complete altitudinal gradients (i.e. connected to the lowlands). Tropical Andean species, in contrast, were more diverse in mid‐elevational belts, where speciation rates are expected to be higher. The influence of these species was more prevalent in internal Andean slopes with no connection to the lowlands. The decline of species richness at high elevations may be related to higher extinction rates and lower resource levels.     

Dispersal,isolation and diversification with continued gene flow in an Andean tropical dry forest

The Andes are the world's longest mountain chain, and the tropical Andes are the world's richest biodiversity hot spot. The origin of the tropical Andean cordillera is relatively recent because the elevation of the mountains was relatively low (400–2500 m palaeoelevations) only 10 MYA with final uplift being rapid. These final phases of the Andean orogeny are thought to have had a fundamental role in shaping processes of biotic diversification and biogeography, with these effects reaching far from the mountains themselves by changing the course of rivers and deposition of mineral‐rich Andean sediments across the massive Amazon basin. In a recent issue of Molecular Ecology, Oswald, Overcast, Mauck, Andersen, and Smith (2017) investigate the biogeography and diversification of bird species in the Andes of Peru and Ecuador. Their study is novel in its focus on tropical dry forests (Figure 1) rather than more mesic biomes such as rain forests, cloud forests and paramos, which tend to be the focus of science and conservation in the Andean hot spot. It is also able to draw powerful conclusions via the first deployment of genomic approaches to a biogeographic question in the threatened dry forests of the New World.     

Selecting for extinction: nonrandom disease-associated extinction homogenizes amphibian biotas

Studying the patterns in which local extinctions occur is critical to understanding how extinctions affect biodiversity at local, regional and global spatial scales. To understand the importance of patterns of extinction at a regional spatial scale, we use data from extirpations associated with a widespread pathogenic agent of amphibian decline, Batrachochytrium dendrobatidis ( Bd ) as a model system. We apply novel null model analyses to these data to determine whether recent extirpations associated with Bd have resulted in selective extinction and homogenization of diverse tropical American amphibian biotas. We find that Bd -associated extinctions in this region were nonrandom and disproportionately, but not exclusively, affected low-occupancy and endemic species, resulting in homogenization of the remnant amphibian fauna. The pattern of extirpations also resulted in phylogenetic homogenization at the family level and ecological homogenization of reproductive mode and habitat association. Additionally, many more species were extirpated from the region than would be expected if extirpations occurred randomly. Our results indicate that amphibian declines in this region are an extinction filter, reducing regional amphibian biodiversity to highly similar relict assemblages and ultimately causing amplified biodiversity loss at regional and global scales.     

Spatial diversity patterns of Pristimantis frogs in the Tropical Andes

Although biodiversity gradients have been widely documented, the factors governing broad‐scale patterns in species richness are still a source of intense debate and interest in ecology, evolution, and conservation biology. Here, we tested whether spatial hypotheses (species–area effect, topographic heterogeneity, mid‐domain null model, and latitudinal effect) explain the pattern of diversity observed along the altitudinal gradient of Andean rain frogs of the genus Pristimantis. We compiled a gamma‐diversity database of 378 species of Pristimantis from the tropical Andes, specifically from Colombia to Bolivia, using records collected above 500 m.a.s.l. Analyses were performed at three spatial levels: Tropical Andes as a whole, split in its two main domains (Northern and Central Andes), and split in its 11 main mountain ranges. Species richness, area, and topographic heterogeneity were calculated for each 500‐m‐width elevational band. Spatial hypotheses were tested using linear regression models. We examined the fit of the observed diversity to the mid‐domain hypothesis using randomizations. The species richness of Pristimantis showed a hump‐shaped pattern across most of the altitudinal gradients of the Tropical Andes. There was high variability in the relationship between area and species richness along the Tropical Andes. Correcting for area effects had little impact in the shape of the empirical pattern of biodiversity curves. Mid‐domain models produced similar gradients in species richness relative to empirical gradients, but the fit varied among mountain ranges. The effect of topographic heterogeneity on species richness varied among mountain ranges. There was a significant negative relationship between latitude and species richness. Our findings suggest that spatial processes partially explain the richness patterns of Pristimantis frogs along the Tropical Andes. Explaining the current patterns of biodiversity in this hot spot may require further studies on other possible underlying mechanisms (e.g., historical, biotic, or climatic hypotheses) to elucidate the factors that limit the ranges of species along this elevational gradient.     

Thermal extremes at high elevations in the Andes: Physiological ecology of frogs

1. 1. Some anurans live in the tropical Andes above 3000 m, a cold and variable environment.

2. 2. Coping with high-elevation climate includes shifts in activity patterns, avoidance of extreme temperatures, and thermoregulation by heliothermy and thigmothermy.

