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Host-associated microbiomes play important roles in host health and pathogen defense. In amphibians, the skin-associated microbiota can contribute to innate immunity with potential implications for disease management. Few studies have examined season-long temporal variation in the amphibian skin-associated microbiome, and the interactions between bacteria and fungi on amphibian skin remain poorly understood. We characterize season-long temporal variation in the skin-associated microbiome of the western tiger salamander ( Ambystoma mavortium ) for both bacteria and fungi between sites and across salamander life stages. Two hundred seven skin-associated microbiome samples were collected from salamanders at two Rocky Mountain lakes throughout the summer and fall of 2018, and 127 additional microbiome samples were collected from lake water and lake substrate. We used 16S rRNA and ITS amplicon sequencing with Bayesian Dirichlet-multinomial regression to estimate the relative abundances of bacterial and fungal taxa, test for differential abundance, examine microbial selection, and derive alpha diversity. We predicted the ability of bacterial communities to inhibit the amphibian chytrid fungus Batrachochytrium dendrobatidis ( Bd ), a cutaneous fungal pathogen, using stochastic character mapping and a database of Bd -inhibitory bacterial isolates. For both bacteria and fungi, we observed variation in community composition through time, between sites, and with salamander age and life stage. We further found that temporal trends in community composition were specific to each combination of salamander age, life stage, and lake. We found salamander skin to be selective for microbes, with many taxa disproportionately represented relative to the environment. Salamander skin appeared to select for predicted Bd -inhibitory bacteria, and we found a negative relationship between the relative abundances of predicted Bd -inhibitory bacteria and Bd . We hope these findings will assist in the conservation of amphibian species threatened by chytridiomycosis and other emerging diseases.
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Phylosymbiosis shapes skin bacterial communities and pathogen-protective function in Appalachian salamanders
Abstract Phylosymbiosis is an association between host-associated microbiome composition and host phylogeny. This pattern can arise via the evolution of host traits, habitat preferences, diets, and the co-diversification of hosts and microbes. Understanding the drivers of phylosymbiosis is vital for modelling disease-microbiome interactions and manipulating microbiomes in multi-host systems. This study quantifies phylosymbiosis in Appalachian salamander skin in the context of infection by the fungal pathogen Batrachochytrium dendrobatidis (Bd), while accounting for environmental microbiome exposure. We sampled ten salamander species representing >150M years of divergence, assessed their Bd infection status, and analysed their skin and environmental microbiomes. Our results reveal a significant signal of phylosymbiosis, whereas the local environmental pool of microbes, climate, geography, and Bd infection load had a smaller impact. Host-microbe co-speciation was not evident, indicating that the effect stems from the evolution of host traits influencing microbiome assembly. Bd infection is correlated with host phylogeny and the abundance of Bd-inhibitory bacterial strains, suggesting that the long-term evolutionary dynamics between salamander hosts and their skin microbiomes affect the present-day distribution of the pathogen, along with habitat-linked exposure risk. Five Bd-inhibitory bacterial strains showed unusual generalism: occurring in most host species and habitats. These generalist strains may enhance the likelihood of probiotic manipulations colonising and persisting on hosts. Our results underscore the substantial influence of host-microbiome eco-evolutionary dynamics on environmental health and disease outcomes.
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- Award ID(s):
- 2131060
- PAR ID:
- 10517009
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- The ISME Journal
- Volume:
- 18
- Issue:
- 1
- ISSN:
- 1751-7362
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Synopsis Emerging infectious diseases have been of particular interest as a major threat to global biodiversity. In amphibians, two fungal sister taxa, Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal), along with the viral pathogen ranavirus, have affected global populations. Factors such as host traits, abiotic and biotic environmental conditions, and pathogen prevalence contribute to species-specific disease susceptibility. The eastern United States is home to the Appalachian Mountain system, known as a “hotspot” for salamander biodiversity. Bd and ranavirus are present throughout the Appalachians, and a Bsal emergence could be imminent. Throughout the Appalachians are the spotted salamanders, Ambystoma maculatum, a mostly terrestrial salamander that participates in mass breeding migration to ponds and vernal pools in the late spring. Previous experimental studies have shown that spotted salamanders appear to be resistant to Bd and Bsal infection, but the mechanisms behind Bd defense remain unknown. Spotted salamanders emerging from their overwintering habitats were hypothesized to have potent anti-Bd function expressed in their mucus and in their skin microbiomes, as a countermeasure to annual Bd re-emergence. We used non-invasive sampling at two pools during the spotted salamander annual breeding event to (I) determine pathogen prevalence, (II) quantify the antifungal potential of salamander skin mucus, and (III) characterize the diversity and composition of the salamander skin microbiome and contrast it to that of the corresponding environmental microbiome. We did not detect any Bd, Bsal, or ranavirus in the salamanders. The salamander mucus did not inhibit Bd growth in vitro, and anti-Bd bacteria were at low relative abundance in the microbiome. The salamander microbiome sourced a proportion of bacteria from the environment and appeared to select rare taxa from their respective pools; however, their functional relevance in pathogen defense is unclear. Our results suggest that the spotted salamander mucosal secretions and skin microbiome are not the mechanisms of defense against Bd. Rather, elements not captured by the mucosome (e.g., immune cell gene expression) may confer resistance. This study contributes to the understanding of salamander intraspecies variation in disease susceptibility.more » « less
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