Amphibian chytridiomycosis in Japan: distribution, haplotypes and possible route of entry into Japan

Widespread occurrence of the amphibian chytrid panzootic lineage in Uruguay is constrained by climate

The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) causes chytridiomycosis, a disease among the main causes of amphibian declines worldwide. However, Bd studies on Neotropical amphibians from temperate areas are scarce. We present a comprehensive survey of Bd in Uruguay, in temperate central eastern South America, carried out between 2006 and 2014. Skin swabs of 535 specimens of 21 native and exotic frogs were tested by PCR. We used individual-level data to examine the relationship between infection, climatic variables, and their effects on body condition and the number of prey items found in stomach contents. Infection was widespread in free-ranging anurans with an overall prevalence of 41.9%, detected in 15 native species, wild American bullfrogs Aquarana catesbeiana, and captive specimens of Ceratophrys ornata and Xenopus laevis. Three haplotypes of the Bd ITS region were identified in native amphibians, all belonging to the global panzootic lineage (BdGPL), of which only one was present in exotic hosts. Despite high infection frequencies in different anurans, we found no evidence of morbidity or mortality attributable to chytridiomycosis, and we observed no discernible impact on body condition or consumed prey. Climatic conditions at the time of our surveys suggested that the chance of infection is associated with monthly mean temperature, mean humidity, and total precipitation. Temperatures below 21°C combined with moderate humidity and pronounced rainfall may increase the likelihood of infection. Multiple haplotypes of BdGPL combined with high frequencies of infection suggest an enzootic pattern in native species, underscoring the need for continued monitoring.

Coevolution of a generalist pathogen with many hosts: the case of the amphibian chytrid Batrachochytrium dendrobatidis

Generalist pathogens maintain infectivity in numerous hosts; how this broad ecological niche impacts host-pathogen coevolution remains to be widely explored. Batrachochytrium dendrobatidis (Bd) is a highly generalist pathogenic fungus that has caused devastating declines in hundreds of amphibian species worldwide. This review examines amphibian chytridiomycosis host-pathogen interactions and available evidence for coevolution between Bd and its numerous hosts. We summarize recent evidence showing that Bd genotypes vary in geographic distribution and virulence, and that amphibian species also vary in Bd susceptibility according to their geographic distribution. How much variation can be explained by phenotypic plasticity or genetic differences remains uncertain. Recent research suggests that Bd genotypes display preferences for specific hosts and that some hosts are undergoing evolution as populations rebound from Bd outbreaks. Taken together, these findings suggest the potential for coevolution to occur and illuminate a path for addressing open questions through integrating historical and contemporary genetic data.

Sequence capture identifies fastidious chytrid fungi directly from host tissue

The chytrid fungus Batrachochytrium dendrobatidis (Bd) was discovered in 1998 as the cause of chytridiomycosis, an emerging infectious disease causing mass declines in amphibian populations worldwide. The rapid population declines of the 1970s-1990s were likely caused by the spread of a highly virulent lineage belonging to the Bd-GPL clade that was introduced to naïve susceptible populations. Multiple genetically distinct and regional lineages of Bd have since been isolated and sequenced, greatly expanding the known biological diversity within this fungal pathogen. To date, most Bd research has been restricted to the limited number of samples that could be isolated using culturing techniques, potentially causing a selection bias for strains that can grow on media and missing other unculturable or fastidious strains that are also present on amphibians. We thus attempted to characterize potentially non-culturable genetic lineages of Bd from distinct amphibian taxa using sequence capture technology on DNA extracted from host tissue and swabs. We focused our efforts on host taxa from two different regions that likely harbored distinct Bd clades: (1) wild-caught leopard frogs (Rana) from North America, and (2) a Japanese Giant Salamander (Andrias japonicus) at the Smithsonian Institution's National Zoological Park that exhibited signs of disease and tested positive for Bd using qPCR, but multiple attempts failed to isolate and culture the strain for physiological and genetic characterization. We successfully enriched for and sequenced thousands of fungal genes from both host clades, and Bd load was positively associated with number of recovered Bd sequences. Phylogenetic reconstruction placed all the Rana-derived strains in the Bd-GPL clade. In contrast, the A. japonicus strain fell within the Bd-Asia3 clade, expanding the range of this clade and generating additional genomic data to confirm its placement. The retrieved ITS locus matched public barcoding data from wild A. japonicus and Bd infections found on other amphibians in India and China, suggesting that this uncultured clade is widespread across Asia. Our study underscores the importance of recognizing and characterizing the hidden diversity of fastidious strains in order to reconstruct the spatiotemporal and evolutionary history of Bd. The success of the sequence capture approach highlights the utility of directly sequencing pathogen DNA from host tissue to characterize cryptic diversity that is missed by culture-reliant approaches.

OCCURRENCE OF PATHOGENIC CHYTRID FUNGI BATRACHOCHYTRIUM SALAMANDRIVORANS AND BATRACHOCHYTRIUM DENDROBATIDIS IN THE HONG KONG NEWT (PARAMESOTRITON HONGKONGENSIS) AND OTHER WILD AND IMPORTED AMPHIBIANS IN A SUBTROPICAL ASIAN REGION

One of the major threats for the massive loss in global amphibian diversity is chytridiomycosis, caused by chytrid fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal). Following its discovery in 2013, Bsal has emerged as a severe threat to the global survival of urodelans. In 2018, a study reported a high prevalence of Bsal (65.6%) in the Hong Kong newts (Paramesotriton hongkongensis, Near Threatened) of a southern China population adjacent to Hong Kong (HK). Uncertainty regarding the Bsal infection status of P. hongkongensis inhabiting HK raised deep concern over the risk of introducing Bsal from that population. We screened the skin swabs from wild individuals of P. hongkongensis, 15 sympatric amphibian species, and 16 imported amphibian species in HK for chytrids. We found that both Bsal and Bd occur in low prevalences in P. hongkongensis (Bsal 1.7%, 5/293; Bd 0.34%, 1/293), Hong Kong cascade frog, Amolops hongkongensis, family Ranidae (Bsal only, 5.26%, 1/19), and Asian common toad, Duttaphrynus melanostictus, family Bufonidae (Bsal only, 5.88%, 1/17), populations of HK, with infected individuals being asymptomatic, suggesting a potential role of these species as reservoirs of Bsal. Conversely, Bd, but not Bsal, was present on 13.2% (9/68) of imported amphibians, indicating a high chytrid introduction risk posed by international amphibian trade. Long-term surveillance of the presence of Bd and Bsal in wild and captive amphibians would be advisable, and we recommend that import and export of nonnative chytrid carriers should be prevented, especially to those regions with amphibian populations naïve to Bd and Bsal.

