The Ulu Temburong region in Bruneian Borneo is an exceptionally diverse, old-growth tropical rainforest that harbours unique species, including cryptic amphibians. In May 2017, we collected three caecilian specimens (Amphibia, Gymnophiona, Ichthyophis) from Ulu Temburong National Park, conducting morphological, molecular and cutaneous microbiome analyses. Comparisons of morphology, including CT scans, and mitochondrial DNA have determined the Temburong specimens to be Ichthyophis asplenius, previously not known from Brunei but documented elsewhere on Borneo. The Temburong specimens had continuous lateral body stripes, lacked splenial teeth and had body folds and grooves that did not cross the back on the anterior portion of the body. The mitochondrial DNA matched published sequences of I. asplenius from Sarawak, Malaysia. Our study pioneers the exploration of caecilian cutaneous microbiomes in the wild, marking the inaugural report from the Asian subcontinent. Microbial communities exhibited specimen-specific differences while maintaining uniformity across body locations. Proteobacteria dominated, aligning with previous studies, whereas Firmicutes and Acidobacteriota displayed intriguing variations between caecilian skin and the environment. This work constitutes the second caecilian species documented in Brunei and provides the initial wild caecilian microbiome description from Asia, contributing valuable insights into the biodiversity and microbial ecology of this important region.

North American salamanders are threatened by intercontinental spread of chytridiomycosis, a deadly disease caused by the fungal pathogenBatrachochytrium salamandrivorans(Bsal). To predict potential dispersal ofBsalspores to salamander habitats, we evaluated the capacity of soil microbial communities to resist invasion. We determined the degree of habitat invasibility using soils from five locations throughout the Great Smoky Mountains National Park, a region with a high abundance of susceptible hosts. Our experimental design consisted of replicate soil microcosms exposed to different propagule pressures of the non-native pathogen,Bsal, and an introduced but endemic pathogen,B. dendrobatidis(Bd). To compare growth and competitive interactions, we used quantitative PCR, live/dead cell viability assays, and full-length 16S rRNA sequencing. We found that soil microcosms with intact bacterial communities inhibited bothBsalandBdgrowth, but inhibitory capacity diminished with increased propagule pressure.Bsalshowed greater persistence thanBd. Linear discriminant analysis (LDA) identified the family Burkolderiaceae as increasing in relative abundance with the decline of both pathogens. Although our findings provide evidence of environmental filtering in soils, such barriers weakened in response to pathogen type and propagule pressure, showing that habitats vary their invasibility based on properties of their local microbial communities.

Abstract The One Health High-Level Expert Panel’s definition of One Health includes optimizing the health of people, animals (wild and domestic) and ecosystems. For many One Health practitioners, wildlife that can spread zoonoses are the focus, particularly if they can come in contact with people. However, ecosystem health is often best-indicated by less-encountered species, for instance, amphibians and reptiles. This review highlights how these taxa can benefit human health and well-being, including cultural significance, as well as their impact on plant, animal and environmental health. We highlight current challenges to the health of these species and the need to include them in the One Health Joint Action Plan. We conclude with a call to action for inclusion of amphibians and reptiles in a One Health approach.

Amphibians face many challenges in their conservation, including threats from emerging infectious pathogens/parasites and habitat degradation. In diverse amphibian communities, where multiple emerging pathogens tend to co-occur, we know little about how the structural partitioning of host specificity impacts population maintenance despite disease. Here, we used field data from amphibian communities in north Florida to investigate host-specific traits influencing the prevalence, intensity, and transmission of three emerging pathogens of amphibians: Batrachochytrium dendrobatidis (Bd), Perkinsea (Pr), and Ranavirus (Rv). We found that Bd exhibited specificity for later developmental stages, and that overall infection patterns differed between ephemeral and semi-permanent sites and across seasons. For each pathogen, we identified key hosts overwhelmingly contributing to community transmission dynamics and found evidence of pathogen interactions that may facilitate Bd-Rv co-infections, and dilution effects of increased host diversity on Pr infection. Our findings confirmed that declining species within the region are routinely infected with emerging pathogens. However, the probability of infection depended on different habitat characteristics and associated host community composition. Thus, our study emphasizes the importance of identifying key and sensitive hosts that drive or succumb to infections in natural communities before reintroducing amphibians into the wild. This approach can help improve conservation efforts in diverse host communities as successful repatriation of sensitive species can benefit from detailed characterization of the established disease dynamics at the release site.

