Population genetics and the microbiome: solving conservation problems

Abstract

Conservation science has long focused on how a target species interacts with its biotic and abiotic environment, however to conserve a species it is important to consider its biotic interactions in their entirety, including the microbes living both on and within it. In particular, gut microbiome communities in the digestive tract of animals play a key role in digestive capabilities, as well as immune function and behavioural responses. This thesis examines how sequencing gut microbiomes of threatened species can inform conservation strategy. Firstly, I review the tools available to a researcher beginning a microbiome investigation in wildlife, with emphasis on how the different methods can be used to solve specific conservation problems. I then apply these methods to a free-ranging population of long-nosed potoroos (Potorous tridactylus), a marsupial in the family Potoroidae. We found that the potoroo gut microbiome is dominated by the bacterial phyla Firmicutes and Bacteroidota, with a mean Firmicutes to Bacteroidota ratio (F:B) of 2.4. We also observed that host inbreeding was associated with changes in the abundance of two bacterial genera within the potoroo gut microbiome. These observations suggest the possibility that inbreeding depression in a small population could feasibly manifest through changes in the microbiome, although the fitness ramifications cannot be determined from our data. Overall, this thesis advances the discussion around microbiome research in conservation and demonstrates the role of the microbiome in the biology of a unique host species. Going forward it is important that the potential of inbreeding depression to manifest via the gut microbiome is considered during population management strategies, through application of a wide variety of analytical tools, especially in species with unique or highly specialised diets.