Oogamochlamys kurilensis sp. nov. (Chlorophyta, Volvocales) from the Soils of Iturup Island (Sakhalin Region, Russia)

A strain of oogamous biflagellate green alga was isolated during a study on soil algal diversity in the Russian Far East (Sakhalin Region, Iturup Island) and examined using an integrative approach. Phylogenetic analyses, based on the SSU rDNA gene, resolved the new strain as a part of the RL clade (sensu Watanabe and Nakada) within Oogamochlamydinia (Volvocales, Chlorophyceae). The strain was similar to members of the genus Oogamochlamys (parietal and massive cup-shaped chloroplasts; two apical contractile vacuoles), but was, however, distinguished from them based on the size and shape of the mature vegetative cells, the flagellar length, the presence of only one pyrenoid in both the mature vegetative cells and the zoospores, the anterior nucleus position, and the spermatozoids' shape. Although a concept of the genus Oogamochlamys has been compromised in recent phylogenetic analysis based on the SSU rDNA sequence data and its likely affinity to anisogamous Chlamydomonas allensworthii, we described the strain from Iturup Island as Oogamochlamys kurilensis sp. nov.

Pathogenic selection promotes adaptive immune variations against serious bottlenecks in early invasions of bullfrogs

Adaptive genetic variations are key for understanding evolutionary processes influencing invasions. However, we have limited knowledge on how adaptive genetic diversity in invasive species responds to new pathogenic environments. Here, we compared variations in immune major histocompatibility complex (MHC) class-II β gene and neutral loci in relation to pathogenic chytrid fungus (Batrachochytrium dendrobatidis, Bd) infection across invasive and native populations of American bullfrog between China and United States (US). Chinese invasive populations show a 60% reduction in neutral cytb variations relative to US native populations, and there were similar MHC variation and functional diversity between them. One MHC allele private to China was under recent positive selection and associated with decreased Bd infection, partly explaining the lower Bd prevalence for Chinese populations than for native US populations. These results suggest that pathogen-mediated selection favors adaptive MHC variations and functional diversity maintenance against serious bottlenecks during the early invasions (within 15 generations) of bullfrogs.

Conserved Evolution of MHC Supertypes among Japanese Frogs Suggests Selection for Bd Resistance

The chytrid fungus Batrachochytrium dendrobatidis (Bd) is a major threat to amphibians, yet there are no reports of major disease impacts in East Asian frogs. Genetic variation of the major histocompatibility complex (MHC) has been associated with resistance to Bd in frogs from East Asia and worldwide. Using transcriptomic data collated from 11 Japanese frog species (one individual per species), we isolated MHC class I and IIb sequences and validated using molecular cloning. We then compared MHC from Japanese frogs and other species worldwide, with varying Bd susceptibility. Supertyping analysis, which groups MHC alleles based on physicochemical properties of peptide binding sites, identified that all examined East Asian frogs contained at least one MHC-IIb allele belonging to supertype ST-1. This indicates that, despite the large divergence times between some Japanese frogs (up to 145 million years), particular functional properties in the peptide binding sites of MHC-II are conserved among East Asian frogs. Furthermore, preliminary analysis using NetMHCIIpan-4.0, which predicts potential Bd-peptide binding ability, suggests that MHC-IIb ST-1 and ST-2 have higher overall peptide binding ability than other supertypes, irrespective of whether the peptides are derived from Bd, other fungi, or bacteria. Our findings suggest that MHC-IIb among East Asian frogs may have co-evolved under the same selective pressure. Given that Bd originated in this region, it may be a major driver of MHC evolution in East Asian frogs.

Major Emerging Fungal Diseases of Reptiles and Amphibians

Emerging infectious diseases (EIDs) are caused by pathogens that have undergone recent changes in terms of geographic spread, increasing incidence, or expanding host range. In this narrative review, we describe three important fungal EIDs with keratin trophism that are relevant to reptile and amphibian conservation and veterinary practice. Nannizziopsis spp. have been mainly described in saurians; infection results in thickened, discolored skin crusting, with eventual progression to deep tissues. Previously only reported in captive populations, it was first described in wild animals in Australia in 2020. Ophidiomyces ophidiicola (formely O. ophiodiicola) is only known to infect snakes; clinical signs include ulcerating lesions in the cranial, ventral, and pericloacal regions. It has been associated with mortality events in wild populations in North America. Batrachochytrium spp. cause ulceration, hyperkeratosis, and erythema in amphibians. They are a major cause of catastrophic amphibian declines worldwide. In general, infection and clinical course are determined by host-related characteristics (e.g., nutritional, metabolic, and immune status), pathogens (e.g., virulence and environmental survival), and environment (e.g., temperature, hygrometry, and water quality). The animal trade is thought to be an important cause of worldwide spread, with global modifications in temperature, hygrometry, and water quality further affecting fungal pathogenicity and host immune response.

Novel chytrid pathogen variants and the global amphibian pet trade

Global wildlife trade spreads emerging infectious diseases that threaten biodiversity. The amphibian chytrid pathogen Batrachochytrium dendrobatidis (Bd) has caused population declines and species extinctions worldwide except in Asia. Fire-bellied toads (Bombina orientalis), exported in large numbers from Asia, are tolerant of Bd and carry hypervirulent ancestral chytrid BdAsia-1 variants. We assayed the virulence of a new isolate of BdAsia-1 on the model Australasian frog host Litoria caerulea. Infected individuals (n = 15) all showed rapid disease progression culminating in death, whereas sham-inoculated individuals (n = 10) presented no clinical signs of disease and all survived (log rank test, χ² = 15.6, df = 1, p < 0.0001). The virulence of the new isolate of BdAsia-1 is comparable to the one we assayed previously (χ² = 0.0, df = 1, p = 0.91). Internationally traded wildlife, even when they appear healthy, can carry hypervirulent variants of pathogens. Once new pathogen variants escape into the environment, native species that have had no opportunity to evolve resistance to them may perish. Our study suggests that hypervirulent pathogens are being spread by the international pet trade. Notifiable wildlife diseases attributable to locally endemic pathogens often fail to generate conservation concern so are rarely subject to border surveillance or import controls. Because of the danger novel variants pose, national border control agencies need to implement disease screening and quarantine protocols to ensure the safety of their endemic fauna.

Environment is associated with chytrid infection and skin microbiome richness on an amphibian rich island (Taiwan)

Growing evidence suggests that the origins of the panzootic amphibian pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) are in Asia. In Taiwan, an island hotspot of high amphibian diversity, no amphibian mass mortality events linked to Bd or Bsal have been reported. We conducted a multi-year study across this subtropical island, sampling 2517 individuals from 30 species at 34 field sites, between 2010 and 2017, and including 171 museum samples collected between 1981 and 2009. We analyzed the skin microbiome of 153 samples (6 species) from 2017 in order to assess any association between the amphibian skin microbiome and the probability of infection amongst different host species. We did not detect Bsal in our samples, but found widespread infection by Bd across central and northern Taiwan, both taxonomically and spatially. Museum samples show that Bd has been present in Taiwan since at least 1990. Host species, geography (elevation), climatic conditions and microbial richness were all associated with the prevalence of infection. Host life-history traits, skin microbiome composition and phylogeny were associated with lower prevalence of infection for high altitude species. Overall, we observed low prevalence and burden of infection in host populations, suggesting that Bd is enzootic in Taiwan where it causes subclinical infections. While amphibian species in Taiwan are currently threatened by habitat loss, our study indicates that Bd is in an endemic equilibrium with the populations and species we investigated. However, ongoing surveillance of the infection is warranted, as changing environmental conditions may disturb the currently stable equilibrium.

