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Diverse communities of symbiotic microbes inhabit the digestive systems of vertebrates and play a crucial role in animal health, and host diet plays a major role in shaping the composition and diversity of these communities. Here, we characterized diet and gut microbiome of fire salamander populations from three Belgian forests. We carried out DNA metabarcoding on fecal samples, targeting eukaryotic 18S rRNA of potential dietary prey items, and bacterial 16S rRNA of the concomitant gut microbiome. Our results demonstrated an abundance of soft-bodied prey in the diet of fire salamanders, and a significant difference in the diet composition between males and females. This sex-dependent effect on diet was also reflected in the gut microbiome diversity, which is higher in males than female animals. Proximity to human activities was associated with increased intestinal pathogen loads. Collectively, the data supports a relationship between diet, environment and intestinal microbiome in fire salamanders, with potential health implications.

The host‐associated microbiome plays a significant role in health. However, the roles of factors such as host genetics and microbial interactions in determining microbiome diversity remain unclear. We examined these factors using amplicon‐based sequencing of 175 Thoropa taophora frog skin swabs collected from a naturally fragmented landscape in southeastern Brazil. Specifically, we examined (1) the effects of geography and host genetics on microbiome diversity and structure; (2) the structure of microbial eukaryotic and bacterial co‐occurrence networks; and (3) co‐occurrence between microeukaryotes with bacterial OTUs known to affect growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). While bacterial alpha diversity varied by both site type and host MHC IIB genotype, microeukaryotic alpha diversity varied only by site type. However, bacteria and microeukaryote composition showed variation according to both site type and host MHC IIB genotype. Our network analysis showed the highest connectivity when both eukaryotes and bacteria were included, implying that ecological interactions may occur among domains. Lastly, anti‐Bd bacteria were not broadly negatively co‐associated with the fungal microbiome and were positively associated with potential amphibian parasites. Our findings emphasize the importance of considering both domains in microbiome research and suggest that for effective probiotic strategies for amphibian disease management, considering potential interactions among all members of the microbiome is crucial., We use a natural laboratory to examine the relationship between host genetic diversity, bacterial diversity, and microeukaryote diversity in the skin microbiome of a Brazilian frog. We find that host immunogenetic diversity is associated with variation in microbiome diversity and structure, and present results that support novel associations between microeukaryotes and bacteria on frog skin. Our results have implications for the relationships between host genetics and health mediated through microbiome diversity and structure. ​

The fields of ecology and conservation have evolved rapidly over the past century. Synthesizing larger trends in these disciplines remains a challenge yet is critical to bridging subdisciplines, guiding research, and informing educational frameworks. Here, we provide what we believe is the largest full‐text culturomic analysis of ecology and conservation journals, covering 80 years, 52 journals, and half a billion words. Our analysis illuminates the boom‐and‐bust of ecological hypotheses and theories; the adoption of statistical, genetic, and social‐science approaches; and the domination of terms that have emerged in recent decades (eg climate change, invasive species, ecosystem services, meta‐analysis, and supplementary material, which largely replaced unpublished data). We track the evolution of ecology from a largely descriptive field focused on natural history and observational studies to a more data‐driven, multidisciplinary field focused on applied environmental issues. Overall, our analysis highlights the increasing breadth of the field, illustrating that there is room for more diversity of ecologists and conservationists today than ever before.

Mucosal defenses are crucial in animals for protection against pathogens and predators. Host defense peptides (antimicrobial peptides, AMPs) as well as skin-associated microbes are key components of mucosal immunity, particularly in amphibians. We integrate microbiology, molecular biology, network-thinking, and proteomics to understand how host and microbially derived products on amphibian skin (referred to as the mucosome) serve as pathogen defenses. We studied defense mechanisms against chytrid pathogens

Variation in the structure of host-associated microbial communities has been correlated with the occurrence and severity of disease in diverse host taxa, suggesting a key role of the microbiome in pathogen defense. However, whether these correlations are typically a cause or consequence of pathogen exposure remains an open question, and requires experimental approaches to disentangle. In amphibians, infection by the fungal pathogen Batrachochytrium dendrobatidis (Bd) alters the skin microbial community in some host species, whereas in other species, the skin microbial community appears to mediate infection dynamics. In this study, we completed experimental Bd exposures in three species of tropical frogs (Agalychnis callidryas, Dendropsophus ebraccatus,andCraugastor fitzingeri) that were sympatric with Bd at the time of the study. For all three species, we identified key taxa within the skin bacterial communities that were linked to Bd infection dynamics. We also measured higher Bd infection intensities in D. ebraccatus and C. fitzingeri that were associated with higher mortality in C. fitzingeri. Our findings indicate that microbially mediated pathogen resistance is a complex trait that can vary within and across host species, and suggest that symbiont communities that have experienced prior selection for defensive microbes may be less likely to be disturbed by pathogen exposure.

