Global Amphibian Declines, Disease, and the Ongoing Battle between Batrachochytrium Fungi and the Immune System

Amphibian cellular immune response to chytridiomycosis at metamorphic climax

The fungal disease chytridiomycosis (caused by Batrachochytrium dendrobatidis [Bd]) is a primary contributor to amphibian declines. The frog metamorphic stages, characterised by extensive physiological reorganisation and energy expenditure, have heightened susceptibility to Bd. However, little is known about how these metamorphic stages respond immunologically to Bd infection. In this study, we examined Bd infection and the cellular immune response of Mixophyes fleayi at Gosner stages 40, 42 and 45, using blood smears and skin and liver histology. Although proportional differences were observed, the impact of Bd exposure appeared negligible prior to Gosner stage 45 (onset of morbidity), with no significant differences observed in absolute leukocyte counts for blood or liver samples between control and Bd-exposed groups at Gosner stages 40 and 42. Animals exhibiting clinical signs at Gosner stage 45 demonstrated significant elevation in liver leukocyte counts, blood neutrophil and monocyte counts and neutrophil-to-lymphocyte ratios. These findings are reminiscent of the amplified inflammatory response characteristic of immunopathology in clinically infected amphibians. Interestingly, a subset of exposed animals that had apparently cleared infections at Gosner stage 45 had similar blood leukocyte counts but reduced liver leukocyte counts compared to naïve controls. This could be a consequence of prior cellular consumption during pathogen removal or effective immune regulation via anti-inflammatory protective feedback mechanisms. We recommend targeted gene expression analyses (e.g. immunomodulatory cytokines) to establish the mechanisms responsible for the varied immune expression and infection outcomes across metamorphosis.

Leveraging machine learning to uncover multi-pathogen infection dynamics across co-distributed frog families

Background

Amphibians are experiencing substantial declines attributed to emerging pathogens. Efforts to understand what drives patterns of pathogen prevalence and differential responses among species are challenging because numerous factors related to the host, pathogen, and their shared environment can influence infection dynamics. Furthermore, sampling across broad taxonomic and geographic scales to evaluate these factors poses logistical challenges, and interpreting the roles of multiple potentially correlated variables is difficult with traditional statistical approaches. In this study, we leverage frozen tissues stored in natural history collections and machine learning techniques to characterize infection dynamics of three generalist pathogens known to cause mortality in frogs.

Methods

We selected 12 widespread and abundant focal taxa within three ecologically distinct, co-distributed host families (Bufonidae, Hylidae, and Ranidae) and sampled them across the eastern two-thirds of the United States of America. We screened and quantified infection loads via quantitative PCR for three major pathogens: the fungal pathogen Batrachochytrium dendrobatidis (Bd), double-stranded viruses in the lineage Ranavirus (Rv), and the alveolate parasite currently referred to as Amphibian Perkinsea (Pr). We then built balanced random forests (RF) models to predict infection status and intensity based on host taxonomy, age, sex, geography, and environmental variables and to assess relative variable importance across pathogens. Lastly, we used one-way analyses to determine directional relationships and significance of identified predictors.

Results

We found approximately 20% of individuals were infected with at least one pathogen (231 single infections and 25 coinfections). The most prevalent pathogen across all taxonomic groups was Bd (16.9%; 95% CI [14.9-19%]), followed by Rv (4.38%; 95% CI [3.35-5.7%]) and Pr (1.06%; 95% CI [0.618-1.82%]). The highest prevalence and intensity were found in the family Ranidae, which represented 74.3% of all infections, including the majority of Rv infection points, and had significantly higher Bd intensities compared to Bufonidae and Hylidae. Host species and environmental variables related to temperature were key predictors identified in RF models, with differences in importance among pathogens and host families. For Bd and Rv, infected individuals were associated with higher latitudes and cooler, more stable temperatures, while Pr showed trends in the opposite direction. We found no significant differences between sexes, but juvenile frogs had higher Rv prevalence and Bd infection intensity compared to adults. Overall, our study highlights the use of machine learning techniques and a broad sampling strategy for identifying important factors related to infection in multi-host, multi-pathogen systems.

Landscape-scale drivers of spatial dynamics and genetic diversity in an emerging wildlife pathogen

Aquatic pathogens often cannot tolerate drying, and thus their spread, and diversity across a landscape may depend on interactions between hydrological conditions and the movement of infected hosts. The aquatic fungus Batrachochytrium dendrobatidis (Bd) is a nearly ubiquitous pathogen of amphibians and particular lineages have been associated with host declines. By coupling amphibian surveys with molecular pathogen detection and genotyping techniques, we characterized the spatial dynamics and genetic diversity of Bd on a landscape containing both permanent and ephemeral ponds. In doing so, we aimed to clarify how pathogen loads and prevalences vary across seasons and among habitat types, and which host species move the pathogen from place to place. At the start of spring breeding, Bd prevalence was lower on amphibians sampled from ephemeral ponds. For the remainder of the amphibian active season, prevalence was similar across both ephemeral and permanent ponds, with variation in prevalence being well-explained by a hump-shaped relationship with host body temperature. The first amphibians to arrive at these ephemeral ponds infected were species that breed in ephemeral ponds and likely emerged infected from terrestrial hibernacula. However, species from permanent ponds, most of which hibernate aquatically, later visited the ephemeral ponds and these animals had a greater prevalence and load of Bd, suggesting that migrants among ponds and pond types also move Bd across the landscape. The Bd we sampled was genetically diverse within ponds but showed little genetic structure among ponds, host species, or seasons. Taken together, our findings suggest that Bd can be diverse even at small scales and moves readily across a landscape with help from a wide variety of hosts.

