Panamanian frog species host unique skin bacterial communities.

Lisa K Belden,Jenifer B Walke,Leanna L House,Eria A Rebollar,Myra C Hughey,Roderick V Jensen,Thomas P Umile,Stephen C Loftus,Reid N Harris,Matthew H Becker,Elizabeth A Burzynski,Roberto Ibáñez,Daniel Medina,Kevin P C Minbiole

doi:10.3389/fmicb.2015.01171

Abstract

Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd), that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panamá, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panamá to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti-fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, ~bacterial species) community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panamá and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panamá, across all four sites, only 35 individuals (~26%) were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west-east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in these skin symbiont microbial systems as it is in many macro-systems.

Highlights

All animals serve as hosts to symbiotic microorganisms that, along with their genetic contributions, constitute their microbiome
We identified 3138 operational taxonomic units (OTUs) from A. callidryas (N = 62 frogs), 2704 OTUs from D. ebraccatus (N = 53 frogs), and 2667 OTUs from C. fitzingeri (N = 21 frogs), based on our 16S rRNA amplicon sequencing
Alpha diversity differed among the three species, with C. fitzingeri harboring the most diverse communities of bacteria in terms of richness (Chisq = 57.3, P < 0.001; posthoc comparisons, A. callidryas–D. ebraccatus, P = 0.002; FIGURE 3 | Mean relative abundance of bacterial phyla present on the skin of (A) three frog species surveyed in Panamá in 2012 (Agalychnis callidryas, Dendropsophus ebraccatus, Craugastor fitzingeri; this study) and (B) a subset of individuals of each of the three frog species surveyed in Panamá compared to three frog species surveyed in Virginia, USA (Anaxyrus americanus, Lithobates catesbeianus, Pseudacris crucifer; Walke et al, 2015; Belden et al unpublished data)

Summary

Introduction

All animals serve as hosts to symbiotic microorganisms that, along with their genetic contributions, constitute their microbiome. Panamanian frog skin microbiota throughout the body (Cho and Blaser, 2012; Ursell et al, 2012) The composition of these microbial communities can strongly influence many facets of host health and disease resistance (Cho and Blaser, 2012; Fierer et al, 2012; McFall-Ngai et al, 2013). Our knowledge in this area is growing in large part because of advances in molecular microbiology that allow us to study these complex microbial communities in much more detail. Culture-independent studies, while initially focused on revealing diversity, clearly indicate complex interactions in these communities both among microbes and among microbes and their host (McFall-Ngai et al, 2013; Boon et al, 2014; Manor et al, 2014)

Methods

Results

Conclusion