Microbiomes are major determinants of host growth, development and survival. In amphibians, host-associated bacteria in the skin can inhibit pathogen infection, but many processes can influence the structure and composition of the community. Here we quantified the shifts in skin-associated bacteria across developmental stages in the striped newt (Notophthalmus perstriatus), a threatened salamander species with a complex life history and vulnerable to infection by the amphibian chytrid fungus Batrachochytrium dendrobatidis and ranavirus. Our analyses show that pre-metamorphic larval and paedomorphic stages share similar bacterial compositions, and that the changes in the microbiome coincided with physiological restructuring during metamorphosis. Newts undergoing metamorphosis exhibited microbiome compositions that were intermediate between paedomorphic and post-metamorphic stages, further supporting the idea that metamorphosis is a major driver of host-associated microbes in amphibians. We did not find support for infection-related disruption of the microbiome, though infection replicates were small for each respective life stage.

While some pathogens are limited to single species, others can colonize many hosts, likely contributing to the emergence of novel disease outbreaks. Despite this biodiversity threat, traits associated with host niche expansions are not well understood in multihost pathogens. Here, we aimed to uncover functional machinery driving multihost invasion by focusing on Batrachochytrium dendrobatidis (Bd), a pathogen that infects the skin of hundreds of amphibians worldwide. We performed a meta-analysis of Bd gene expression using data from published infection experiments and newly generated profiles. We analysed Bd transcriptomic landscapes across the skin of 14 host species, reconstructed Bd isolates phylogenetic relationships, and inferred the origin and evolutionary history of differentially expressed genes under a phylogenetic framework comprising other 12 zoosporic fungi. Bd displayed plastic infection strategies when challenged by hosts with different disease susceptibility. Our analyses identified sets of differentially expressed genes under host environments with similar infection outcome. We stressed nutritional immunity and gene silencing as important processes required to overcome challenging skin environments in less susceptible hosts. Overall, Bd genes expressed during amphibian skin exploitation have arisen mainly via gene duplications with great family expansions, increasing the gene copy events previously described for this fungal species. Finally, we provide a comprehensive gene data set that can be used to further examine eco-evolutionary hypotheses for this host-pathogen system. Our study supports the idea that host environments exert contrasting selective pressures, such that gene expression plasticity could be one of the evolutionary keys leading to the success of multihost pathogens.

Detection of cryptic, arboreal amphibians requires specialized survey devices to account for taxa-specific climbing and hiding life histories. Hylid treefrogs are typically surveyed via tubes, wherein a polyvinyl chloride (PVC) pipe is placed upright in the ground or attached to a tree, which frogs then use as a shelter. Traditional survey methods typically require removal of amphibians for identification, adding time to data collection and stress to survey animals. As an alternative, we developed a novel shelter that includes a clear, acrylic tube nested within PVC pipe. Frogs can be identified through the clear tubing, eliminating the need for removal or handling. Here, we compare the efficacy of these novel devices to traditional PVC pipes in the field to determine any differences in device occupancy by hylid treefrogs. We placed 30 tubes of each type for 6 mo at a pond site in midwestern Virginia, USA. We found 23 frogs of two species (Gray Treefrogs, Hyla twrsicolor, and Spring Peepers, Pseudacris crucifer) in tubes. We found no significant difference in tube occupancy between device types. This demonstrates our novel design as a valid surveying method for these hylid species, particularly H. versicolor, though further research should examine the effectiveness of these devices for other species and habitats. The efficacy, ease of use, and minimally invasive nature of this trap design make it useful not only for hylid surveys but also for educational outreach and public engagement, which are key components for addressing ongoing amphibian population declines.