Amphibians rise to flourishing under climate change on the Qinghai-Tibetan Plateau

Amphibian populations are declining globally due to climate change. However, the impacts on the geographic distribution of amphibians on the Qinghai-Tibetan Plateau (QTP), a global biodiversity hotspot with 112 species of amphibians that is sensitive to global climate change, remains unclear. In this study, MaxEnt and barycentre shift analyses were performed to reveal the impact of climate change on the potential future habitats of amphibians on the QTP using the BCC-CSM2-MR global climate model of the Coupled Model Intercomparison Projects Phase 6 (CMIP6) climate pattern with three shared socioeconomic pathways (SSP). In contrast to the widespread decline in the amphibian population, the future scenarios projected an increase in most amphibian habitats on the QTP, accompanied by migration to higher elevations or latitudes under three climatic projections (SSP 1-2.6, 3-7.0, and 5-8.5). Average annual precipitation was the most crucial environmental variable impacting the future distribution of amphibians. The findings indicate that amphibians would flourish under climate change on the QTP, which is of great significance for the protection of amphibians and biodiversity on the QTP.

Evolutionary analysis of major histocompatibility complex variants in chytrid-resistant and susceptible amphibians

An amphibian emerging infectious disease (EID), chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), originated in Asia but primarily led to declines and extinctions in amphibian populations outside of Asia. Host major histocompatibility complex (MHC) molecules exhibit high polymorphism, and the evolution of MHC can be influenced by recombination and pathogens. Previous studies have indicated that host MHC class II is associated with Bd resistance. In this study, I conducted recombination and selection tests on functional MHC IIß1 alleles from an Asian Bd-resistant anuran species (Bufo gargarizans) and an Australasian Bd-susceptible species (Litoria caerulea). Recombination at the same site was identified in both species, supporting the hypothesis that recombination contributes to MHC IIß1 diversity in amphibians. Positive selection was observed in MHC IIß1 alleles in both species. In L. caerulea, at least four amino acid sites were identified under significant positive selection in the MHC IIß1, whereas these sites were either negatively selected or conserved in B. gargarizans. This suggests these sites might be selected for Bd resistance. Hydrophobicity was detected in certain amino acid sites relating to Bd resistance, suggesting this physicochemical property may be a factor selected to counteract Bd infection. These findings of this study provide an evolutionary basis for understanding how amphibian MHC IIß1 may undergo selection in response to chytrid infection.

Effects of temperature on the interaction between amphibian skin bacteria and Batrachochytrium dendrobatidis

Symbiotic relationships between animals and microbes are important for a range of functions, from digestion to protection from pathogens. However, the impact of temperature variation on these animal-microbe interactions remains poorly understood. Amphibians have experienced population declines and even extinctions on a global scale due to chytridiomycosis, a disease caused by chytrid fungi in the genus Batrachochytrium. Variation in susceptibility to this disease exists within and among host species. While the mechanisms generating differences in host susceptibility remain elusive, differences in immune system components, as well as variation in host and environmental temperatures, have been associated with this variation. The symbiotic cutaneous bacteria of amphibians are another potential cause for variation in susceptibility to chytridiomycosis, with some bacterial species producing antifungal metabolites that prevent the growth of Bd. The growth of both Bd and bacteria are affected by temperature, and thus we hypothesized that amphibian skin bacteria may be more effective at preventing Bd growth at certain temperatures. To test this, we collected bacteria from the skins of frogs, harvested the metabolites they produced when grown at three different temperatures, and then grew Bd in the presence of those metabolites under those same three temperatures in a three-by-three fully crossed design. We found that both the temperature at which cutaneous bacteria were grown (and metabolites produced) as well as the temperature at which Bd is grown can impact the ability of cutaneous bacteria to inhibit the growth of Bd. While some bacterial isolates showed the ability to inhibit Bd growth across multiple temperature treatments, no isolate was found to be inhibitive across all combinations of bacterial incubation or Bd challenge temperatures, suggesting that temperature affects both the metabolites produced and the effectiveness of those metabolites against the Bd pathogen. These findings move us closer to a mechanistic understanding of why chytridiomycosis outbreaks and related amphibian declines are often limited to certain climates and seasons.