Microflora Influence: The Aquatic Environment Changes Grouping Risk and Development Speed of Toad Tadpoles

In addition to habitat loss and fragmentation, behavioral traits and the deterioration of water environments also contribute to the local extinction of amphibians. Abundant microflora in urban ponds may cause fatal diseases, whereas symbiotic bacteria may protect the host from pathogens; these effects may vary with group size. In this study, I monitored the growth of Japanese common toad (Bufo japonicus) larvae in Tokyo using three different group sizes: 1 (solitary), 2 (pair), and 15. Although there was no genetic bias in the major histocompatibility complex (MHC) class II genes or microsatellite loci to the survival of the larvae, the mortality risk of the larvae reared in pond water was higher than that of those reared in tap water. According to the survival analysis, the risk was more significant when the group size was 15. This result would be unwelcomed for the B. japonicus tadpoles, which have habits of social aggregation. Furthermore, larval metamorphosis took longer to complete in pond than tap water without any difference in body length or mass. These findings provide fundamental insight into the impact of the aquatic environment and the effect of the group size on animal health and conservation.

Host species is linked to pathogen genotype for the amphibian chytrid fungus (Batrachochytrium dendrobatidis)

Host-pathogen specificity can arise from certain selective environments mediated by both the host and pathogen. Therefore, understanding the degree to which host species identity is correlated with pathogen genotype can help reveal historical host-pathogen dynamics. One animal disease of particular concern is chytridiomycosis, typically caused by the global panzootic lineage of the amphibian chytrid fungus (Batrachochytrium dendrobatidis, Bd), termed Bd-GPL. This pathogen lineage has caused devastating declines in amphibian communities around the world. However, the site of origin for the common ancestor of modern Bd-GPL and the fine-scale transmission dynamics of this lineage have remained a mystery. This is especially the case in North America where Bd-GPL is widespread, but disease outbreaks occur sporadically. Herein, we use Bd genetic data collected throughout the United States from amphibian skin swabs and cultured isolate samples to investigate Bd genetic patterns. We highlight two case studies in Pennsylvania and Nevada where Bd-GPL genotypes are strongly correlated with host species identity. Specifically, in some localities bullfrogs (Rana catesbeiana) are infected with Bd-GPL lineages that are distinct from those infecting other sympatric amphibian species. Overall, we reveal a previously unknown association of Bd genotype with host species and identify the eastern United States as a Bd diversity hotspot and potential site of origin for Bd-GPL.

New Species of Chloroidium (Trebouxiophyceae, Chlorophyta) from East Asia

Chlorella-like green algae that reproduce only asexually by immotile autospores or motile zoospores are the most typical inhabitants of non-aquatic environments. They have a simple morphology that hampers their differentiation, but algae of such habit represent a diverse array of lineages, which are mostly in the classes Chlorophyceae and Trebouxiophyceae. One of these lineages is the order Watanabeales (Watanabea clade; Trebouxiophyceae), which comprises 10 genera that share a distinct mode of reproduction through unequally sized autospores. Most of these genera account for a few species that are rarely recorded in nature. In contrast, the genus Chloroidium is one of the most species-rich and widely distributed members of the order. Three strains of coccoid green alga were isolated during a study of soil algae in the temperate monsoon climate zone of Asia. These strains are described here as a new species, Chloroidium orientalis. SSU and ITS rDNA sequence data, morphological characteristics, and life cycle features differentiate these strains from known members of the genus.

Alien Smooth Newts (Lissotriton vulgaris) in Australia Are Infected with Batrachochytrium dendrobatidis but Test Negative for Ranaviruses

Smooth newts (Lissotriton vulgaris) established recently in Melbourne, Australia. Previously, the population's disease status was unknown. Samples from 34 adults and 78 larvae, collected 2011-2016, were tested for two pathogens driving the global amphibian extinction crisis. The fungus Batrachochytrium dendrobatidis was identified (6.3% qPCR positive); ranaviruses were not detected.

Chytridiomycosis Outbreak in a Chilean Giant Frog (Calyptocephalella gayi) Captive Breeding Program: Genomic Characterization and Pathological Findings

Emerging infectious diseases in wildlife are increasingly associated with animal mortality and species declines, but their source and genetic characterization often remains elusive. Amphibian chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), has been associated with catastrophic and well-documented amphibian population declines and extinctions at the global scale. We used histology and whole-genome sequencing to describe the lesions caused by, and the genetic variability of, two Bd isolates obtained from a mass mortality event in a captive population of the threatened Chilean giant frog (Calyptocephalella gayi). This was the first time an association between Bd and high mortality had been detected in this charismatic and declining frog species. Pathological examinations revealed that 30 dead metamorphosed frogs presented agnathia or brachygnathia, a condition that is reported for the first time in association with chytridiomycosis. Phylogenomic analyses revealed that Bd isolates (PA1 and PA2) from captive C. gayi group with other Bd isolates (AVS2, AVS4, and AVS7) forming a single highly supported Chilean Bd clade within the global panzootic lineage of Bd (BdGPL). These findings are important to inform the strengthening of biosecurity measures to prevent the impacts of chytridiomycosis in captive breeding programs elsewhere.

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.

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.

Distribution and Genetic Diversity of the Amphibian Chytrid in Japan

While research on frog chytrid fungus Batrachochytrium dendrobatidis (Bd), an infectious disease that threatens amphibian diversity, continues to advance worldwide, little progress has been made in Japan since around 2010. The reason for this is, which we pointed out in 2009, that the origin of frog chytrid fungus may be in the East Asian region, including Japan based on the Bd ITS-DNA variation, and as few cases of mass mortality caused by this fungus have been observed in wild amphibian populations in Japan, the interest of the Japanese government and the general public in Bd has waned. However, we believe that organizing the data obtained so far in Japan and distributing the status of frog chytrid fungus in Japan to the world will provide useful insight for future risk management of this pathogen. We collected more than 5500 swab samples from wild amphibians throughout Japan from 2009 to 2010. Then, we investigated the infection status using the Nested-PCR method. We sequenced the obtained DNA samples and constructed a maximum-parsimony (MP) tree to clarify the phylogenetic diversity of Bd. We detected Bd infection in 11 (nine native and two alien) amphibian species in Japan and obtained 44 haplotypes of Bd ITS-DNA. The MP tree showed a high diversity of Bd strains in Japan, suggesting that some strains belong to Bd-GPL and Bd-Brazil. Except for local populations of the Japanese giant salamanders Andrias japonicus in Honshu Island and the sword tail newts Cynops ensicauda in Okinawa Island, the Bd infection prevalence in native amphibian species was very low. The alien bullfrog Aquarana catesbeiana had high Bd infection rates in all areas where they were sampled. No Bd infection was detected in other native amphibians in the areas where giant salamanders, sword tail newts, and bullfrogs were collected, suggesting that many native amphibians are resistant to Bd infection. The sword tail newt of Okinawa Island had both the highest infectious incidence and greatest number of haplotypes. The giant salamanders also showed relatively high infection prevalence, but the infected strains were limited to those specific to this species. These two Caudata species are endemic to a limited area of Japan, and it was thought that they may have been refugia for Bd, which had been distributed in Japan Islands for a long time.

