Seasonal and ontogenetic transitions trigger skin dysbioses in declining amphibians affected by chytridiomycosis

Background/Question/Methods

Skin microbial communities provide protection against pathogens, and regulate physiological processes and immune responses. We hypothesized that ontogenetic and seasonal shifts can alter the balance between “protective” and “harmful” bacteria (also known as dysbiosis), leading to increased rates of infection to pathogens. To test our hypothesis, we examined the transition of skin microbial communities between periods of immunesupression, either caused by development or environmental stress, in declining amphibians affected by the pathogenic fungus Batrachochytrium dendrobatidis. We used automated ribosomal intergenic spacer analyses (ARISA) and Illumina MiSeq sequencing to quantify microbial diversity and composition in Eleutherodactylus coqui and Lithobates yavapaiensis, two anurans with well-characterized infection dynamics but different life histories.

 Results/Conclusions

Using ARISA, we found similar responses in both species where immune-suppressed hosts (juveniles and winter-collected frogs) exhibited increased operational taxonomic unit (OTU) richness, diversity, and evenness. In addition, skin microbial community structure overlapped very little between ages in E. coqui and seasons in L. yavapaiensis, suggesting drastic shifts driven by the addition or loss of specific OTUs or by changes in their relative abundances. Juvenile E. coqui frogs lost eight unique OTUs not present in adults, whereas adult L. yavapaiensis gained 13 unique OTUs from summer to winter. By amplifying the V4 region of 16S ribosomal RNA, we found significant differences in core microbiota for E. coqui. Acinetobacter johnsonii formed part of the core microbiome of juveniles, whereas Pseudomonadaceae dominated in adults. Unfortunately, due to insufficient template material, we were only able to sequence four winter-collected L. yavapaiensis, precluding phylotype analyses between seasons. Our findings indicate that immune suppression during susceptible states is accompanied by the addition of new microbial taxa which causes skin dysbioses in amphibians. Identifying whether these microbial community changes promote health or disease requires further functional investigation, particularly if future conservation strategies are to include the use of probiotics in successful disease mitigation.