Predicting fungal infection rate and severity with skin-associated microbial communities on amphibians

The costs and benefits of a dynamic host microbiome

All species host a rich community of microbes. This microbiome is dynamic, and displays seasonal, daily, and even hourly changes, but also needs to be resilient to fulfill important roles for the host. In evolutionary ecology, the focus of microbiome dynamism has been on how it can facilitate host adaptation to novel environments. However, an hitherto largely overlooked issue is that the host needs to keep its microbiome in check, which is costly and leads to trade-offs with investing in other fitness-related traits. Investigating these trade-offs in natural vertebrate systems by collecting longitudinal data will lead to deeper insight into the evolutionary mechanisms that shape host-microbiome interactions.

Skin microbiomes of frogs vary among individuals and body regions, revealing differences that reflect known patterns of chytrid infection

The amphibian skin microbiome is an important line of defense against pathogens including the deadly chytrid fungus, Batrachochytrium dendrobatidis (Bd). Intra-species variation in disease susceptibility and intra-individual variation in infection distribution across the skin, therefore, may relate to differences in skin microbiomes. However, characterization of microbiome variation within and among amphibian individuals is needed. We utilized 16S rRNA gene amplicon sequencing to compare microbiomes of ten body regions from nine captive R. sierrae individuals and their tank environments. While frogs harbored distinct microbial communities compared to their tank environments, tank identity was associated with more variation in frog microbiomes than individual frog identity. Within individuals, we detected differences between microbiomes of body regions where Bd infection would be expected compared to regions that infrequently experience infection. Notably, the bacterial families Burkholderiaceae (phylum Proteobacteria) and Rubritaleaceae (phylum Verrucomicrobia) were dominant on frog skin, and the relative abundances of undescribed members of these families were important to describing differences among and within individuals. Two undescribed Burkholderiaceae taxa were found to be putatively Bd-inhibitory, and both showed higher relative abundance on body regions where Bd infection is often localized. These findings highlight the importance of considering intrapopulation and intraindividual heterogeneities, which could provide insights relevant to predicting localized interactions with pathogens.

Skin microbiome disturbance linked to drought-associated amphibian disease

The onset of global climate change has led to abnormal rainfall patterns, disrupting associations between wildlife and their symbiotic microorganisms. We monitored a population of pumpkin toadlets and their skin bacteria in the Brazilian Atlantic Forest during a drought. Given the recognized ability of some amphibian skin bacteria to inhibit the widespread fungal pathogen Batrachochytrium dendrobatidis (Bd), we investigated links between skin microbiome health, susceptibility to Bd and host mortality during a die-off event. We found that rainfall deficit was an indirect predictor of Bd loads through microbiome disruption, while its direct effect on Bd was weak. The microbiome was characterized by fewer putative Bd-inhibitory bacteria following the drought, which points to a one-month lagged effect of drought on the microbiome that may have increased toadlet susceptibility to Bd. Our study underscores the capacity of rainfall variability to disturb complex host-microbiome interactions and alter wildlife disease dynamics.

Dietary carotenoid supplementation has long-term and community-wide effects on the amphibian skin microbiome

The amphibian skin microbiome plays a crucial role in host immunity and pathogen defence, yet we know little about the environmental drivers of skin microbial variation across host individuals. Inter-individual variation in the availability of micro-nutrients such as dietary carotenoids, which are involved in amphibian immunity, may be one factor that influences skin microbial assembly across different life history stages. We compared the effect of four carotenoid supplementation regimes during different life stages on the adult skin microbiome using a captive population of the critically endangered southern corroboree frog, Pseudophryne corroboree. We applied 16S rRNA sequencing paired with joint-species distribution models to examine the effect of supplementation on taxon abundances. We found that carotenoid supplementation had subtle yet taxonomically widespread effects on the skin microbiome, even 4.5 years post supplementation. Supplementation during any life-history stage tended to have a positive effect on the number of bacterial taxa detected, although explanatory power was low. Some genera were sensitive to supplementation pre-metamorphosis, but most demonstrated either additive or dominant effects, whereby supplementation during one life history stage had intermediate or similar effects, respectively, to supplementation across life. Carotenoid supplementation increased abundances of taxa belonging to lactic acid bacteria, including Lactococcus and Enterococcus, a group of bacteria that have previously been linked to protection against the amphibian fungal pathogen Batrachochytrium dendrobatidis (Bd). While the fitness benefits of these microbial shifts require further study, these results suggest a fundamental relationship between nutrition and the amphibian skin microbiome which may be critical to amphibian health and the development of novel conservation strategies.

Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts

Amphibian skin harbors microorganisms that are associated with the fungal pathogen Batrachochytrium dendrobatidis (Bd), which causes chytridiomycosis, one of the most significant wildlife diseases known. This pathogen originated in Asia, where diverse Bd lineages exist; hence, native amphibian hosts have co-existed with Bd over long time periods. Determining the nuances of this co-existence is crucial for understanding the prevalence and spread of Bd from a microbial context. However, associations of Bd with the natural skin microbiome remain poorly understood for Asian hosts, especially in relation to skin-associated fungi. We used 16 S rRNA and fungal internal transcribed spacer (ITS) gene sequencing to characterize the skin microbiome of four native Asian amphibian species and examined the relationships between Bd infection and their skin bacterial and fungal communities; we also analyzed the correlates of the putative anti-Bd bacteria. We show that both skin bacterial and fungal community structure and composition had significant associations with infection status (Bd presence/absence) and infection intensity (frequency of Bd sequence reads). We also found that the putative anti-Bd bacterial richness was correlated with Bd infection status and infection intensity, and observed that the relative abundance of anti-Bd bacteria roughly correspond with changes in both Bd prevalence and mean infection intensity in populations. Additionally, the microbial co-occurrence network of infected frogs was significantly different from that of uninfected frogs that were characterized by more keystone nodes (connectors) and larger proportions in correlations between bacteria, suggesting stronger inter-module bacterial interactions. These results indicate that the mutual effects between Bd and skin-associated microbiome, including the interplay between bacteria and fungi, might vary with Bd infection in susceptible amphibian species. This knowledge will help in understanding the dynamics of Bd from a microbial perspective, potentially contributing to mitigate chytridiomycosis in other regions of the world.

The adaptive microbiome hypothesis and immune interactions in amphibian mucus

The microbiome is known to provide benefits to hosts, including extension of immune function. Amphibians are a powerful immunological model for examining mucosal defenses because of an accessible epithelial mucosome throughout their developmental trajectory, their responsiveness to experimental treatments, and direct interactions with emerging infectious pathogens. We review amphibian skin mucus components and describe the adaptive microbiome as a novel process of disease resilience where competitive microbial interactions couple with host immune responses to select for functions beneficial to the host. We demonstrate microbiome diversity, specificity of function, and mechanisms for memory characteristic of an adaptive immune response. At a time when industrialization has been linked to losses in microbiota important for host health, applications of microbial therapies such as probiotics may contribute to immunotherapeutics and to conservation efforts for species currently threatened by emerging diseases.

Metabarcoding approaches in amphibian disease ecology: Disentangling the functional contributions of skin bacteria on disease outcome

Molecular technologies have revolutionized the field of wildlife disease ecology, allowing the detection of outbreaks, novel pathogens, and invasive strains. In particular, metabarcoding approaches, defined here as tools used to amplify and sequence universal barcodes from a single sample (e.g., 16S rRNA for bacteria, ITS for fungi, 18S rRNA for eukaryotes), are expanding our traditional view of host-pathogen dynamics by integrating microbial interactions that modulate disease outcome. Here, I provide an analysis from the perspective of the field of amphibian disease ecology, where the emergence of multi-host pathogens has caused global declines and species extinctions. I re-analyzed an experimental mesocosm dataset to infer the functional profiles of the skin microbiomes of coqui frogs (Eleutherodactylus coqui), an amphibian species that is consistently found infected with the fungal pathogen Batrachochytrium dendrobatidis and has high turnover of skin bacteria driven by seasonal shifts. I found that the metabolic activities of microbiomes operate at different capacities depending on the season. Global enrichment of predicted functions was more prominent during the warm-wet season, indicating that microbiomes during the cool-dry season were either depauperate, resistant to new bacterial colonization, or that their functional space was more saturated. These findings suggest important avenues to investigate how microbes regulate population growth and contribute to host physiological processes. Overall, this study highlights the current challenges and future opportunities in the application of metabarcoding to investigate the causes and consequences of disease in wild systems.