Biobanks, offspring fitness and the influence of developmental plasticity in conservation biology

Mitigation of the widely known threats to the world's biodiversity is difficult, despite the strategies and actions proposed by international agreements such as the United Nations Framework Convention on Climate Change (UNFCCC) and the Convention on Biological Diversity (CBD). Nevertheless, many scientists devote their time and effort to finding and implementing various solutions to the problem. One potential way forward that is gaining popularity involves the establishment of biobank programs aimed at preserving and storing germplasm from threatened species, and then using it to support the future viability and health of threatened populations. This involves developing and using assisted reproductive technologies to achieve their goals. Despite considerable advances in the effectiveness of reproductive technologies, differences between the reproductive behavior and physiology of widely differing taxonomic groups mean that this approach cannot be applied with equal success to many species. Moreover, evidence that epigenetic influences and developmental plasticity, whereby it is now understood that embryonic development, and subsequent health in later life, can be affected by peri-conceptional environmental conditions, is raising the possibility that cryopreservation methods themselves may have to be reviewed and revised when planning the biobanks. Here, I describe the benefits and problems associated with germplasm biobanking across various species, but also offer some realistic assessments of current progress and applications.

Effects of exogenous elevation of corticosterone on immunity and the skin microbiome of eastern newts (Notophthalmus viridescens)

The amphibian chytrid fungus, Batrachochytrium salamandrivorans (Bsal) threatens salamander biodiversity. The factors underlying Bsal susceptibility may include glucocorticoid hormones (GCs). The effects of GCs on immunity and disease susceptibility are well studied in mammals, but less is known in other groups, including salamanders. We used Notophthalmus viridescens (eastern newts) to test the hypothesis that GCs modulate salamander immunity. We first determined the dose required to elevate corticosterone (CORT; primary GC in amphibians) to physiologically relevant levels. We then measured immunity (neutrophil lymphocyte ratios, plasma bacterial killing ability (BKA), skin microbiome, splenocytes, melanomacrophage centres (MMCs)) and overall health in newts following treatment with CORT or an oil vehicle control. Treatments were repeated for a short (two treatments over 5 days) or long (18 treatments over 26 days) time period. Contrary to our predictions, most immune and health parameters were similar for CORT and oil-treated newts. Surprisingly, differences in BKA, skin microbiome and MMCs were observed between newts subjected to short- and long-term treatments, regardless of treatment type (CORT, oil vehicle). Taken together, CORT does not appear to be a major factor contributing to immunity in eastern newts, although more studies examining additional immune factors are necessary. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.

Ranavirus infection does not reduce heat tolerance in a larval amphibian

Extreme heat events and emerging infectious diseases negatively impact wildlife populations, but the interacting effects of infection and host heat tolerance remain understudied. The few studies covering this subject have demonstrated that pathogens lower the heat tolerance of their hosts, which places infected hosts at a greater risk experiencing lethal heat stress. Here, we studied how ranavirus infection influenced heat tolerance in larval wood frogs (Lithobates sylvaticus). In line with similar studies, we predicted the elevated costs of ranavirus infection would lower heat tolerance, measured as critical thermal maximum (CT_max), compared to uninfected controls. Ranavirus infection did not reduce CT_max and there was a positive relationship between CT_max and viral loads. Our results demonstrate that ranavirus-infected wood frog larvae had no loss in heat tolerance compared to uninfected larvae, even at viral loads associated with high mortality rates, which contradicts the common pattern for other pathogenic infections in ectotherms. Larval anurans may prioritize maintenance of their CT_max when infected with ranavirus to promote selection of warmer temperatures during behavioral fever that can improve pathogen clearance. Our study represents the first to examine the effect of ranavirus infection on host heat tolerance, and because no decline in CT_max was observed, this suggests that infected hosts would not be under greater risk of heat stress.

Unraveling disparate roles of organisms, from plants to bacteria, and viruses on built cultural heritage

The different organisms, ranging from plants to bacteria, and viruses that dwell on built cultural heritage can be passive or active participants in conservation processes. For the active participants, particular attention is generally given to organisms that play a positive role in bioprotection, bioprecipitation, bioconsolidation, bioremediation, biocleaning, and biological control and to those involved in providing ecosystem services, such as reducing temperature, pollution, and noise in urban areas. The organisms can also evolve or mutate in response to changes, becoming tolerant and resistant to biocidal treatments or acquiring certain capacities, such as water repellency or resistance to ultraviolet radiation. Our understanding of the capacities and roles of these active organisms is constantly evolving as bioprotection/biodeterioration, and biotreatment studies are conducted and new techniques for characterizing species are developed. This brief review article aims to shed light on interesting research that has been abandoned as well as on recent (some ongoing) studies opening up new scopes of research involving a wide variety of organisms and viruses, which are likely to receive more attention in the coming years. KEY POINTS: • Organisms and viruses can be active or passive players in heritage conservation • Biotreatment and ecosystem service studies involving organisms and viruses are shown • Green deal, health, ecosystem services, and global change may shape future research.

