Skin microbiome composition and diversity across Anaxyrus boreas developmental stages

In the last decade our understanding of host-associated microbes has grown immensely, however there are still many questions to be answered. Few studies have examined the assembly of the microbiome throughout organismal development, and even fewer have attempted to observe this phenomenon through a natural study. We sampled three high elevation wetland habitats in Colorado, USA, where boreal toads (Anaxyrus boreas) had successfully reproduced and deposited egg masses. In total, we sampled 12 distinct life stages ranging from eggs to adults along with two types of environmental samples during May through September 2015. We used barcoded sequencing of the 16S rRNA marker gene to characterize the diversity and composition of bacterial taxa living on the skin of the boreal toads. We found that microbiome composition was highly dependent on amphibian life stage. The bacterial communities on egg stages and early tadpoles were very similar to the environmental bacterial community. The skin community on later-stage tadpoles began to diverge from the environmental community as development continued, then shifted again following metamorphosis. Bacterial diversity on the A. boreas decreased soon after the tadpoles hatched form the egg but then increased following metamorphosis. The relative proportion of the bacterial order Burkholderiales increased during the tadpole stages and decreased after metamorphosis. Stramenopiles were dominant during the egg stage but nearly absent on adults. Actinomycetales were absent or rare throughout development until becoming the most proportionally abundant order of bacteria on the subadult and adult stages. Our results suggest that the microbiome of amphibians is deterministic and extremely selective as tadpoles develop which indicates that the skin microbiome of larval amphibians may perform specific functions for the host