The Influence of Habitat and Phylogeny on the Skin Microbiome of Amphibians in Guatemala and Mexico

Abstract

Microbial symbionts are increasingly recognized as playing a critical role in organismal health across a wide range of hosts. Amphibians are unique hosts in that their skin helps to regulate the exchange of water, ions, and gases, and it plays an active role in defense against pathogens through the synthesis of anti-microbial peptides. The microbiome of amphibian skin includes a diverse community of bacteria known to defend against pathogens, including the global pandemic lineage of Batrachochytrium dendrobatidis associated with mass amphibian die-offs. The relative influence of host phylogeny and environment in determining the composition of the amphibian skin microbiome remains poorly understood. We collected skin swabs from montane amphibians in Mexico and Guatemala, focusing on two genera of plethodontid salamanders and one genus of frogs. We used high throughput sequencing to characterize the skin bacterial microbiome and tested the impact of phylogeny and habitat on bacterial diversity. Our results show that phylogenetic history strongly influences the diversity and community structure of the total bacterial microbiome at higher taxonomic levels (between orders), but on lower scales (within genera and species), the effect of habitat predominates. These results add to a growing consensus that habitat exerts a strong effect on microbiome structure and composition, particularly at shallow phylogenetic scales.

Composition of the North American Wood Frog (Rana sylvatica) Bacterial Skin Microbiome and Seasonal Variation in Community Structure

“…Changes in environmental conditions are known to influence the microbiome [4,6,7], potentially affecting the hosts ability to resist infection by a pathogen [18,19]. In this study we have reported on the microbial community associated with R. sylvatica skin over the course of multiple seasons to observe the changes in community composition and structure.…”

“…Core taxa were determined for each group of seasonal frog skin communities, and for the overall frog skin microbiome, using the core-features command in QIIME2. Core taxa were defined as those found to be present in 90% or more of the samples within a given group, as this is a commonly used threshold [6,38] which meets the definition of core microbiota as those which are commonly present within samples from a given environment [39]. Venn diagrams depicting the overlap of seasonally core microbiota were prepared using the online Venn diagram tool provided by the University of Ghent (http://bioinformatics.psb.ugent.be/webtools/Venn/).…”

“…Additionally, species which dominate the skin-associated community are not generally those which are dominant in the environment at large, and therefore must be selected for by the skin microenvironment [1]. Further microbiome studies have shown that frogs of the same species sampled during different seasons or from different habitats can have large differences in the diversity of bacteria present on their skin [4,6,7], underscoring the influence of environmental factors on the microbial community. Most studies of amphibian microbiota have been performed on amphibian species from tropical or subtropical climates, meaning data on temperate amphibian species is less comprehensive.…”

Characterization of the Skin Cultivable Microbiota Composition of the Frog Pelophylax perezi Inhabiting Different Environments

“…The establishment of the microbial skin community in amphibians is mainly obtained on the vertical transmission of parental microbes, horizontal transmission (e.g., during mating), pool of microbes present in the external environment (both aquatic and terrestrial), and on the interaction between the host’s immune system/mucous composition with bacteria [ 21 , 29 , 34 , 35 ]. Beyond this, the skin microbial community can be influenced by several biotic and abiotic environmental factors like chemical contamination [ 4 , 33 , 35 , 36 , 37 , 38 ]. However, the research about the influence of pollution on the skin microbiome composition is starting to understand how these changes are achieved.…”

Assembly of the amphibian microbiome is influenced by the effects of land-use change on environmental reservoirs

“…This coincided with variation in both the bacterial and fungal communities of salamanders found at these sites. We believe our findings provide valuable insight into the exogenous factors often confounded by host species identity, a well-supported predictor of microbial composition (Ellison et al, 2018;Jani & Briggs, 2018;Muletz-Wolz et al, 2018). Additionally, this study reveals the important roles that dispersal, drift, and heterogeneous selection play in driving dissimilarity between individual hosts.…”