The increasing study of emerging wildlife pathogens and a lack of policy or legislation regulating their translocation and use has heightened concerns about laboratory escape, species spillover, and subsequent epizootics among animal populations. Responsible self-regulation by research laboratories, in conjunction with institutional-level safeguards, has an important role in mitigating pathogen transmission and spillover, as well as potential interspecies pathogenesis. A model system in disease ecology that highlights these concerns and related amelioration efforts is research focused on amphibian emerging infectious diseases. Whereas laboratory escape of amphibian pathogens has not been reported and may be rare compared with introduction events from trade or human globalization, the threat that novel disease outbreaks with mass mortality effects pose to wild populations warrants thorough biosecurity measures to ensure containment and prevent spillover. Here, we present a case study of the laboratory biosecurity concerns for the emerging amphibian fungal pathogen Batrachochytrium salamandrivorans. We conclude that proactive biosecurity strategies are needed to integrate researcher and institutional oversight of aquatic wildlife pathogens generally, and we call for increased national and international policy and legislative enforcement. Furthermore, taking professional responsibility beyond current regulations is needed as development of legal guidance can be slow at national and international levels. We outline the need for annual laboratory risk assessments, comprehensive training for all laboratory personnel, and appropriate safeguards specific to pathogens under study. These strategies are critical for upholding the integrity and credibility of the scientific community and maintaining public support for research on wildlife diseases.

Detecting and quantifying pathogens with quick, cost-efficient and sensitive methods is needed across disease systems for addressing pertinent epidemiological questions. Typical methods rely on extracting DNA from collected samples. Here we develop and test an extraction-free method from water bath samples that is both sensitive and efficient for 2 major amphibian pathogens—Batrachochytrium dendrobatidis and B. salamandrivorans. We tested mock samples with known pathogen quantities as well as comparatively assessed detection from skin swabs and water baths from field sampled amphibians. Quantitative PCR (qPCR) directly on lyophilized water baths was able to reliably detect low loads of 10 and 1 zoospores for both pathogens, and detection rates were greater than those of swabs from field samples. Further concentration of samples did not improve detection, and collection container type did not influence pathogen load estimates. This method of lyophilization (i.e. freeze-drying) followed by direct qPCR offers an effective and efficient tool from detecting amphibian pathogens, which is crucial for surveillance efforts and estimating shedding rates for robust epidemiological understanding of transmission dynamics. Furthermore, water bath samples have multiple functions and can be used to evaluate mucosal function against pathogens and characterize mucosal components. The multifunctionality of water bath samples and reduced monetary costs and time expenditures make this method an optimal tool for amphibian disease research and may also prove to be useful in other wildlife disease systems.

Emerging infectious wildlife diseases have caused devastating declines, particularly when pathogens have been introduced in naïve host populations. The outcome of disease emergence in any host population will be dictated by a series of factors including pathogen virulence, host susceptibility, and prior opportunity for coevolution between hosts and pathogens. Historical coevolution can lead to increased resistance in hosts and/or reduced virulence in endemic pathogens that allows stable persistence of host and pathogen populations. Adaptive coevolution may also occur on relatively short time scales following introduction of a novel pathogen. Here, we performed a meta-analysis of multi-strain