Chytridiomycosis in Asian Amphibians, a Global Resource for Batrachochytrium dendrobatidis (Bd) Research

Chytridiomycosis is an emerging infectious disease affecting amphibians globally and it is caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd). Chytridiomycosis has caused dramatic declines and even extinctions in wild amphibian populations in Europe, Australia, Central and North America. Spanning over two and a half decades, extensive research has led to discovery of epizootic and enzootic lineages of this pathogen. However, the Bd–amphibian system had garnered less attention in Asia until recently when an ancestral Bd lineage was identified in the Korean peninsula. Amphibians co-exist with the pathogen in Asia, only sub-lethal effects have been documented on hosts. Such regions are ‘coldspots’ of infection and are an important resource to understand the dynamics between the enzootic pathogen—Bd and its obligate host—amphibians. Insights into the biology of infection have provided new knowledge on the multi-faceted interaction of Bd in a hyperdiverse Asian amphibian community. We present the findings and highlight the knowledge gap that exists, and propose the ways to bridge them. We emphasize that chytridiomycosis in Asia is an important wildlife disease and it needs focussed research, as it is a dynamic front of pathogen diversity and virulence.

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

Environmental DNA (eDNA) is becoming an indispensable tool in biodiversity monitoring, including the monitoring of invasive species and pathogens. Aquatic chytrid fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal) are major threats to amphibians. However, the use of eDNA for detecting these pathogens has not yet become widespread, due to technological and economic obstacles. Using the enhanced eDNA approach (a simple and cheap sampling protocol) and the universally accepted qPCR assay, we confirmed the presence of Bsal and Bd in previously identified sites in Spain, including four sites that were new for Bsal. The new approach was successfully tested in laboratory conditions using manufactured gene fragments (gBlocks) of the targeted DNA sequence. A comparison of storage methods showed that samples kept in ethanol had the best DNA yield. Our results showed that the number of DNA copies in the Internal Transcribed Spacer region was 120 copies per Bsal cell. Eradication of emerging diseases requires quick and cost-effective solutions. We therefore performed cost-efficiency analyses of standard animal swabbing, a previous eDNA approach, and our own approach. The procedure presented here was evaluated as the most cost-efficient. Our findings will help to disseminate information about efforts to prevent the spread of chytrid fungi.

First Report of Binucleate Rhizoctonia AG-L Causing Root and Stem Rot of Wishbone Flower (Torenia fournieri) in Taiwan

Wishbone flower (Torenia fournieri L.) is a common ornamental plant for flower bed in Taiwan. In August 2018, root and stem rot of wishbone flower occurred on the flower bed in the campus of National Chung Hsing University, Taichung city, with 100% incidence. Symptoms were dark brown discoloration of basal stems and brown necrosis of roots. Lesions from base of stems were excised into 5 mm long fragments, which were then surface sterilized in 1% sodium hydrochloride for 1 min, rinsed in sterile distilled water, dried on filter paper and thereafter placed onto 2% water agar. After 24 h, hyphae characteristic of Rhizoctonia (Sneh et al. 1991) appeared and dominated in every isolation. Hyphal tips were transferred to potato dextrose agar (PDA). After 5 days of incubation at 28°C, characteristic brown colonies of Rhizoctonia (Sneh et al. 1991) were observed. Hyphal width was 4.29±0.52 μm. No sclerotia were visibly present after 21 days of growth on PDA at 28°C. Hyphae were stained by 0.3% safranin-O and 1% KOH. There were two nuclei in each hyphal compartment, suggesting a binucleate Rhizoctonia fungus. ITS sequence has been used as the best tool to identify specific anastomosis group (AG) of Rhizoctonia as shown by Sharon et al. (2006, 2008). ITS sequence was amplified using the primers Bd1a and ITS4 (Goka et al. 2009; White et al. 1990). Blast search analysis of this acquired sequence (acc. no. LC498494) revealed the highest similarity (98.75 to 99.83%) with the reference sequences (acc. nos. AB286934, AB286933, and AB196653) of binucleate Rhizoctonia AG-L, namely Ceratobasidium sp. AG-L. Pathogenicity test was carried out using seedlings of 4-week-old wishbone flower each grown in a pot of 6.35 cm diameter. To prepare the inoculum, a PDA agar block (6 mm in diameter) excised from the growing front of 5-day-old colony was transferred into a flask with 200 ml of potato dextrose broth (PDB) incubated in a shaker at 26°C and 120 rpm for 6 days. The PDB broth was then blended into slurry. Ten pots each with a seedling were inoculated by pouring 50 ml of slurry onto the potting medium. Five pots were served as the controls by pouring PDB only. Pots were maintained in a greenhouse (26 to 33°C). Three days after inoculation, all inoculated plants exhibited symptom of root and stem rot. The same fungus was reisolated and confirmed by sequencing rDNA-ITS. This is the first report of root and stem rot of wishbone flower caused by binucleate Rhizoctonia AG-L in Taiwan and in the world. Although this is the second cases, since Wang and Hsieh (1993), for binucleate Rhizoctonia AG-L to be pathogenic, this study shows that this fungus has the potential to cause damages and is worth of further investigations.

First Detection of Batrachochytrium dendrobatidis in Wild Frogs from Bangladesh

Global amphibian populations are facing a novel threat, chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), which is responsible for the severe decline of a number of species across several continents. Chytridiomycosis in Asia is a relatively recent discovery yet there have been no reports on Bd-presence in Bangladeshi amphibians. We conducted a preliminary study on 133 wild frogs from seven sites in Bangladesh between April and July 2018. Nested PCR analysis showed 20 samples (15.04%) and 50% of the tested taxa (9 species from 6 genera and 4 families) as Bd-positive. Eight of the nine species are discovered as newly infected hosts. Analysis of Bd-positive samples shows prevalence does not significantly vary among different land cover categories, although the occurrence is higher in forested areas. The prevalence rate is similar in high and low disturbed areas, but the range of occurrence is statistically higher in low disturbance areas. Maximum entropy distribution modeling indicates high probabilities of Bd occurrence in hilly and forested areas in southeast and central-north Bangladesh. The Bd-specific ITS1-5.8S-ITS2 ribosomal gene sequence from the Bd-positive samples tested is completely identical. A neighbor-joining phylogenetic tree reveals that the identified strain shares a common ancestry with strains previously discovered in different Asian regions. Our results provide the first evidence of Bd-presence in Bangladeshi amphibians, inferring that diversity is at risk. The effects of environmental and climatic factors along with quantitative PCR analysis are required to determine the infection intensity and susceptibility of amphibians in the country.

