Bacterial metacommunities of San Francisco Bay Area salamanders are structured by host taxonomy and habitat quality

Metacommunity theory aims to integrate both small-scale and large-scale dynamics to better understand patterns of composition and function in host-associated microbiomes. The composition of the cutaneous microbiome can determine what roles bacterial symbionts play for their hosts, including contributing to infectious disease resistance. For example, some bacteria on the skin of amphibians produce antifungal compounds that inhibit two lethal amphibian skin fungal pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal). These fungal pathogens have caused extirpations of amphibian populations across the world and continue to spread. Of particular interest is the potential impact of Bsal if it becomes introduced into the United States - the largest hotspot of salamander diversity in the world. This study applies 16S rRNA sequencing to characterize the skin microbiomes of terrestrial salamanders native to the San Francisco Bay Area. By applying metacommunity structure analysis, we identified dispersal barriers for these influential bacteria between salamander genera and localities. Each genus had a somewhat distinct community of anti-Bd skin bacteria, suggesting that the salamander skin may select for a functional assembly of symbionts that could differ in their ability to protect these salamanders from disease.