The emerging fungal pathogen Batrachochytrium salamandrivorans (Bsal) is a major threat to amphibian species worldwide with potential to infect many species if it invades salamander biodiversity hotspots in the Americas. Bsal can cause the disease chytridiomycosis, and it is important to assess the risk of Bsal-induced chytridiomycosis to species in North America. We evaluated the susceptibility to Bsal of the common and widespread spotted salamander, Ambystoma maculatum, across life history stages and monitored the effect of Bsal exposure on growth rate and response of the stress hormone, corticosterone. We conclude that spotted salamanders appear resistant to Bsal because they showed no indication of disease or infection, and experienced minor effects on growth upon exposure. While we focused on a single population for this study, results were consistent across conditions of exposure including high or repeated doses of Bsal, life-stage at exposure, environmental conditions including two temperatures and two substrates, and promoting pathogen infectivity by conditioning Bsal cultures with thyroid hormone. Exposure to high levels of Bsal elicited an acute but not chronic increase in corticosterone in spotted salamanders, and reduced growth. We hypothesize that the early acute increase in corticosterone facilitated mounting an immune response to the pathogen, perhaps through immunoredistribution to the skin, but further study is needed to determine immune responses to Bsal. These results will contribute to development of appropriate Bsal management plans to conserve species at risk of emerging disease.

Significance Batrachochytrium dendrobatidis [Bd] is one of the most devastating wildlife pathogens ever documented. Most surveys for Bd report only the presence/absence of the pathogen. However, Bd has distinct genetic lineages that vary in geographic extent and virulence, thus reporting Bd presence alone is not particularly informative. Our study uses a custom method for genotyping degraded Bd DNA samples, such as those nondestructively collected from live animal or museum specimen skin swabs, and presents the discovery of a divergent lineage of Bd—BdASIA3. This study advances our understanding of the evolutionary origins of Bd, highlights areas of the world where Bd lineages are coming into contact, and opens the door to affordable, rapid genetic monitoring of this pathogen., Biodiversity loss is one major outcome of human-mediated ecosystem disturbance. One way that humans have triggered wildlife declines is by transporting disease-causing agents to remote areas of the world. Amphibians have been hit particularly hard by disease due in part to a globally distributed pathogenic chytrid fungus (Batrachochytrium dendrobatidis [Bd]). Prior research has revealed important insights into the biology and distribution of Bd; however, there are still many outstanding questions in this system. Although we know that there are multiple divergent lineages of Bd that differ in pathogenicity, we know little about how these lineages are distributed around the world and where lineages may be coming into contact. Here, we implement a custom genotyping method for a global set of Bd samples. This method is optimized to amplify and sequence degraded DNA from noninvasive skin swab samples. We describe a divergent lineage of Bd, which we call BdASIA3, that appears to be widespread in Southeast Asia. This lineage co-occurs with the global panzootic lineage (BdGPL) in multiple localities. Additionally, we shed light on the global distribution of BdGPL and highlight the expanded range of another lineage, BdCAPE. Finally, we argue that more monitoring needs to take place where Bd lineages are coming into contact and where we know little about Bd lineage diversity. Monitoring need not use expensive or difficult field techniques but can use archived swab samples to further explore the history—and predict the future impacts—of this devastating pathogen.

Animal-associated microbiomes are integral to host health, yet key biotic and abiotic factors that shape host-associated microbial communities at the global scale remain poorly understood. We investigated global patterns in amphibian skin bacterial communities, incorporating samples from 2,349 individuals representing 205 amphibian species across a broad biogeographic range. We analysed how biotic and abiotic factors correlate with skin microbial communities using multiple statistical approaches. Global amphibian skin bacterial richness was consistently correlated with temperature-associated factors. We found more diverse skin microbiomes in environments with colder winters and less stable thermal conditions compared with environments with warm winters and less annual temperature variation. We used bioinformatically predicted bacterial growth rates, dormancy genes and antibiotic synthesis genes, as well as inferred bacterial thermal growth optima to propose mechanistic hypotheses that may explain the observed patterns. We conclude that temporal and spatial characteristics of the host’s macro-environment mediate microbial diversity. National Science Foundation/[DEB-1146284]/NSF/Estados Unidos National Science Foundation/[IOS-1121758]/NSF/Estados Unidos National Science Foundation/[DEB-1310036]/NSF/Estados Unidos John Templeton Foundation/[]/JTF/Estados Unidos Deutsche Forschungsgemeinschaft/[]/DFG/Alemania Deutsche Forschungsgemeinschaft/[VE247/9-1]/DFG/Alemania Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/[]/CAPES/Brasil Fundação de Amparo à Pesquisa do Estado de São Paulo/[#2013/50741-7]/FAPESP/Brasil Conselho Nacional de Desenvolvimento Científico e Tecnológico/[]/CNPq/Brasil Simons Foundation/[429440, WTW]//Estados Unidos Deutscher Akademischer Austauschdienst/[]/DAAD/Alemania Universidad de Costa Rica/[801-B2-029]/UCR/Costa Rica Ministerio de Ciencia, Tecnología y Telecomunicaciones/[849-PINN-2015]/MICITT/Costa Rica National Research Foundation of Korea/[2015R1D1A1A01057282]/NRF/Corea del Sur UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Biología Celular y Molecular (CIBCM) UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Estructuras Microscópicas (CIEMIC)

