The amphibian skin‐associated microbiome across species, space and life history stages

Abstract

Skin-associated bacteria of amphibians are increasingly recognized for their role in defence against pathogens, yet we have little understanding of their basic ecology. Here, we use high-throughput 16S rRNA gene sequencing to examine the host and environmental influences on the skin microbiota of the cohabiting amphibian species Anaxyrus boreas, Pseudacris regilla, Taricha torosa and Lithobates catesbeianus from the Central Valley in California. We also studied populations of Rana cascadae over a large geographic range in the Klamath Mountain range of Northern California, and across developmental stages within a single site. Dominant bacterial phylotypes on amphibian skin included taxa from Bacteroidetes, Gammaproteobacteria, Alphaproteobacteria, Firmicutes, Sphingobacteria and Actinobacteria. Amphibian species identity was the strongest predictor of microbial community composition. Secondarily, within a given amphibian species, wetland site explained significant variation. Amphibian-associated microbiota differed systematically from microbial assemblages in their environments. Rana cascadae tadpoles have skin bacterial communities distinct from postmetamorphic conspecifics, indicating a strong developmental shift in the skin microbes following metamorphosis. Establishing patterns observed in the skin microbiota of wild amphibians and environmental factors that underlie them is necessary to understand skin symbiont community assembly, and ultimately, the role skin microbiota play in the extended host phenotype including disease resistance.

Fecal Bacterial Composition of the Endangered Yangtze Finless Porpoises Living Under Captive and Semi-natural Conditions

“…These results were congruent with the existing findings, which demonstrated a natural environment contained a higher diversity of microorganisms than that in closed-system aquaria [16,21]. Moreover, there were also several studies indicating that microbiome diversity varied from diverse geographical locations [22,36]. The results could suggest that the diversity of host microbial communities may be correlated with the complexity of environment.…”

Inhibitory bacteria reduce fungi on early life stages of endangered Colorado boreal toads (Anaxyrus boreas)

“…The pattern of alpha diversity by life stage suggests that microbial colonization at the tadpole stage is restricted and that the community undergoes a restructuring after metamorphosis. Evidence supporting reduced and bacterially restrictive communities was also found for tadpoles of frog species Rana cascadae (Kueneman et al, 2014). Tadpoles of R. cascadae had microbial communities with lower alpha diversity than the lake water they inhabited, suggesting that tadpoles of some species maintain restrictive bacterial communities compared to other developmental stages.…”

“…Our knowledge of amphibian skin microbiomes is rapidly increasing (Jani and Briggs, 2014;Kueneman et al, 2014;Walke et al, 2014). Exploring skin bacterial communities across different amphibian developmental stages and the defensive functions those microbes play, particularly prior to the development of the adaptive immune function, is an important and understudied area.…”

The pathogen Batrachochytrium dendrobatidis disturbs the frog skin microbiome during a natural epidemic and experimental infection

“…Several of the bacterial taxa affected by Bd infection in the current study, such as the Pseudomonadaceae, Opitutae, and Comamonadaceae, are common members of the amphibian microbiome, both in this and other studies (44)(45)(46), and it would be interesting to find out whether these taxa respond similarly to Bd infection in different amphibian species. In general, it will be important to determine if the disturbance effect of Bd on the R. sierrae microbiome that we observed is generally true for other amphibian species.…”

“…A second knowledge gap is the paucity of comprehensive culture-independent assessments of the amphibian microbiome, which are important because the vast majority of environmental and symbiotic microbes are not readily cultured, and culture-based methods can lead to severe underestimates of diversity and biased assessment of community composition (43). Few studies have applied next-generation sequencing methods to characterize the microbial communities on amphibian skin (44)(45)(46)(47), and, to our knowledge, none have done so in the context of Bd infection. A final challenge to understanding interactions between Bd and bacteria stems from the difficulties of drawing direct connections between laboratory and field studies.…”