Background The amphibian skin microbiome is an important mediator of host health and serves as a potential source of undiscovered scientifically significant compounds. However, the underlying modalities of how amphibian hosts obtain their initial skin-associated microbiome remains unclear. Here, we explore microbial transmission patterns in foam-nest breeding tree frogs from Southeast Asia (Genus: Polypedates ) whose specialized breeding strategy allows for better delineation between vertically and environmentally derived microbes. To facilitate this, we analyzed samples associated with adult frog pairs taken after mating—including adults of each sex, their foam nests, environments, and tadpoles before and after environmental interaction—for the bacterial communities using DNA metabarcoding data (16S rRNA). Samples were collected from frogs in-situ in Brunei, Borneo, a previously unsampled region for amphibian-related microbial diversity. Results Adult frogs differed in skin bacterial communities among species, but tadpoles did not differ among species. Foam nests had varying bacterial community composition, most notably in the nests’ moist interior. Nest interior bacterial communities were discrete for each nest and overall displayed a narrower diversity compared to the nest exteriors. Tadpoles sampled directly from the foam nest displayed a bacterial composition less like the nest interior and more similar to that of the adults and nest exterior. After one week of pond water interaction the tadpole skin microbiome shifted towards the tadpole skin and pond water microbial communities being more tightly coupled than between tadpoles and the internal nest environment, but not to the extent that the skin microbiome mirrored the pond bacterial community. Conclusions Both vertical influence and environmental interaction play a role in shaping the tadpole cutaneous microbiome. Interestingly, the interior of the foam nest had a distinct bacterial community from the tadpoles suggesting a limited environmental effect on tadpole cutaneous bacterial selection at initial stages of life. The shift in the tadpole microbiome after environmental interaction indicates an interplay between underlying host and ecological mechanisms that drive community formation. This survey serves as a baseline for further research into the ecology of microbial transmission in aquatic animals.

Experiment is an online platform for funding and sharing scientific discoveries. Push the boundaries of knowledge in biology, chemistry, medicine, physics, computer science, paleontology, economics, engineering, neuroscience, and more.

Abstract Rapid advances in genomic tools for use in ecological contexts and non‐model systems allow unprecedented insight into interactions that occur beyond direct observation. We developed an approach that couples microbial forensics with molecular dietary analysis to identify species interactions and scavenging by invasive rats on native and introduced birds in Hawaii. First, we characterized bacterial signatures of bird carcass decay by conducting 16S rRNA high‐throughput sequencing on chicken (Gallus gallus domesticus) tissues collected over an 11‐day decomposition study in natural Hawaiian habitats. Second, we determined if field‐collected invasive black rats (Rattus rattus; n = 51, stomach and fecal samples) had consumed birds using molecular diet analysis with two independent PCR assays (mitochondrial Cytochrome Oxidase I and Cytochrome b genes) and Sanger sequencing. Third, we characterized the gut microbiome of the same rats using 16S rRNA high‐throughput sequencing and identified 15 bacterial taxa that were (a) detected only in rats that consumed birds (n = 20/51) and (b) were indicative of decaying tissue in the chicken decomposition experiment. We found that 18% of rats (n = 9/51) likely consumed birds as carrion by the presence of bacterial biomarkers of decayed tissue in their gut microbiome. One species of native bird (Myadestes obscurus) and three introduced bird species (Lophura leucomelanos, Meleagris gallopavo, Zosterops japonicus) were detected in the rats’ diets, with individuals from these species (except L. nycthemera) likely consumed through scavenging. Bacterial biomarkers of bird carcass decay can persist through rat digestion and may serve as biomarkers of scavenging. Our approach can be used to reveal trophic interactions that are challenging to measure through direct observation.