Biological invasions are on the rise, with each invader carrying a plethora of associated microbes. These microbes play important, yet poorly understood, ecological roles that can include assisting the hosts in colonization and adaptation processes or as possible pathogens. Understanding how these communities differ in an invasion scenario may help to understand the host’s resilience and adaptability. The Asian common toad, Duttaphrynus melanostictus is an invasive amphibian, which has recently established in Madagascar and is expected to pose numerous threats to the native ecosystems. We characterized the skin and gut bacterial communities of D. melanostictus in Toamasina (Eastern Madagascar), and compared them to those of a co-occurring native frog species, Ptychadena mascareniensis, at three sites where the toad arrived in different years. Microbial composition did not vary among sites, showing that D. melanostictus keeps a stable community across its expansion but significant differences were observed between these two amphibians. Moreover, D. melanostictus had richer and more diverse communities and also harboured a high percentage of total unique taxa (skin: 80%; gut: 52%). These differences may reflect the combination of multiple host-associated factors including microhabitat selection, skin features and dietary preferences.

The coronavirus pandemic is more fully exposing ubiquitous economic and social inequities that pervade conservation science. In this time of prolonged stress on members of the research community, primary investigators or project leaders (PLs) have a unique opportunity to adapt their programs to jointly create more equitable and productive research environments for their teams. Institutional guidance for PLs pursuing field and laboratory work centers on the physical safety of individuals while in the lab or field, but largely ignores the vast differences in how team members may be experiencing the pandemic. Strains on mental, physical, and emotional health; racial trauma; familial responsibilities; and compulsory productivity resources, such as high-speed internet, quiet work spaces, and support are unequally distributed across team members. The goal of this paper is to summarize the shifting dynamics of leadership and mentorship during the coronavirus pandemic and highlight opportunities for increasing equity in conservation research at the scale of the project team. Here, we (1) describe how the pandemic differentially manifests inequity on project teams, particularly for groups that have been structurally excluded from conservation science, (2) consider equitable career advancement during the coronavirus pandemic, and (3) offer suggestions for PLs to provide mentorship that prioritizes equity and wellbeing during and beyond the pandemic. We aim to support PLs who have power and flexibility in how they manage research, teaching, mentoring, consulting, outreach, and extension activities so that individual team members' needs are met with compassion and attention to equity.

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., Author summary 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.

Discovered in 2013, Batrachochytrium salamandrivorans (Bsal) is an emerging amphibian pathogen that causes ulcerative skin lesions and multifocal erosion. A closely related pathogen, Batrachochytrium dendrobatidis (Bd), has devastated amphibian populations worldwide, suggesting that Bsal poses a significant threat to global salamander biodiversity. To expedite research into this emerging threat, we seek to standardize protocols across the field so that results of laboratory studies are reproducible and comparable. We have collated data and experience from multiple labs to standardize culturing practices of Bsal. Here we outline common culture practices including a media for optimal Bsal growth, standard culture protocols, and a method for isolating Bsal from infected tissue.

