Establishing the core microbiota of Oregon spotted frogs: distribution, potential function and stability

Amphibians have bacteria on their skins that can protect against the fungal pathogen, Batrachochytrium dendrobatidis (Bd). Oregon spotted frogs (OSF) are an endangered amphibian that are in captive breeding and head start programs in British Columbia. In the wild OSF are resistant to Bd. Skin bacteria can mediate resistance to Bd in some amphibians, but little is known about OSF bacteria and whether they are associated with Bd. Furthermore, captivity changes the microbiome of many animals, including amphibians, which may have implications for reintroducing endangered amphibians into the wild. Here we survey the microbiota of wild and captive OSF. We show that wild OSF have three core bacteria that are absent from the environment but found on other sympatric amphibians. These core bacteria are also on captive frogs, but two are lower in abundance. Two of the core bacteria are also detected at a low relative abundance on some wild egg masses, although they are absent, or rare, on egg masses in captivity. Using qPCR, we detected Bd in wild populations, allowing me to test the hypothesis that Bd alters microbiota structure. Bd intensity weakly correlates with overall microbiota composition, and the core bacterium Rhizobacter positively correlates with Bd. Lastly, we experimentally test the role of environmental reservoirs in maintaining OSF microbiota. Housing frogs in low diversity settings resulted in subtle bacterial community changes, with most community members remaining stable. Furthermore reducing the diversity of the environmental reservoir did not reduce diversity on frogs or change the predicted antifungal function of OSF communities. Overall, we show that OSF have a handful of specific bacteria that are dominant, stable, and associated with a wide range of amphibians.