Colonization order of bacterial isolates on treefrog embryos impacts microbiome structure in tadpoles

Priority effects, or impacts of colonization order, may have lasting influence on ecological community composition. The embryonic microbiome is subject to stochasticity in colonization order of bacteria. Stochasticity may be especially impactful for embryos developing in bacteria-rich environments, such as the embryos of many amphibians. To determine if priority effects experienced as embryos impacted bacterial community composition in newly hatched tadpoles, we selectively inoculated the embryos of laboratory-raised hourglass treefrogs, Dendropsophus ebraccatus, with bacteria initially isolated from the skin of wild D. ebraccatus adults over 2 days. First, embryos were inoculated with two bacteria in alternating sequences. Next, we evaluated the outcomes of priority effects in an in vitro co-culture assay absent of host factors. We then performed a second embryo experiment, inoculating embryos with one of three bacteria on the first day and a community of five target bacteria on the second. Through 16S rRNA gene amplicon sequencing, we observed relative abundance shifts in tadpole bacteria communities due to priority effects. Our results suggest that the initial bacterial source pools of embryos shape bacterial communities at later life stages; however, the magnitude of those changes is dependent on the host environment and the identity of bacterial colonists.

Immune priming prior to pathogen exposure sheds light on the relationship between host, microbiome and pathogen in disease

Dynamic interactions between host, pathogen and host-associated microbiome dictate infection outcomes. Pathogens including Batrachochytrium dendrobatidis (Bd) threaten global biodiversity, but conservation efforts are hindered by limited understanding of amphibian host, Bd and microbiome interactions. We conducted a vaccination and infection experiment using Eastern hellbender salamanders (Cryptobranchus alleganiensis alleganiensis) challenged with Bd to observe infection, skin microbial communities and gene expression of host skin, pathogen and microbiome throughout the experiment. Most animals survived high Bd loads regardless of their vaccination status and vaccination did not affect pathogen load, but host gene expression differed based on vaccination. Oral vaccination (exposure to killed Bd) stimulated immune gene upregulation while topically and sham-vaccinated animals did not significantly upregulate immune genes. In early infection, topically vaccinated animals upregulated immune genes but orally and sham-vaccinated animals downregulated immune genes. Bd increased pathogenicity-associated gene expression in late infection when Bd loads were highest. The microbiome was altered by Bd, but there was no correlation between anti-Bd microbe abundance or richness and pathogen burden. Our observations suggest that hellbenders initially generate a vigorous immune response to Bd, which is ineffective at controlling disease and is subsequently modulated. Interactions with antifungal skin microbiota did not influence disease progression.

When Defenses Fail: Atelopus zeteki Skin Secretions Increase Growth of the Pathogen Batrachochytrium dendrobatidis

To combat the threat of emerging infectious diseases in wildlife, ecoimmunologists seek to understand the complex interactions among pathogens, their hosts, and their shared environments. The cutaneous fungal pathogen Batrachochytrium dendrobatidis (Bd), has led to the decline of innumerable amphibian species, including the Panamanian golden frog (Atelopus zeteki). Given that Bd can evade or dampen the acquired immune responses of some amphibians, nonspecific immune defenses are thought to be especially important for amphibian defenses against Bd. In particular, skin secretions constitute a vital component of amphibian innate immunity against skin infections, but their role in protecting A. zeteki from Bd is unknown. We investigated the importance of this innate immune component by reducing the skin secretions from A. zeteki and evaluating their effectiveness against Bd in vitro and in vivo. Following exposure to Bd in a controlled inoculation experiment, we compared key disease characteristics (e.g., changes in body condition, prevalence, pathogen loads, and survival) among groups of frogs that had their skin secretions reduced and control frogs that maintained their skin secretions. Surprisingly, we found that the skin secretions collected from A. zeteki increased Bd growth in vitro. This finding was further supported by infection and survival patterns in the in vivo experiment where frogs with reduced skin secretions tended to have lower pathogen loads and survive longer compared to frogs that maintained their secretions. These results suggest that the skin secretions of A. zeteki are not only ineffective at inhibiting Bd but may enhance Bd growth, possibly leading to greater severity of disease and higher mortality in this highly vulnerable species. These results differ from those of previous studies in other amphibian host species that suggest that skin secretions are a key defense in protecting amphibians from developing severe chytridiomycosis. Therefore, we suggest that the importance of immune components cannot be generalized across all amphibian species or over time. Moreover, the finding that skin secretions may be enhancing Bd growth emphasizes the importance of investigating these immune components in detail, especially for species that are a conservation priority.

Long-amplicon MinION-based sequencing study in a salt-contaminated twelfth century granite-built chapel

The irregular damp dark staining on the stonework of a salt-contaminated twelfth century granite-built chapel is thought to be related to a non-homogeneous distribution of salts and microbial communities. To enhance understanding of the role of microorganisms in the presence of salt and damp stains, we determined the salt content and identified the microbial ecosystem in several paving slabs and inner wall slabs (untreated and previously bio-desalinated) and in the exterior surrounding soil. Soluble salt analysis and culture-dependent approaches combined with archaeal and bacterial 16S rRNA and fungal ITS fragment as well as with the functional genes nirK, dsr, and soxB long-amplicon MinION-based sequencing were performed. State-of-the-art technology was used for microbial identification, providing information about the microbial diversity and phylogenetic groups present and enabling us to gain some insight into the biological cycles occurring in the community key genes involved in the different geomicrobiological cycles. A well-defined relationship between microbial data and soluble salts was identified, suggesting that poorly soluble salts (CaSO4) could fill the pores in the stone and lead to condensation and dissolution of highly soluble salts (Ca(NO3)2 and Mg(NO3)2) in the thin layer of water formed on the stonework. By contrast, no direct relationship between the damp staining and the salt content or related microbiota was established. Further analysis regarding organic matter and recalcitrant elements in the stonework should be carried out. KEY POINTS : • Poorly (CaSO4) and highly (Ca(NO3)2, Mg(NO3)2) soluble salts were detected • Halophilic and mineral weathering microorganisms reveal ecological impacts of salts • Microbial communities involved in nitrate and sulfate cycles were detected.