Genotyping and differential bacterial inhibition of Batrachochytrium dendrobatidis in threatened amphibians in Costa Rica

Amphibians have declined around the world in recent years, in parallel with the emergence of an epidermal disease called chytridiomycosis, caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd). This disease has been associated with mass mortality in amphibians worldwide, including in Costa Rica, and Bd is considered an important contributor to the disappearance of this group of vertebrates. While many species are susceptible to the disease, others show tolerance and manage to survive infection with the pathogen. We evaluated the pathogen Bd circulating in Costa Rica and the capacity of amphibian skin bacteria to inhibit the growth of the pathogen in vitro. We isolated and characterized - genetically and morphologically - several Bd isolates from areas with declining populations of amphibians. We determined that the circulating chytrid fungus in Costa Rica belongs to the virulent strain Bd-GPL-2, which has been related to massive amphibian deaths worldwide; however, the isolates obtained showed genetic and morphological variation. Furthermore, we isolated epidermal bacteria from 12 amphibian species of surviving populations, some in danger of extinction, and evaluated their inhibitory activity against the collection of chytrid isolates. Through bioassays we confirmed the presence of chytrid-inhibitory bacterial genera in Costa Rican amphibians. However, we observed that the inhibition varied between different isolates of the same bacterial genus, and each bacterial isolation inhibited fungal isolation differently. In total, 14 bacterial isolates belonging to the genera Stenotrophomonas, Streptomyces, Enterobacter, Pseudomonas and Klebsiella showed inhibitory activity against all Bd isolates. Given the observed variation both in the pathogen and in the bacterial inhibition capacity, it is highly relevant to include local isolates and to consider the origin of the microorganisms when performing in vivo infection tests aimed at developing and implementing mitigation strategies for chytridiomycosis.

Early presence of Batrachochytrium dendrobatidis in Mexico with a contemporary dominance of the global panzootic lineage

Chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), is a devastating infectious disease of amphibians. Retrospective studies using museum vouchers and genetic samples supported the hypothesis that Bd colonized Mexico from North America and then continued to spread into Central and South America, where it led to dramatic losses in tropical amphibian biodiversity (the epizootic wave hypothesis). While these studies suggest that Bd has been in Mexico since the 1970s, information regarding the historical and contemporary occurrence of different pathogen genetic lineages across the country is limited. In the current study, we investigated the historical and contemporary patterns of Bd in Mexico. We combined the swabbing of historical museum vouchers and sampling of wild amphibians with a custom Bd genotyping assay to assess the presence, prevalence, and genetic diversity of Bd over time in Mexico. We found Bd-positive museum specimens from the late 1800s, far earlier than previous records and well before recent amphibian declines. With Bd genotypes from samples collected between 1975-2019, we observed a contemporary dominance of the global panzootic lineage in Mexico and report four genetic subpopulations and potential for admixture among these populations. The observed genetic variation did not have a clear geographic signature or provide clear support for the epizootic wave hypothesis. These results provide a framework for testing new questions regarding Bd invasions and their temporal relationship to observed amphibian declines in the Americas.

Mechanisms underlying host persistence following amphibian disease emergence determine appropriate management strategies

Emerging infectious diseases have caused many species declines, changes in communities and even extinctions. There are also many species that persist following devastating declines due to disease. The broad mechanisms that enable host persistence following declines include evolution of resistance or tolerance, changes in immunity and behaviour, compensatory recruitment, pathogen attenuation, environmental refugia, density-dependent transmission and changes in community composition. Here we examine the case of chytridiomycosis, the most important wildlife disease of the past century. We review the full breadth of mechanisms allowing host persistence, and synthesise research on host, pathogen, environmental and community factors driving persistence following chytridiomycosis-related declines and overview the current evidence and the information required to support each mechanism. We found that for most species the mechanisms facilitating persistence have not been identified. We illustrate how the mechanisms that drive long-term host population dynamics determine the most effective conservation management strategies. Therefore, understanding mechanisms of host persistence is important because many species continue to be threatened by disease, some of which will require intervention. The conceptual framework we describe is broadly applicable to other novel disease systems.

Genetic analysis of post-epizootic amphibian chytrid strains in Bolivia: Adding a piece to the puzzle

The evolutionary history and dispersal pattern of Batrachochytrium dendrobatidis (Bd), an emergent fungal pathogen responsible for the decline and extinctions of many species of amphibians worldwide, is still not well understood. In South America, the tropical Andes are known as an important site for amphibian diversification, but also for being a place where hosts are at greater risk of chytridiomycosis. In an attempt to understand the history and the geographic pattern of Bd-associated amphibian declines in Bolivia, we isolated Bd from hosts at two locations that differ in their chronology of Bd prevalence and host survival outcome, the cloud forests of the Amazonian slopes of the Andes and Lake Titicaca in the altiplano. We genotyped Bd from both locations and sequenced the genome from the cloud forest isolate and then compared them to reference sequences of other Bd strains across the world. We found that the Bolivian chytrid isolates were nearly genotypically identical and that they belong to the global panzootic lineage (Bd-GPL). The Bolivian Bd strain grouped with other tropical New World strains but was closest to those from the Brazilian Atlantic Forest. Our results extend the presence of Bd-GPL to the central Andes in South America and report this hypervirulent strain at Lago Titicaca, where Bd has been detected since 1863, without evidence of amphibian declines. These findings suggest a more complex evolutionary history for this pathogen in Bolivia and may point to the existence of an old lineage of Bd that has since been extirpated following the arrival of the panzootic Bd-GPL or that the timing of Bd-GPL emergence is earlier than generally acknowledged.

Chytrid fungi and global amphibian declines

Discovering that chytrid fungi cause chytridiomycosis in amphibians represented a paradigm shift in our understanding of how emerging infectious diseases contribute to global patterns of biodiversity loss. In this Review we describe how the use of multidisciplinary biological approaches has been essential to pinpointing the origins of amphibian-parasitizing chytrid fungi, including Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans, as well as to timing their emergence, tracking their cycles of expansion and identifying the core mechanisms that underpin their pathogenicity. We discuss the development of the experimental methods and bioinformatics toolkits that have provided a fuller understanding of batrachochytrid biology and informed policy and control measures.

Genetic assessment of the internal transcribed spacer region (ITS1.2) in Mangifera indica L. landraces

Mango (Mangifera indica) is one of the most important tropical fruits in the world. Twenty-two genotypes of native mangoes from different regions of southern Iran (Hormozgan and Kerman) were collected and analyzed for the ribosomal genes. GC content was found to be 55.5%. Fu and Li's D* test statistic (0.437), Fu and Li's F* test statistic (0.500) and Tajima's D (1.801) were positive and nonsignificant. A total of 769 positions were identified (319 with insertion or deletion including 250 polymorphic and 69 monomorphic loci; 450 loci without any insertion or deletion including 35 Singletons and 22 haplotypes). Nucleotide diversity of 0.309 and a high genetic differentiation including Chi square of 79.8; P value of 0.3605 and df value of 76 was observed among mango genotypes studied. The numerical value of the ratio dN/dS (0.45) indicated a pure selection in the examined gene and the absence of any key changes. Cluster analysis differentiated the mango used in this research (M. indica L.) into two genotypes but could not differentiate their geographical locations. The results of this study indicated that a high genetic distance exists between HajiGholam (Manojan) and Arbabi (Rodan) genotypes and showed higher genetic diversity in mango of Rodan region. Results of present study suggested that for successful breeding, the genotypes of Rodan region mango especially Arbabi mango can be used as a gene donor and ITS can be a suitable tool for genetic evaluations of inter and intra species.

