title: Seasonal and spatial dynamics of the diet and rumen microbiome of roe deer in Scotland
Creators: name: Hirst, Christopher M.
Publisher: name: The University of Edinburgh
Year: 2025
Subjects: subject: roe deer
subject: digestive processes
subject: seasonal dietary changes
subject: winter bacterial communities
subject: seasonally variable associations
subject: stomach bacteria

description: Roe deer (Capreolus capreolus) are the most abundant and widespread wild ungulate species in Europe and play a significant role in shaping ecosystems through their browsing activities. Their impact on vegetation can lead to conflicts with forestry and landscape conservation objectives, which require effective management strategies. However, developing these methods requires a comprehensive understanding of the nutritional ecology of roe deer, which characterises how their diets and digestive processes respond to varying environmental conditions. Despite extensive research on roe deer ecology, significant knowledge gaps persist, particularly regarding the intricate relationships among their diet, local habitats, and gut microbiome across seasons and spatial scales. This research addresses these knowledge gaps by providing a multifaceted investigation into the nutritional ecology of roe deer in Scotland. This research employs a combination of molecular techniques, including DNA metabarcoding, alongside remote sensing methodologies to characterise roe deer diets, rumen microbial communities, and local habitat composition across Scotland. By integrating these approaches, this thesis aims to elucidate how roe deer modify their foraging strategies and rumen microbiome in response to varying environmental conditions, with implications for both ecological understanding and management practices. This thesis begins with a broad-scale biogeographical review of roe deer diets across Europe, setting the context for the subsequent focused study of Scottish populations. It then delves into a detailed analysis of the diet of roe deer across six sites in Scotland, using DNA metabarcoding of rumen contents to examine the composition and diversity of roe deer diets across different sites and seasons. The influence of local habitat characteristics on diet is then explored by integrating high-resolution remote sensing data with molecular diet analysis. The composition and diversity of the rumen microbiome are characterised, along with how it varies spatially and seasonally, and with intrinsic factors such as sex, age, and body weight. Finally, the interactions between diet composition and the rumen microbiome are explored via both taxonomic and functional analyses. This multifaceted approach allows for an improved understanding of how roe deer modulate their foraging strategies and digestive processes in response to varying environmental conditions across Scotland. Key findings include the following: 1) Regional differences in the diet of roe deer across Europe. 2) There are significant seasonal and spatial variations in the diet composition and diversity of roe deer in Scotland, with summer diets being the most diverse and winter diets the least diverse. 3) There are strong associations between local habitat composition and diet, with certain habitat types predicting the presence and abundance of specific plant genera in the diet. 4) Seasonal shifts in rumen microbiome composition and diversity, with winter microbiomes being the most diverse. 5) An inverse relationship between dietary diversity and microbiome diversity, challenging previous assumptions about diet-microbiome interactions. 6) Individuals with similar diet compositions tend to harbor more similar rumen microbiome communities. 7) Complex, seasonally dynamic associations between specific plant genera and microbial taxa, suggesting interactions between the microbiome and dietary components. This research advances the ecological understanding of roe deer and herbivore nutritional ecology more broadly, providing insights for wildlife management in Scotland and beyond. By exploring the complex relationships among habitat, diet, and the rumen microbiome, this thesis offers valuable insights into how wild ruminants respond to seasonal and spatial variations in resource availability. The integrated approach developed here, which combines DNA metabarcoding, remote sensing, and microbiome analysis, highlights the importance of considering both extrinsic environmental factors and intrinsic host characteristics in understanding wildlife nutrition. This multifaceted methodology offers a template for future studies, paving the way for more comprehensive approaches to wildlife ecology, conservation, and management.