Genetic variability and ontogeny predict microbiome structure in a disease-challenged montane amphibian

Griffiths, Sarah M; Harrison, Xavier A; Weldon, Ché; Wood, Michael D; Pretorius, Abigail; Hopkins, Kevin; Fox, Graeme; Preziosi, Richard F; Antwis, Rachael E

Abstract

Amphibian populations worldwide are at risk of extinction from infectious diseases, including chytridiomycosis caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd). Amphibian cutaneous microbiomes interact with Bd and can confer protective benefits to the host. The composition of the microbiome itself is influenced by many environment- and host-related factors. However, little is known about the interacting effects of host population structure, genetic variation and developmental stage on microbiome composition and Bd prevalence across multiple sites. Here we explore these questions in Amietia hymenopus, a disease-affected frog in southern Africa. We use microsatellite genotyping and 16S amplicon sequencing to show that the microbiome associated with tadpole mouthparts is structured spatially, and is influenced by host genotype and developmental stage. We observed strong genetic structure in host populations based on rivers and geographic distances, but this did not correspond to spatial patterns in microbiome composition. These results indicate that demographic and host genetic factors affect microbiome composition within sites, but different factors are responsible for host population structure and microbiome structure at the between-site level. Our results help to elucidate complex within- and among- population drivers of microbiome structure in amphibian populations. That there is a genetic basis to microbiome composition in amphibians could help to inform amphibian conservation efforts against infectious diseases.

Citation

Griffiths, S. M., Harrison, X. A., Weldon, C., Wood, M. D., Pretorius, A., Hopkins, K., …Antwis, R. E. (2018). Genetic variability and ontogeny predict microbiome structure in a disease-challenged montane amphibian. ISME Journal, 12(10), 2506-2517. https://doi.org/10.1038/s41396-018-0167-0

• Journal Article Type: Article
• Acceptance Date: Mar 10, 2018
• Online Publication Date: Jun 25, 2018
• Publication Date: Oct 1, 2018
• Deposit Date: Jun 26, 2018
• Publicly Available Date: Jun 26, 2018
• Journal: The ISME Journal
• Print ISSN: 1751-7362
• Publisher: Nature Publishing Group
• Volume: 12
• Issue: 10
• Pages: 2506-2517
• DOI: https://doi.org/10.1038/s41396-018-0167-0
• Publisher URL: https://doi.org/10.1038/s41396-018-0167-0
• Related Public URLs: https://www.nature.com/ismej/