Bullfrog farms release virulent zoospores of the frog-killing fungus into the natural environment

Bullfrog farming and trade practices are well-established, globally distributed, and economically valuable, but pose risks for biodiversity conservation. Besides their negative impacts on native amphibian populations as an invasive species, bullfrogs play a key role in spreading the frog-killing fungus Batrachochytrium dendrobatidis (Bd) in the natural environment. Bullfrogs are tolerant to Bd, meaning that they can carry high infection loads without developing chytridiomycosis. To test the potential of bullfrog farms as reservoirs for diverse and virulent chytrid genotypes, we quantified Bd presence, prevalence and infection loads across approximately 1,500 farmed bullfrogs and in the water that is released from farms into the environment. We also described Bd genotypic diversity within frog farms by isolating Bd from dozens of infected tadpoles. We observed individuals infected with Bd in all sampled farms, with high prevalence (reaching 100%) and high infection loads (average 71,029 zoospore genomic equivalents). Average outflow water volume from farms was high (60,000 L/day), with Bd zoospore concentration reaching approximately 50 million zoospores/L. Because virulent pathogen strains are often selected when growing in tolerant hosts, we experimentally tested whether Bd genotypes isolated from bullfrogs are more virulent in native anuran hosts compared to genotypes isolated from native host species. We genotyped 36 Bd isolates from two genetic lineages and found that Bd genotypes cultured from bullfrogs showed similar virulence in native toads when compared to genotypes isolated from native hosts. Our results indicate that bullfrog farms can harbor high Bd genotypic diversity and virulence and may be contributing to the spread of virulent genotypes in the natural environment. We highlight the urgent need to implement Bd monitoring and mitigation strategies in bullfrog farms to aid in the conservation of native amphibians.

Ancestral chytrid pathogen remains hypervirulent following its long coevolution with amphibian hosts

Many amphibian species around the world, except in Asia, suffer morbidity and mortality when infected by the emerging infectious pathogen Batrachochytrium dendrobatidis (Bd). A lineage of the amphibian chytrid fungus isolated from South Korean amphibians (BdAsia-1) is evolutionarily basal to recombinant global pandemic lineages (BdGPL) associated with worldwide amphibian population declines. In Asia, the Bd pathogen and its amphibian hosts have coevolved over 100 years or more. Thus, resilience of Asian amphibian populations to infection might result from attenuated virulence of endemic Bd lineages, evolved immunity to the pathogen or both. We compared susceptibilities of an Australasian amphibian, Litoria caerulea, known to lack resistance to BdGPL, with those of three Korean species, Bufo gargarizans, Bombina orientalis and Hyla japonica, after inoculation with BdAsia-1, BdGPL or a blank solution. Subjects became infected in all experimental treatments but Korean species rapidly cleared themselves of infection, regardless of Bd lineage. They survived with no apparent secondary effects. By contrast, L. caerulea, after infection by either BdAsia-1 or BdGPL, suffered deteriorating body condition and carried progressively higher Bd loads over time. Subsequently, most subjects died. Comparing their effects on L. caerulea, BdAsia-1 induced more rapid disease progression than BdGPL. The results suggest that genomic recombination with other lineages was not necessary for the ancestral Bd lineage to evolve hypervirulence over its long period of coevolution with amphibian hosts. The pathogen's virulence may have driven strong selection for immune responses in endemic Asian amphibian host species.

Enzootic frog pathogen Batrachochytrium dendrobatidis in Asian tropics reveals high ITS haplotype diversity and low prevalence

Emerging Infectious Diseases (EIDs) are a major threat to wildlife and a key player in the declining amphibian populations worldwide. One such EID is chytridiomycosis caused by Batrachochytrium dendrobatidis (Bd), a fungal pathogen. Aetiology of Bd infection is poorly known from tropical frogs in Asian biodiversity hotspots. Surveys were carried out in four biodiversity hotspots to ascertain the status of Bd fungus. We collected a total of 1870 swab samples from frogs representing 32 genera and 111 species. Nested PCRs revealed low prevalence (8.4%) and high Bd haplotype richness was revealed after sequencing. We document 57 Bd Internal Transcribed Spacer region (ITS) haplotypes, of which 46 were unique to the global database. Bd ITS region showed indels at the Taqman binding site and qPCR reverse primer binding site, suggesting qPCR is unsuitable for diagnosis in Asian Bd coldspots. Our median-joining network and Bayesian tree analyses reveal that the Asian haplotypes, with the exception of Korea, formed a separate clade along with pandemic BdGPL (Bd Global Panzootic Lineage) haplotype. We hypothesise that the frog populations in Asian tropics might harbour several endemic strains of Bd, and the high levels of diversity and uniqueness of Bd haplotypes in the region, probably resulted from historical host-pathogen co-evolution.

Hybrids of amphibian chytrid show high virulence in native hosts

Hybridization of parasites can generate new genotypes with high virulence. The fungal amphibian parasite Batrachochytrium dendrobatidis (Bd) hybridizes in Brazil’s Atlantic Forest, a biodiversity hotspot where amphibian declines have been linked to Bd, but the virulence of hybrid genotypes in native hosts has never been tested. We compared the virulence (measured as host mortality and infection burden) of hybrid Bd genotypes to the parental lineages, the putatively hypovirulent lineage Bd-Brazil and the hypervirulent Global Pandemic Lineage (Bd-GPL), in a panel of native Brazilian hosts. In Brachycephalus ephippium, the hybrid exceeded the virulence (host mortality) of both parents, suggesting that novelty arising from hybridization of Bd is a conservation concern. In Ischnocnema parva, host mortality in the hybrid treatment was intermediate between the parent treatments, suggesting that this species is more vulnerable to the aggressive phenotypes associated with Bd-GPL. Dendropsophus minutus showed low overall mortality, but infection burdens were higher in frogs treated with hybrid and Bd-GPL genotypes than with Bd-Brazil genotypes. Our experiment suggests that Bd hybrids have the potential to increase disease risk in native hosts. Continued surveillance is needed to track potential spread of hybrid genotypes and detect future genomic shifts in this dynamic disease system.

Distribution modeling and lineage diversity of the chytrid fungus Batrachochytrium dendrobatidis (Bd) in a central African amphibian hotspot

The amphibian disease chytridiomycosis in amphibians is caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd) and has resulted in dramatic declines and extinctions of amphibian populations worldwide. A hypervirulent, globally-dispersed pandemic lineage (Bd-GPL) is thought to be largely responsible for population declines and extinctions, although numerous endemic lineages have also been found. Recent reports of amphibian declines have been linked to the emergence of Bd in Cameroon, a major hotspot of African amphibian diversity. However, it is not known whether Bd-GPL or other lineages have been found in this region. This study therefore aims to examine Bd lineage diversity in the region and predict the distribution of this pathogen under current and future climate conditions using data from this study and from historical records. Almost 15% (52/360) of individuals tested positive for Bd using a standard quantitative PCR diagnostic. Infected amphibians were found at all eight sites sampled in this study. Species distribution models generated in BIOMOD2 indicate that areas with highest predicted environmental suitability occur in the Cameroon highlands and several protected areas throughout the country. These areas of high environmental suitability for Bd are projected to shift or decrease in size under future climate change. However, montane regions with high amphibian diversity are predicted to remain highly suitable. Phylogenetic analysis of the ITS sequences obtained from a set of positive Bd samples indicate that most fall within the Bd-GPL lineage while the remainder group with isolates from either Brazil or South Korea. Although more in depth phylogenetic analyses are needed, identification of Bd-GPL lineages in areas of high amphibian diversity emphasizes the need to continue to monitor for Bd and develop appropriate conservation strategies to prevent its further spread.