3. 3. Behavior alone does not allow for full compensation of low environmental temperatures.

4. 4. Modifications of metabolic physiology allow high-elevation frogs to be active at low temperatures. However at warm temperatures their thermal physiology is similar to that of low-elevation forms.

     

Susceptibility of amphibians to chytridiomycosis is associated with MHC class II conformation

The pathogenic chytrid fungus Batrachochytrium dendrobatidis (Bd) can cause precipitous population declines in its amphibian hosts. Responses of individuals to infection vary greatly with the capacity of their immune system to respond to the pathogen. We used a combination of comparative and experimental approaches to identify major histocompatibility complex class II (MHC-II) alleles encoding molecules that foster the survival of Bd-infected amphibians. We found that Bd-resistant amphibians across four continents share common amino acids in three binding pockets of the MHC-II antigen-binding groove. Moreover, strong signals of selection acting on these specific sites were evident among all species co-existing with the pathogen. In the laboratory, we experimentally inoculated Australian tree frogs with Bd to test how each binding pocket conformation influences disease resistance. Only the conformation of MHC-II pocket 9 of surviving subjects matched those of Bd-resistant species. This MHC-II conformation thus may determine amphibian resistance to Bd, although other MHC-II binding pockets also may contribute to resistance. Rescuing amphibian biodiversity will depend on our understanding of amphibian immune defence mechanisms against Bd. The identification of adaptive genetic markers for Bd resistance represents an important step forward towards that goal.     

Distribution of the disease pathogen Batrachochytrium dendrobatidis in non‐epidemic amphibian communities of western Canada

Chytridiomycosis is an emerging infectious disease of amphibians caused by the waterborne pathogen Batrachochytrium dendrobatidis (Bd) and is responsible for the recent decline of species worldwide. Elucidating patterns in disease prevalence has proved challenging, as small‐scale studies to date have provided conflicting results. We present data on the prevalence of Bd (the proportion of individuals with Bd) collected from amphibians sampled throughout British Columbia. We had two different datasets: our original dataset includes 1129 individuals sampled in 103 sites representing 14 species. A second dataset has 839 individuals sampled in 19 sites representing 10 species. We use a Bayesian state‐space occupancy modelling approach to estimate the probability that an individual is Bd+ as a function of individual and site characteristics. Cross‐validation techniques and the original dataset were used to find the best model: this model includes species, life stage, and geographic location. Our results suggest that Bd prevalence is not strongly related to seasonality, latitude or site type. Within a species, Bd prevalence depended on life stage; the watershed in which a site occurs may also usefully predict prevalence. Overall observed infection prevalence was ～16%. Our best model accurately assigns Bd status to an individual ～ 42% of the time. Taking advantage of the Bayesian framework, we ran an analysis with the second dataset using estimates from the original model as prior values. We present posterior density distributions for those sites and species with narrow credible intervals, and show that sites tend to be either highly likely or highly unlikely to have individuals with Bd, while individuals of some stages of some species have an intermediate likelihood of being Bd‐positive. The Bayesian model using informed priors had increased accuracy rates in assigning Bd status to both individuals and groups of individuals.     

Fungal disease and temperature alter skin microbiome structure in an experimental salamander system

Pathogens compete with host microbiomes for space and resources. Their shared environment impacts pathogen–microbiome–host interactions, which can lead to variation in disease outcome. The skin microbiome of red‐backed salamanders (Plethodon cinereus) can reduce infection by the pathogen Batrachochytrium dendrobatidis (Bd) at moderate infection loads, with high species richness and high abundance of competitors as putative mechanisms. However, it is unclear if the skin microbiome can reduce epizootic Bd loads across temperatures. We conducted a laboratory experiment to quantify skin microbiome and host responses (P. cinereus: n = 87) to Bd at mimicked epizootic loads across temperatures (13, 17 and 21°C). We quantified skin microbiomes using 16S rRNA gene metabarcoding and identified operational taxonomic units (OTUs) taxonomically similar to culturable bacteria known to kill Bd (anti‐Bd OTUs). Prior to pathogen exposure, temperature changed the microbiome (OTU richness decreased by 12% and the abundance of anti‐Bd OTUs increased by 18% per degree increase in temperature), but these changes were not predictive of disease outcome. After exposure, Bd changed the microbiome (OTU richness decreased by 0.1% and the abundance of anti‐Bd OTUs increased by 0.2% per 1% increase in Bd load) and caused high host mortality across temperatures (35/45: 78%). Temperature indirectly impacted microbiome change and mortality through its direct effect on pathogen load. We did not find support for the microbiome impacting Bd load or host survival. Our research reveals complex host, pathogen, microbiome and environmental interactions to demonstrate that during epizootic events the microbiome will be unlikely to reduce pathogen invasion, even for putatively Bd‐resistant species.