Gut microorganisms are crucial for many biological functions playing a pivotal role in the host’s well-being. We studied gut bacterial community structure of marine iguana populations across the Galápagos archipelago. Marine iguanas depend heavily on their specialized gut microbiome for the digestion of dietary algae, a resource whose growth was strongly reduced by severe “El Niño”-related climatic fluctuations in 2015/2016. As a consequence, marine iguana populations showed signs of starvation as expressed by a poor body condition. Body condition indices (BCI) varied between island populations indicating that food resources (i.e., algae) are affected differently across the archipelago during ‘El Niño’ events. Though this event impacted food availability for marine iguanas, we found that reductions in body condition due to “El Niño”-related starvation did not result in differences in bacterial gut community structure. Species richness of gut microorganisms was instead correlated with levels of neutral genetic diversity in the distinct host populations. Our data suggest that marine iguana populations with a higher level of gene diversity and allelic richness may harbor a more diverse gut microbiome than those populations with lower genetic diversity. Since low values of these diversity parameters usually correlate with small census and effective population sizes, we use our results to propose a novel hypothesis according to which small and genetically less diverse host populations might be characterized by less diverse microbiomes. Whether such genetically depauperate populations may experience additional threats from reduced dietary flexibility due to a limited intestinal microbiome is currently unclear and calls for further investigation. Supplementary Information The online version contains supplementary material available at 10.1007/s00114-020-01714-w.

Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacterial communities have the potential to elucidate global-scale patterns of microbial community structure and function. It is possible that host surface-associated (external) microbiomes respond more strongly to variations in environmental factors, whereas internal microbiomes are more tightly linked to host factors.Here, we use the dataset from the Earth Microbiome Project and accumulate data from 50 additional studies totaling 654 host species and over 15,000 samples to examine global-scale patterns of bacterial diversity and function. We analyze microbiomes from non-captive hosts sampled from natural habitats and find patterns with bioclimate and geophysical factors, as well as land use, host phylogeny, and trophic level/diet. Specifically, external microbiomes are best explained by variations in mean daily temperature range and precipitation seasonality. In contrast, internal microbiomes are best explained by host factors such as phylogeny/immune complexity and trophic level/diet, plus climate.Internal microbiomes are predominantly associated with top-down effects, while climatic factors are stronger determinants of microbiomes on host external surfaces. Host immunity may act on microbiome diversity through top-down regulation analogous to predators in non-microbial ecosystems. Noting gaps in geographic and host sampling, this combined dataset represents a global baseline available for interrogation by future microbial ecology studies.

BackgroundHost-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacterial communities have the potential to elucidate global-scale patterns of microbial community structure and function. It is possible that host surface-associated (external) microbiomes respond more strongly to variations in environmental factors, whereas internal microbiomes are more tightly linked to host factors.ResultsHere, we use the dataset from the Earth Microbiome Project and accumulate data from 50 additional studies totaling 654 host species and over 15,000 samples to examine global-scale patterns of bacterial diversity and function. We analyze microbiomes from non-captive hosts sampled from natural habitats and find patterns with bioclimate and geophysical factors, as well as land use, host phylogeny, and trophic level/diet. Specifically, external microbiomes are best explained by variations in mean daily temperature range and precipitation seasonality. In contrast, internal microbiomes are best explained by host factors such as phylogeny/immune complexity and trophic level/diet, plus climate.ConclusionsInternal microbiomes are predominantly associated with top-down effects, while climatic factors are stronger determinants of microbiomes on host external surfaces. Host immunity may act on microbiome diversity through top-down regulation analogous to predators in non-microbial ecosystems. Noting gaps in geographic and host sampling, this combined dataset represents a global baseline available for interrogation by future microbial ecology studies.

Animal-associated bacterial communities play essential roles for their host's ecology, physiology and health. Temporal dynamics of these communities are poorly understood, but might be of high relevance for amphibians with a well-expressed biphasic biology of adults where the structure of their skin changes drastically between the aquatic and terrestrial phases. Here, we investigated the temporal dynamics of cutaneous bacterial communities of Lissotriton boscai and Triturus marmoratus by monthly sampling populations from a pond and surrounding terrestrial habitats near A Coruña, Spain. These communities were characterized by 16S rRNA gene amplicons from DNA isolated from skin swabs. Newt bacterial communities displayed variation at three levels: between larvae and aquatic adults, between adult life phases (terrestrial versus aquatic), and temporally within life phases. The skin bacterial communities tended to differ to a lesser extent temporally and between larvae and adults, and more strongly between life phases. Larvae had a higher proportion of reads associated with antifungal taxa compared with adults, while no differences were found among adult life phases. Terrestrial specimens exhibited the highest community diversity. The regular transitions of adult newts between aquatic and terrestrial environments might contribute to the diversity of their skin microbiota and could increase disease resistance.