Does the thermal mismatch hypothesis predict disease outcomes in different morphs of a terrestrial salamander?

Many aspects of ectotherm physiology are temperature-dependent. The immune system of temperate-dwelling ectothermic host species is no exception and their immune function is often downregulated in cold temperatures. Likewise, species of ectothermic pathogens experience temperature-mediated effects on rates of transmission and/or virulence. Although seemingly straightforward, predicting the outcomes of ectothermic host-pathogen interactions is quite challenging. A recent hypothesis termed the thermal mismatch hypothesis posits that cool-adapted host species should be most susceptible to pathogen infection during warm temperature periods whereas warm-adapted host species should be most susceptible to pathogens during periods of cool temperatures. We explore this hypothesis using two ecologically and physiologically differentiated color morphs of the Eastern Red-backed Salamander (Plethodon cinereus) and a pathogenic chytrid fungus (Batrachochytrium dendrobatidis; hereafter "Bd") using a fully factorial laboratory experiment. At cool temperatures, unstriped salamanders (i.e., those that are tolerant of warm temperatures) had a significantly higher probability of Bd infection compared with cool-tolerant striped salamanders, consistent with the thermal mismatch hypothesis. However, we found no support for this hypothesis when salamanders were exposed to Bd at warm temperatures: the probability of Bd infection in the cool-tolerant striped salamanders was nearly identical in both cool and warm temperatures, opposite the predictions of the thermal mismatch hypothesis. Our results are most consistent with the fact that Bd grows poorly at warm temperatures. Alternatively, our data could indicate that the two color morphs do not differ in their tolerance to warm temperatures but that striped salamanders are more tolerant to cool temperatures than unstriped salamanders.

Electrolyte imbalances and dehydration play a key role in Batrachochytrium salamandrivorans chytridiomycosis

Introduction

One of the most important emerging infectious diseases of amphibians is caused by the fungal pathogen Batrachochytrium salamandrivorans (Bsal). Bsal was recently discovered and is of global concern due to its potential to cause high mortality in amphibians, especially salamander species. To date, little has been reported on the pathophysiological effects of Bsal; however, studies of a similar fungus, B. dendrobatidis (Bd), have shown that electrolyte losses and immunosuppression likely play a key role in morbidity and mortality associated with this disease. The goal of this study was to investigate pathophysiological effects and immune responses associated with Bsal chytridiomycosis using 49 rough-skinned newts (Taricha granulosa) as the model species.

Methods

Taricha granulosa were exposed to a 1 × 107 per 10 mL dose of Bsal zoospores and allowed to reach various stages of disease progression before being humanely euthanized. At the time of euthanasia, blood was collected for biochemical and hematological analyses as well as protein electrophoresis. Ten standardized body sections were histologically examined, and Bsal-induced skin lesions were counted and graded on a scale of 1-5 based on severity.

Results

Results indicated that electrolyte imbalances and dehydration induced by damage to the epidermis likely play a major role in the pathogenesis of Bsal chytridiomycosis in this species. Additionally, Bsal-infected, clinically diseased T. granulosa exhibited a systemic inflammatory response identified through alterations in complete blood counts and protein electrophoretograms.

Discussion

Overall, these results provide foundational information on the pathogenesis of this disease and highlight the differences and similarities between Bsal and Bd chytridiomycosis.

Opportunities and Limitations for Reproductive Science in Species Conservation

Reproductive science in the context of conservation biology is often understood solely in terms of breeding threatened species. Although technologies developed primarily for agriculture or biomedicine have a potentially important role in species conservation, their effectiveness is limited if we regard the main objective of animal conservation as helping to support populations rather than to breed a small number of individuals. The global threats facing wild species include the consequences of climate change, population growth, urbanization, atmospheric and water pollution, and the release of chemicals into the environment, to cite but a few. Reproductive sciences provide important and often unexpected windows into many of these consequences, and our aim here is both to demonstrate the breadth of reproductive science and the importance of basic knowledge and to suggest where some of the insights might be useful in mitigating the problems. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Early-diverging fungal phyla: taxonomy, species concept, ecology, distribution, anthropogenic impact, and novel phylogenetic proposals

The increasing number of new fungal species described from all over the world along with the use of genetics to define taxa, has dramatically changed the classification system of early-diverging fungi over the past several decades. The number of phyla established for non-Dikarya fungi has increased from 2 to 17. However, to date, both the classification and phylogeny of the basal fungi are still unresolved. In this article, we review the recent taxonomy of the basal fungi and re-evaluate the relationships among early-diverging lineages of fungal phyla. We also provide information on the ecology and distribution in Mucoromycota and highlight the impact of chytrids on amphibian populations. Species concepts in Chytridiomycota, Aphelidiomycota, Rozellomycota, Neocallimastigomycota are discussed in this paper. To preserve the current application of the genus Nephridiophaga (Chytridiomycota: Nephridiophagales), a new type species, Nephridiophaga blattellae, is proposed.