Selective constraint acting on TLR2 and TLR4 genes of Japanese Rana frogs

Toll-like receptors (TLRs) are an important component of innate immunity, the first line of pathogen defence. One of the major roles of TLRs includes recognition of pathogen-associated molecular patterns. Amphibians are currently facing population declines and even extinction due to chytridiomycosis caused by the Batrachochytrium dendrobatidis (Bd) fungus. Evidence from other vertebrates shows that TLR2 and TLR4 are involved in innate immunity against various fungi. Such genes therefore may play a functional role in amphibian-chytridiomycosis dynamics. Frogs from East Asia appear to be tolerant to Bd, so we examined the genetic diversity that underlies TLR2 and TLR4 from three Japanese Ranidae frog species, Rana japonica, R. ornativentris and R. tagoi tagoi (n = 5 per species). We isolated 27 TLR2 and 20 TLR4 alleles and found that these genes are evolutionarily conserved, with overall evidence supporting purifying selection. In contrast, site-by-site analysis of selection identified several specific codon sites under positive selection, some of which were located in the variable leucine rich repeat domains. In addition, preliminary expression levels of TLR2 and TLR4 from transcriptome data showed overall low expression. Although it remains unclear whether infectious pathogens are a selective force acting on TLRs of Japanese frogs, our results support that certain sites in TLRs of these species may have experienced pathogen-mediated selection.

Recent Asian origin of chytrid fungi causing global amphibian declines

Globalized infectious diseases are causing species declines worldwide, but their source often remains elusive. We used whole-genome sequencing to solve the spatiotemporal origins of the most devastating panzootic to date, caused by the fungus Batrachochytrium dendrobatidis, a proximate driver of global amphibian declines. We traced the source of B. dendrobatidis to the Korean peninsula, where one lineage, BdASIA-1, exhibits the genetic hallmarks of an ancestral population that seeded the panzootic. We date the emergence of this pathogen to the early 20th century, coinciding with the global expansion of commercial trade in amphibians, and we show that intercontinental transmission is ongoing. Our findings point to East Asia as a geographic hotspot for B. dendrobatidis biodiversity and the original source of these lineages that now parasitize amphibians worldwide.

Invasive African clawed frogs in California: A reservoir for or predator against the chytrid fungus?

Amphibian species are experiencing population declines due to infection by the fungal pathogen, Batrachochytrium dendrobatidis (Bd). The African clawed frog (Xenopus laevis), an asymptomatic carrier of Bd, has been implicated in the spread of this pathogen through global trade and established invasive populations on several continents. However, research has not explored the relationships of both life stages of this amphibian with Bd. While the post-metamorphic individuals may act as a reservoir, spreading the infection to susceptible species, the filter-feeding larvae may consume the motile Bd zoospores from the water column, potentially reducing pathogen abundance and thus the likelihood of infection. We explore these contrasting processes by assessing Bd prevalence and infection intensities in field populations of post-metamorphic individuals, and performing laboratory experiments to determine if larval X. laevis preyed upon Bd zoospores. The water flea, Daphnia magna, was included in the Bd consumption trials to compare consumption rates and to explore whether intraguild predation between the larval X. laevis and Daphnia may occur, potentially interfering with control of Bd zoospores by Daphnia. Field surveys of three X. laevis populations in southern California, in which 70 post-metamorphic individuals were tested for Bd, found 10% infection prevalence. All infected individuals had very low infection loads (all Bd loads were below 5 zoospore equivalents). Laboratory experiments found that larval X. laevis consume Bd zoospores and therefore may reduce Bd abundance and transmission between amphibians. However, metamorphic and juvenile X. laevis exhibited intraguild predation by consuming Daphnia, which also prey upon Bd zoospores. The results suggest that X laevis is not a large reservoir for Bd and its larval stage may offer some reduction of Bd transmission through direct predation.

Comparison of methods for detection of chytrid fungus (Batrachochytrium dendrobatidis) in bullfrog tadpole mouthparts

We previously reported that the tadpole of bullfrog (Lithobates catesbeiana) is a useful model for the field surveillance of the Batrachochytrium dendrobatidis (Bd) distribution. In the present study, we compared Bd detection rates in swab-scraped and resected mouthpart samples, using nested polymerase chain reaction (PCR). The resulting detection rates for swab-scraped and resected specimens were 67 and 65%, respectively, with no significant difference. Furthermore, we performed a histopathological examination for Bd distribution in the mouthparts; we found that Bd infection occurred in the tip and basement of the jaw sheaths and tooth rows. We recommend using swab-scraped samples for Bd detection. Moreover, careful attention should be paid to scraping the tip and basement of the jaw sheaths and the entire oral cavity to reduce the rates of false-negative results on nested PCR of the mouthparts of bullfrog tadpoles.

Skin Bacterial Community Reorganization Following Metamorphosis of the Fire-Bellied Toad (Bombina orientalis)

In organisms with complex life histories, dramatic changes in microbial community structure may occur with host development and immune system maturation. Amphibian host susceptibility to diseases such as chytridiomycosis may be affected by the reorganization of skin microbial community structure that occurs during metamorphosis. We tracked changes in the bacterial communities inhabiting skin of Korean fire-bellied toads (Bombina orientalis) that we infected as tadpoles with different strains of Batrachochytrium dendrobatidis (Bd), the pathogenic fungus that causes chytridiomycosis. We found that B. orientalis undergoes a major change in skin bacterial community composition between 5 and 15 days following metamorphosis. Richness indices and phylogenetic diversity measures began to diverge earlier, between aquatic and terrestrial stages. Our results further reveal differences in skin bacterial community composition among infection groups, suggesting that the effect of Bd infection on skin microbiome composition may differ by Bd strain. Additional studies are needed to further investigate the structural and temporal dynamics of microbiome shifts during metamorphosis in wild and captive amphibian populations. Analyses of the ontogeny of microbiome shifts may contribute to an understanding of why amphibians vary in their susceptibility to chytridiomycosis.

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.

Probiotic consortia are not uniformly effective against different amphibian chytrid pathogen isolates

Symbiotic bacterial communities can protect their hosts from infection by pathogens. Treatment of wild individuals with protective bacteria (probiotics) isolated from hosts can combat the spread of emerging infectious diseases. However, it is unclear whether candidate probiotic bacteria can offer consistent protection across multiple isolates of globally distributed pathogens. Here, we use the lethal amphibian fungal pathogen Batrachochytrium dendrobatidis to investigate whether probiotic richness (number of bacteria) or genetic distance among consortia members influences broad-scale in vitro inhibitory capabilities of probiotics across multiple isolates of the pathogen. We show that inhibition of multiple pathogen isolates by individual bacteria is rare, with no systematic pattern among bacterial genera in ability to inhibit multiple B. dendrobatidis isolates. Bacterial consortia can offer stronger protection against B. dendrobatidis compared to single strains, and this tended to be more pronounced for consortia containing multiple genera compared with those consisting of bacteria from a single genus (i.e., with lower genetic distance), but critically, this effect was not uniform across all B. dendrobatidis isolates. These novel insights have important implications for the effective design of bacterial probiotics to mitigate emerging infectious diseases.