Host-associated microbiomes are increasingly recognized to contribute to host disease resistance; the temporal dynamics of their community structure and function, however, are poorly understood. We investigated the cutaneous bacterial communities of three newt species, Ichthyosaura alpestris, Lissotriton vulgaris and Triturus cristatus, at approximately weekly intervals for 3 months using 16S ribosomal RNA amplicon sequencing. We hypothesized cutaneous microbiota would vary across time, and that such variation would be linked to changes in predicted fungal-inhibitory function. We observed significant temporal variation within the aquatic phase, and also between aquatic and terrestrial phase newts. By keeping T. cristatus in mesocosms, we demonstrated that structural changes occurred similarly across individuals, highlighting the non-stochastic nature of the bacterial community succession. Temporal changes were mainly associated with fluctuations in relative abundance rather than full turnover of bacterial operational taxonomic units (OTUs). Newt skin microbe fluctuations were not correlated with that of pond microbiota; however, a portion of community variation was explained by environmental temperature. Using a database of amphibian skin bacteria that inhibit the pathogen Batrachochytrium dendrobatidis (Bd), we found that the proportion of reads associated with ‘potentially’ Bd-inhibitory OTUs did not vary temporally for two of three newt species, suggesting that protective function may be maintained despite temporal variation in community structure.

Andrias japonicus, the Japanese giant salamander, is the second largest amphibian species in the world. The biology of this long-lived, fully aquatic salamander is still incompletely known, and studying the threats it experiences is important for conservation management. We used 16S amplicon sequencing to provide the first data on the composition and diversity of the cutaneous microbiome of this species. Skin bacterial communities of adult and larval giant salamanders were composed primarily of taxa belonging to the phyla Proteobacteria and Bacteroidetes, and, their community structure differed significantly from that of two other syntopic amphibians (Cynops pyrrhogaster and Glandirana rugosa). We also found differences between wild A. japonicus and captive individuals, with the latter having an increased bacterial diversity. The fungal pathogen Batrachochytrium dendrobatidis (Bd) was detected only in captive individuals (40% prevalence), and did not correlate with a particular bacterial community structure. We identified eight bacteria that were significantly more abundant on A. japonicus compared to syntopic amphibians, one of which was Janthinobacterium lividum, a bacterial species known to exert Bd-inhibiting effects. Our study provides baseline data for future in-depth studies on the microbial ecology of cutaneous bacteria and the contribution of cutaneous bacteria to Bd resistance in giant salamanders.

Dramatic global amphibian declines have recently led to an increased concern for many species of this animal class. The enigmatic Hula painted frog (Latonia nigriventer), the first amphibian to be declared extinct but unexpectedly rediscovered in 2011, has remained one of the rarest and most poorly understood amphibians worldwide. Gathering basic biological information on this species, along with an understanding of its disease-related threats remains fundamental for developing risk assessments and conservation strategies. Our surveys in recent years confirmed that L. nigriventer is a localised species with elusive habits. The species appears to follow an opportunistic breeding phenology and has a tadpole morphology similar to its well-studied sister group Discoglossus. However, the adults’ extended annual presence in the aquatic habitat is a major difference from species of Discoglossus. We detected the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd), in northern Israel and on Hula painted frogs but did not observe any signs of chytridiomycosis in this species. Our preliminary data on aspects of the innate immunity of L. nigriventer suggest that the skin mucosome of this species contains antimicrobial peptides and a bacterial community differing from other syntopic frogs (Pelophylax bedriagae). The combined knowledge of both natural history and innate immunity of L. nigriventer provides valuable insights to direct future research and conservation management of this critically endangered frog species.

Novel outbreaks of emerging pathogens require rapid responses to enable successful mitigation. We simulated a 1‐day emergency meeting where experts were engaged to recommend mitigation strategies for a new outbreak of the amphibian fungal pathogen Batrachochytrium salamandrivorans. Despite the inevitable uncertainty, experts suggested and discussed several possible strategies. However, their recommendations were undermined by imperfect initial definitions of the objectives and scope of management. This problem is likely to arise in most real‐world emergency situations. The exercise thus highlighted the importance of clearly defining the context, objectives, and spatial–temporal scale of mitigation decisions. Managers are commonly under pressure to act immediately. However, an iterative process in which experts and managers cooperate to clarify objectives and uncertainties, while collecting more information and devising mitigation strategies, may be slightly more time consuming but ultimately lead to better outcomes.