Host gene expression in wildlife disease: making sense of species-level responses

Emerging infectious diseases are significant threats to wildlife conservation, yet the impacts of pathogen exposure and infection can vary widely among host species. As such, conservation biologists and disease ecologists have increasingly aimed to understand species-specific host susceptibility using molecular methods. In particular, comparative gene expression assays have been used to contrast the transcriptomic responses of disease-resistant and disease-susceptible hosts to pathogen exposure. This work usually assumes that the gene expression responses of disease-resistant species will reveal the activation of molecular pathways contributing to host defence. However, results often show that disease-resistant hosts undergo little gene expression change following pathogen challenge. Here, we discuss the mechanistic implications of these "null" findings and offer methodological suggestions for future molecular studies of wildlife disease. First, we highlight that muted transcriptomic responses with minimal immune system recruitment may indeed be protective for nonsusceptible hosts if they limit immunopathology and promote pathogen tolerance in systems where susceptible hosts suffer from genetic dysregulation. Second, we argue that overly narrow investigation of responses to pathogen exposure may overlook important, constitutively active molecular pathways that underlie species-specific defences. Finally, we outline alternative study designs and approaches that complement interspecific transcriptomic comparisons, including intraspecific gene expression studies and genomic methods to detect signatures of selection. Collectively, these insights will help ecologists extract maximal information from conservation-relevant transcriptomic data sets, leading to a deeper understanding of host defences and, ultimately, the implementation of successful conservation interventions.

Global Patterns of the Fungal Pathogen Batrachochytrium dendrobatidis Support Conservation Urgency

The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) is a skin pathogen that can cause the emerging infectious disease chytridiomycosis in susceptible species. It has been considered one of the most severe threats to amphibian biodiversity. We aimed to provide an updated compilation of global Bd occurrences by host taxon and geography, and with the larger global Bd dataset we reanalyzed Bd associations with environmental metrics at the world and regional scales. We also compared our Bd data compilation with a recent independent assessment to provide a more comprehensive count of species and countries with Bd occurrences. Bd has been detected in 1,375 of 2,525 (55%) species sampled, more than doubling known species infections since 2013. Bd occurrence is known from 93 of 134 (69%) countries at this writing; this compares to known occurrences in 56 of 82 (68%) countries in 2013. Climate-niche space is highly associated with Bd detection, with different climate metrics emerging as key predictors of Bd occurrence at regional scales; this warrants further assessment relative to climate-change projections. The accretion of Bd occurrence reports points to the common aims of worldwide investigators to understand the conservation concerns for amphibian biodiversity in the face of potential disease threat. Renewed calls for better mitigation of amphibian disease threats resonate across continents with amphibians, especially outside Asia. As Bd appears to be able to infect about half of amphibian taxa and sites, there is considerable room for biosecurity actions to forestall its spread using both bottom-up community-run efforts and top-down national-to-international policies. Conservation safeguards for sensitive species and biodiversity refugia are continuing priorities.

TEMPERATURE AS A DRIVER OF THE PATHOGENICITY AND VIRULENCE OF AMPHIBIAN CHYTRID FUNGUS BATRACHOCHYTRIUM DENDROBATIDIS: A SYSTEMATIC REVIEW

Chytridiomycosis, caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd), is a leading cause of global amphibian declines. Severe infections with Bd can lead to cardiac arrest, and mass deaths during epidemics have been reported. Temperature, pH, salinity, and moisture are important determinants of the survival, growth, reproduction, and pathogenicity of Bd, as well as its effect on amphibian populations. Here, we synthesize current knowledge on the role of temperature as a driver of the pathogenicity and virulence of Bd to better understand the effects of temperature on amphibian defense mechanisms against infection. This review advises on research direction and management approaches to benefit amphibian populations affected by Bd. We conclude by offering guidelines for four levels of temperature monitoring in amphibian field studies to improve consistency between studies: regional climate, habitat, microhabitat, and amphibian host.

Design of Protected Area by Tracking and Excluding the Effects of Climate and Landscape Change: A Case Study Using Neurergus derjugini

This study aimed to use the applications of Ensemble Species Distribution Modelling (eSDM), Geographical Information Systems (GISs), and Multi-Criteria Decision Analysis (MCDA) for the design of a protected area (PA) for the critically endangered yellow-spotted mountain newt, Neurergus derjugini, by tracking and excluding the effects of climate and landscape changes in western Iran and northeastern Iraq. Potential recent and future distributions (2050 and 2070) were reconstructed by eSDM using eight algorithms with MRI-CGCM3 and CCSM4 models. The GIS-based MCDA siting procedure was followed inside habitats with high eSDM suitability by eliminating the main roads, cities, high village density, dams, poor vegetation, low stream density, agricultural lands and high ridge density. Then, within the remaining relevant areas, 10 polygons were created as “nominations” for PAs (NPAs). Finally, for 10 different NPAs, the suitability score was ranked based on ratings and weights (analytical hierarchy process) of the number of newt localities, NPA connectivity, NPA shape, NPA habitat suitability in 2070, NPA size, genetic diversity, village density and distance to nearest PAs, cities, and main roads. This research could serve as a modern realistic approach for environmental management to plan conservation areas using a cost-effective and affordable technique.

