Investigating the effects of diversity, distribution and chytrid load on Uperoleia frog skin microbial communities

Image: Stewart Macdonald

Ignition Grant Round 5 (Sept 2015)

Amphibian skin-associated microbial communities (“skin microbiomes”) are recognised for their role in mediating disease susceptibility, yet we have little understanding of the diversity and distribution of microbiomes across the Australian landscape.

Few studies have applied high-throughput DNA sequencing methods to characterize frog skin microbiomes and, to our knowledge, none have explicitly incorporated the context of host genetic, morphological, and acoustic variation, or phylogeographic history.

This project will start to address this knowledge gap by analysing skin microbiome diversity across four species pairs of a widely-distributed frog genus, and address a set of exemplar questions that will inform future collaborative research proposals.

This project seeks to capitalise on an externally-funded ANU-administered grant to Renee Catullo. That grant funds the study of molecular and morphological diversity within Uperoleia frogs across a large geographic range in Northern Queensland, in addition to surveying for the prevalence of chytrid fungus.

CBA funding will allow for the analysis of additional frog skin swab samples, and for a subset of 200 frogs, use high-throughput DNA sequencing to characterise their skin-associated microbiomes. The results from this subset of samples will provide proof-of-concept support for future collaborative proposals to sequence the full range of collected samples, which will include exhaustive sampling of entire frog communities at selected sites.

Our results will also help to establish new collaborations between CSIRO, ANU and external partners applying these techniques to other disease-susceptible species, such as northern corroboree frogs (Pseudophryne pengilleyi). 

This project will address three primary research questions:

1) Does host genetic variation explain within-species variance in skin microbiome composition?
Cohabiting frogs maintain species-specific microbiome communities even when they occur in the same ponds. These frogs likely source these communities from the same environmental pool of microbial candidates, and so observed species-specific differences may be attributed to genetic (e.g. genes affecting skin pH or defence peptides) or behavioural characteristics of each host species.

Within-species variation in frog skin microbiomes is also seen across geographic sampling sites, but environmental factors known to influence microbial distributions explain little of this variance. How much within-species variance can be explained by genetic variation in the host species is currently unknown.

2) Do differences in skin-microbiome composition correlate with host evolutionary history?
Skin microbiomes are highly distinct from the microbial communities of the surrounding environment, are species-specific and exhibit within-species variation that is poorly explained by environmental variables. These properties imply that skin microbiomes may be useful in differentiating lineages with independent evolutionary histories.

We will use the combined datasets to assess correspondence of skin-microbiomes diversity and the evolutionary history of host species. For example, are chytrid loads higher in species or populations that have faced more intense population bottlenecks? Is there greater intraspecific variation in skin microbiomes communities in species that have maintained higher population sizes over time? Can we differentiate cryptic host species or populations from each other?

3) Does chytridiomycosis alter the skin microbiome in Uperoleia frogs? Can we identify specific microbiome elements that increase disease resistance?
Chytridiomycosis is a fatal disease affecting amphibians caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd). Recent research efforts have examined the potential for bacterial components of the skin microbiome to increase resistance to Bd infection.

This work has tended to be performed on isolated cultured bacterial strains, and little is known about how Bd interacts with or alters the structure of skin microbiomes in the wild. We will use the microbiome data in combination with the chytrid monitoring and challenge assay data obtained by our team to assess the impact of chytrid infection on the skin microbiome in a wild population.

We will also screen our sequence libraries for bacterial taxa with known Bd-suppressing properties in order to assess whether natural resistance is present in these populations.