Emerging Chytrid Fungal Pathogen, Batrachochytrium Dendrobatidis, in Zoo Amphibians in Thailand

Chytridiomycosis, a disease in amphibians caused by Batrachochytrium dendrobatidis (Bd), has led to a population decline and extinction of frog species since 1996. The objective of this study was to determine the prevalence of and the need for establishing a surveillance system for monitoring chytridiomycosis in five national zoos and five free ranging protected areas across Thailand. A total of 492 skin swab samples were collected from live and dead animals and tested by polymerase chain reaction (PCR) for the presence of Bd. The positive specimens were confi rmed by amplicon sequencing and examined by histopathology and immunohistochemistry. From July 2009 to August 2012, the prevalence of Bd from frog skin samples was low (4.27%), monitored by PCR. All samples from live amphibians were negative. The positive cases were only from dead specimens (21/168, 12.5% dead samples) of two non-native captive species, poison dart frog (Dendrobates tinctorius) and tomato frog (Dyscophus antongilii) in one zoo. Immunohistochemistry and histopathology revealed the typical feature of fl ask-shaped zoosporangia and septate thalli, supporting the PCR-based evidence of chytridiomycosis in captive amphibians in Thailand, but detected Bd in only 7/21 of the PCR-positive samples. Although the introduction of a pathogenic strain of Bd from imported carriers might have a serious impact on the native amphibian populations in Thailand, chytridiomycosis has not currently been detected in native Thai amphibians. An active surveillance system is needed for close monitoring of the fungus crossing into Thai amphibian populations

Transcriptome analyses of immune tissues from three Japanese frogs (genus Rana ) reveals their utility in characterizing major histocompatibility complex class II

Background

In Japan and East Asia, endemic frogs appear to be tolerant or not susceptible to chytridiomycosis, a deadly amphibian disease caused by the chytrid fungus Batrachochytridium dendrobatidis (Bd). Japanese frogs may have evolved mechanisms of immune resistance to pathogens such as Bd. This study characterizes immune genes expressed in various tissues of healthy Japanese Rana frogs.

Results

We generated transcriptome data sets of skin, spleen and blood from three adult Japanese Ranidae frogs (Japanese brown frog Rana japonica, the montane brown frog Rana ornativentris, and Tago’s brown frog Rana tagoi tagoi) as well as whole body of R. japonica and R. ornativentris tadpoles. From this, we identified tissue- and stage-specific differentially expressed genes; in particular, the spleen was most enriched for immune-related genes. A specific immune gene, major histocompatibility complex class IIB (MHC-IIB), was further characterized due to its role in pathogen recognition. We identified a total of 33 MHC-IIB variants from the three focal species (n = 7 individuals each), which displayed evolutionary signatures related to increased MHC variation, including balancing selection. Our supertyping analyses of MHC-IIB variants from Japanese frogs and previously studied frog species identified potential physiochemical properties of MHC-II that may be important for recognizing and binding chytrid-related antigens.

Conclusions

This is one of the first studies to generate transcriptomic resources for Japanese frogs, and contributes to further understanding the immunogenetic factors associated with resistance to infectious diseases in amphibians such as chytridiomycosis. Notably, MHC-IIB supertyping analyses identified unique functional properties of specific MHC-IIB alleles that may partially contribute to Bd resistance, and such properties provide a springboard for future experimental validation.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4404-0) contains supplementary material, which is available to authorized users.

Overview of chytrid emergence and impacts on amphibians

Chytridiomycosis is an emerging infectious disease of amphibians that affects over 700 species on all continents where amphibians occur. The amphibian-chytridiomycosis system is complex, and the response of any amphibian species to chytrid depends on many aspects of the ecology and evolutionary history of the amphibian, the genotype and phenotype of the fungus, and how the biological and physical environment can mediate that interaction. Impacts of chytridiomycosis on amphibians are varied; some species have been driven extinct, populations of others have declined severely, whereas still others have not obviously declined. Understanding patterns and mechanisms of amphibian responses to chytrids is critical for conservation and management. Robust estimates of population numbers are needed to identify species at risk, prioritize taxa for conservation actions, design management strategies for managing populations and species, and to develop effective measures to reduce impacts of chytrids on amphibians.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.

Prevalence and genetic diversity of Batrachochytrium dendrobatidis in Central African island and continental amphibian communities

The fungal pathogen Batrachochytrium dendrobatidis (Bd) infects hundreds of amphibian species and is implicated in global amphibian declines. Bd is comprised of several lineages that differ in pathogenicity, thus, identifying which Bd strains are present in a given amphibian community is essential for understanding host–pathogen dynamics. The presence of Bd has been confirmed in Central Africa, yet vast expanses of this region have not yet been surveyed for Bd prevalence, and the genetic diversity of Bd is largely unknown in this part of the world. Using retrospective surveys of museum specimens and contemporary field surveys, we estimated the prevalence of Bd in Central African island and continental amphibian assemblages, and genotyped strains of Bd present in each community. Our sampling of museum specimens included just a few individuals collected in the Gulf of Guinea archipelago prior to 1998, yet one of these individuals was Bd‐positive indicating that the pathogen has been on Bioko Island since 1966. We detected Bd across all subsequent sample years in our study and found modest support for a relationship between host life history and Bd prevalence, a positive relationship between prevalence and host community species richness, and no significant relationship between elevation and prevalence. The Global Panzootic Lineage (BdGPL) was present in all the island and continental amphibian communities we surveyed. Our results are consistent with a long‐term and widespread distribution of Bd in amphibian communities of Gabon and the Gulf of Guinea archipelago.

Major histocompatibility complex variation and the evolution of resistance to amphibian chytridiomycosis

Chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), has been implicated in population declines and species extinctions of amphibians around the world. Susceptibility to the disease varies both within and among species, most likely attributable to heritable immunogenetic variation. Analyses of transcriptional expression in hosts following their infection by Bd reveal complex responses. Species resistant to Bd generally show evidence of stronger innate and adaptive immune system responses. Major histocompatibility complex (MHC) class I and class II genes of some susceptible species are up-regulated following host infection by Bd, but resistant species show no comparable changes in transcriptional expression. Bd-resistant species share similar pocket conformations within the MHC-II antigen-binding groove. Among susceptible species, survivors of epizootics bear alleles encoding these conformations. Individuals with homozygous resistance alleles appear to benefit by enhanced resistance, especially in environmental conditions that promote pathogen virulence. Subjects that are repeatedly infected and subsequently cleared of Bd can develop an acquired immune response to the pathogen. Strong directional selection for MHC alleles that encode resistance to Bd may deplete genetic variation necessary to respond to other pathogens. Resistance to chytridiomycosis incurs life-history costs that require further study.