The Fungicide Chlorothalonil Changes the Amphibian Skin Microbiome: A Potential Factor Disrupting a Host Disease-Protective Trait

The skin microbiome is an important part of amphibian immune defenses and protects against pathogens such as the chytrid fungus Batrachochytrium dendrobatidis (Bd), which causes the skin disease chytridiomycosis. Alteration of the microbiome by anthropogenic factors, like pesticides, can impact this protective trait, disrupting its functionality. Chlorothalonil is a widely used fungicide that has been recognized as having an impact on amphibians, but so far, no studies have investigated its effects on amphibian microbial communities. In the present study, we used the amphibian Lithobates vibicarius from the montane forest of Costa Rica, which now appears to persist despite ongoing Bd-exposure, as an experimental model organism. We used 16S rRNA amplicon sequencing to investigate the effect of chlorothalonil on tadpoles’ skin microbiome. We found that exposure to chlorothalonil changes bacterial community composition, with more significant changes at a higher concentration. We also found that a larger number of bacteria were reduced on tadpoles’ skin when exposed to the higher concentration of chlorothalonil. We detected four presumed Bd-inhibitory bacteria being suppressed on tadpoles exposed to the fungicide. Our results suggest that exposure to a widely used fungicide could be impacting host-associated bacterial communities, potentially disrupting an amphibian protective trait against pathogens.

Winter is coming-Temperature affects immune defenses and susceptibility to Batrachochytrium salamandrivorans

Environmental temperature is a key factor driving various biological processes, including immune defenses and host-pathogen interactions. Here, we evaluated the effects of environmental temperature on the pathogenicity of the emerging fungal pathogen, Batrachochytrium salamandrivorans (Bsal), using controlled laboratory experiments, and measured components of host immune defense to identify regulating mechanisms. We found that adult and juvenile Notophthalmus viridescens died faster due to Bsal chytridiomycosis at 14°C than at 6 and 22°C. Pathogen replication rates, total available proteins on the skin, and microbiome composition likely drove these relationships. Temperature-dependent skin microbiome composition in our laboratory experiments matched seasonal trends in wild N. viridescens, adding validity to these results. We also found that hydrophobic peptide production after two months post-exposure to Bsal was reduced in infected animals compared to controls, perhaps due to peptide release earlier in infection or impaired granular gland function in diseased animals. Using our temperature-dependent susceptibility results, we performed a geographic analysis that revealed N. viridescens populations in the northeastern United States and southeastern Canada are at greatest risk for Bsal invasion, which shifted risk north compared to previous assessments. Our results indicate that environmental temperature will play a key role in the epidemiology of Bsal and provide evidence that temperature manipulations may be a viable disease management strategy.

In 2010, a new skin-eating fungus, Batrachochytrium salamandrivorans (Bsal), was discovered killing salamanders in the Netherlands. Since then, the pathogen has spread to other European countries. Bsal is believed to be from Asia and is being translocated through the international trade of amphibians. To our knowledge, Bsal has not arrived to North America. As a proactive strategy for disease control, we evaluated how a range of environmental temperatures in North America could affect invasion risk of Bsal into a widely distributed salamander species, the eastern newt (Notophthalmus viridescens). Our results show that northeastern USA, southeastern Canada, and the higher elevations of the Appalachian Mountains have the greatest likelihood of Bsal invasion, when temperature-dependent susceptibility is included in risk analyses. Changes in eastern newt susceptibility to Bsal infection associated with temperature are likely an interaction between pathogen replication rate and host immune defenses, including changes in skin microbiome composition and the host’s ability to produce Bsal-killing proteins on the skin. Our study provides new insights into how latitude, elevation and season can impact the epidemiology of Bsal, and suggests that strategies that manipulate microclimate of newt habitats could be useful in managing Bsal outbreaks and that climate change will impact Bsal invasion probability.

Preparatory immunity: Seasonality of mucosal skin defences and Batrachochytrium infections in Southern leopard frogs