Resistance is not futile The fungal disease chytridiomycosis has wreaked havoc on amphibians worldwide. The disease is caused by the organism Batrachochytrium dendrobatidis and was first identified in the late 1990s. Voyles et al. revisited protected areas in Panama where catastrophic amphibian losses were recorded a decade ago (see the Perspective by Collins). Although disease theory predicts that epidemics should result in reduced pathogenicity, they found no evidence for such a reduction. Despite this, the amphibian community is displaying signs of recovery—including some species presumed extinct after the outbreak. Increased host resistance may be responsible for this recovery. Science , this issue p. 1517 ; see also p. 1458

The bacterial communities colonizing amphibian skin have been intensively studied due to their interactions with pathogenic chytrid fungi that are causing drastic amphibian population declines. Bacteria of the family Alcaligenaceae, and more specifically of the genus Pigmentiphaga, have been found to be associated specifically to arboreal frogs. Here we analyze their occurrence in a previously assembled global skin microbiome dataset from 205 amphibian species. Pigmentiphaga made up about 5% of the total number of reads in this global dataset. They were mostly found in unrelated arboreal frogs from Madagascar (Mantellidae and Hyperoliidae), but also occurred at low abundances on Neotropical frogs. Based on their 16S sequences, most of the sequences belong to a clade within Pigmentiphaga not assignable to any type strains of the five described species of the genus. One isolate from Madagascar clustered with Pigmentiphaga aceris (>99% sequence similarity on 16S rRNA gene level). Here, we report the full genome sequence of this bacterium which, based on 16S sequences of >97% similarity, has previously been found on human skin, floral nectar, tree sap, stream sediment and soil. Its genome consists of a single circular chromosome with 6,165,255 bp, 5,300 predicted coding sequences, 57 tRNA genes, and three rRNA operons. In comparison with other known Pigmentiphaga genomes it encodes a higher number of genes associated with environmental information processing and cellular processes. Furthermore, it has a biosynthetic gene cluster for a nonribosomal peptide syntethase, and bacteriocin biosynthetic genes can be found, but clusters for β-lactones present in other comparative Pigmentiphaga genomes are lacking.

We describe a new frog species of the Spinomantis bertini species complex based on congruent genetic evidence from mitochondrial and nuclear DNA sequences as well as minor morphological differences. A molecular phylogeny derived from the mitochondrial 16S rRNA gene revealed that Spinomantis mirus sp. nov. is sister to a clade containing the other two described species of the species complex, S. bertini and S. beckei, but strongly differentiated from these two species by 8.1–9.8% pairwise distances in this gene. DNA sequences from two nuclear genes revealed that S. mirus sp. nov. shares no alleles with these two species. Phenotypically, S. mirus sp. nov. differs from the other species of the complex by its larger size and some aspects of its coloration, including clear mottling on the flanks, tri-color banding on the legs, and distinct brown dots on the dorsum. The new species is so far only known from Pic d’Ivohibe Special Reserve. Its distribution thus appears to not overlap with those of the other two species, which as far as known are restricted to the Andohahela Massif in the extreme South-East of Madagascar, at a distance of about 250 km from Ivohibe.

We describe a new species of arboreal microhylid frog from northern Madagascar. The new species is assigned to the genus Cophyla based on molecular phylogeny and morphological similarities to other species of this genus. Molecular phylogenetic analysis resolved Cophyla fortuna sp. nov. as closely related to C. noromalalae. However, the two species were reciprocally monophyletic both in a tree reconstructed from a combination of mitochondrial genes, and in a tree based on the nuclear RAG-1 gene. The new species, previously identified as candidate species Cophyla sp. Ca4, occurs in lowland bamboo forests around the Marojejy Massif in northeastern Madagascar. It differs from the allopatric C. noromalalae, so far only known from the Montagne d’Ambre Massif in northern Madagascar, by slightly smaller body size and shorter duration and higher spectral frequency of advertisement calls. Several additional genetically divergent mitochondrial lineages of Cophyla, related to the C. fortuna/noromalalae complex and to C. phyllodactyla, occur in intervening areas between Montagne d’Ambre and Marojejy, and their status requires further study.