Accurately predicting the impacts of climate change on wildlife health requires a deeper understanding of seasonal rhythms in host-pathogen interactions. The amphibian pathogen, Batrachochytrium dendrobatidis (Bd), exhibits seasonality in incidence; however, the role that biological rhythms in host defences play in defining this pattern remains largely unknown. The aim of this study was to examine whether host immune and microbiome defences against Bd correspond with infection risk and seasonal fluctuations in temperature and humidity. Over the course of a year, five populations of Southern leopard frogs (Rana [Lithobates] sphenocephala) in Tennessee, United States, were surveyed for host immunity, microbiome and pathogen dynamics. Frogs were swabbed for pathogen load and skin bacterial diversity and stimulated to release stored antimicrobial peptides (AMPs). Secretions were analysed to estimate total hydrophobic peptide concentrations, presence of known AMPs and effectiveness of Bd growth inhibition in vitro. The diversity and proportion of bacterial reads with a 99% match to sequences of isolates known to inhibit Bd growth in vitro were used as an estimate of predicted anti-Bd function of the skin microbiome. Batrachochytrium dendrobatidis dynamics followed the expected seasonal fluctuations-peaks in cooler months-which coincided with when host mucosal defences were most potent against Bd. Specifically, the concentration and expression of stored AMPs cycled synchronously with Bd dynamics. Although microbiome changes followed more linear trends over time, the proportion of bacteria that can function to inhibit Bd growth was greatest when risk of Bd infection was highest. We interpret the increase in peptide storage in the fall and the shift to a more anti-Bd microbiome over winter as a preparatory response for subsequent infection risk during the colder periods when AMP synthesis and bacterial growth is slow and pathogen pressure from this cool-adapted fungus is high. Given that a decrease in stored AMP concentrations as temperatures warm in spring likely means greater secretion rates, the subsequent decrease in prevalence suggests seasonality of Bd in this host may be in part regulated by annual immune rhythms, and dominated by the effects of temperature.

Preparing for invasion: Assessing risk of infection by chytrid fungi in southeastern plethodontid salamanders

Understanding the responses of naïve communities to the invasion of multihost pathogens requires accurate estimates of susceptibility across taxa. In the Americas, the likely emergence of a second amphibian pathogenic fungus (Batrachochytrium salamandrivorans, Bsal) calls for new ways of prioritizing disease mitigation among species due to the high diversity of naïve hosts with prior B. dendrobatidis (Bd) infections. Here, we applied the concept of pathogenic potential to quantify the virulence of chytrid fungi on naïve amphibians and evaluate species for conservation efforts in the event of an outbreak. The benefit of this measure is that it combines and summarizes the variation in disease effects into a single numerical index, allowing for comparisons across species, populations or groups of individuals that may inherently exhibit differences in susceptibility. As a proof of concept, we obtained standardized responses of disease severity by performing experimental infections with Bsal on five plethodontid salamanders from southeastern United States. Four out of five species carried natural infections of Bd at the start of the experiments. We showed that Bsal exhibited its highest value of pathogenic potential in a species that is already declining (Desmognathus auriculatus). We find that this index provides additional information beyond the standard measures of disease prevalence, intensity, and mortality, because it leveraged these disease parameters within each categorical group. Scientists and practitioners could use this measure to justify research, funding, trade, or conservation measures.

Immunological Aspects of Chytridiomycosis

Amphibians are currently the most threatened vertebrate class, with the disease chytridiomycosis being a major contributor to their global declines. Chytridiomycosis is a frequently fatal skin disease caused by the fungal pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal). The severity and extent of the impact of the infection caused by these pathogens across modern Amphibia are unprecedented in the history of vertebrate infectious diseases. The immune system of amphibians is thought to be largely similar to that of other jawed vertebrates, such as mammals. However, amphibian hosts are both ectothermic and water-dependent, which are characteristics favouring fungal proliferation. Although amphibians possess robust constitutive host defences, Bd/Bsal replicate within host cells once these defences have been breached. Intracellular fungal localisation may contribute to evasion of the induced innate immune response. Increasing evidence suggests that once the innate defences are surpassed, fungal virulence factors suppress the targeted adaptive immune responses whilst promoting an ineffectual inflammatory cascade, resulting in immunopathology and systemic metabolic disruption. Thus, although infections are contained within the integument, crucial homeostatic processes become compromised, leading to mortality. In this paper, we present an integrated synthesis of amphibian post-metamorphic immunological responses and the corresponding outcomes of infection with Bd, focusing on recent developments within the field and highlighting future directions.

The amphibian complement system and chytridiomycosis

Understanding host immune function and ecoimmunology is increasingly important at a time when emerging infectious diseases (EIDs) threaten wildlife. One EID that has emerged and spread widely in recent years is chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), which is implicated unprecedented amphibian declines around the world. The impacts of Bd have been severe for many amphibian species, but some populations have exhibited signs of persistence, and even recovery, in some regions. Many mechanisms may underpin this pattern and amphibian immune responses are likely one key component. Although we have made great strides in understanding amphibian immunity, the complement system remains poorly understood. The complement system is a nonspecific, innate immune defense that is known to enhance other immune responses. Complement activation can occur by three different biochemical pathways and result in protective mechanisms, such as inflammation, opsonization, and pathogen lysis, thereby providing protection to the host. We currently lack an understanding of complement pathway activation for chytridiomycosis, but several studies have suggested that it may be a key part of an early and robust immune response that confers host resistance. Here, we review the available research on the complement system in general as well as amphibian complement responses to Bd infection. Additionally, we propose future research directions that will increase our understanding of the amphibian complement system and other immune responses to Bd. Finally, we suggest how a deeper understanding of amphibian immunity could enhance the conservation and management of amphibian species that are threatened by chytridiomycosis.