Date of Award
5-2025
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
Biological Sciences
Committee Chair/Advisor
Dr. Sharon Bewick
Committee Member
Dr. Barb Campbell
Committee Member
Dr. Kyle Barrett
Committee Member
Dr. Cathy Jachowski
Abstract
Many organisms rely upon the internal and/or external microbial communities they harbor. Microbial communities which depend upon other organisms for survival are known as host-associated (HA) microbial communities. HA microbial communities differ in diversity and composition from surrounding environmental microbiota and are generally less diverse than surrounding soil microbiomes. Although distinct bacterial profiles exist between host and environment, microbial scale dispersal often links the two. For this reason, host and environmental microbial communities can be correlated (e.g., dominant taxa in HA microbiota are dominant in the host microenvironment or vice versa). Eukaryotic hosts act as islands for HA microbiota. Unlike environmental microbial communities, HA microbiota are often maintained by a host organism and may undergo selection based upon host anatomy, physiology, and behavior. Said differently, hosts directly and indirectly curate their microbial communities, retaining the microbiota that are beneficial for survival, while becoming refractory to those that compromise it. Thus, HA microbiota experience evolutionary histories separate from environmental microbiota and are classified as distinct communities. Importantly, HA microbial communities are often subject to perturbation based on a plethora of factors, making beneficial microbes subject to extirpation on both individual host and host-population scales. Throughout this dissertation I investigate the effects of spatial variation on the variation of HA microbiota in wild populations of ectotherms. I begin first with a theoretical model where I interconnect variable host and microbe dynamics within a iii nested multiple-scale metapopulation system. This model incorporates dynamics across host and microbial scales in a spatially implicit framework to obtain a baseline understanding of how changes in colonization/extinction ratios at one scale impacts the other. Importantly, the newly developed theoretical model explicitly accounts for colonization and extinction dynamics at both the microbe and host scales. Explicit accounting of dynamics at both scales reveals complex interactions which significantly influenced persistence and stability within multiscale metapopulations. I then extend insights from my theoretical model into a small-scale spatially explicit system Green Salamander (Aneides aeneus) metapopulation across a relatively homogenous landscape with low environmental variation. My findings demonstrate that the spatial distribution of skin microbiota in green salamanders is not a mere reflection of the surrounding environmental microbial pool but is instead distinctly shaped by host metapopulation structure and dispersal limitation. Despite consistent alpha diversity across populations, I observed a clear pattern of distance-decay in HA but not environmental microbiota similarity with increasing spatial distances, underscoring the role of host dispersal limitations in shaping HA microbial community structure. Amphibian conservation implications of the observed variability in composition and distance-decay of HA microbiota include that putative Chytrid-inhibitory microbiota richness substantiality varied (twofold increase across populations). For my following investigation I once again consider a smaller spatial scale, but I incorporate substantial environmental heterogeneity and explicitly consider host iv relatedness using a species of Aphaenogaster ant found within a montane system which I argue should experience less dispersal limitation than my Green Salamanders. Similar to my Green Salamander system, genetic isolation by distance was detected between host and spatial distance. Interestingly, this correlation was even detected between host phylogeny and environmental dissimilarity. Compositional impacts on HA microbiota resulting from distance-decay of host phylogeny, host spatial distance, or host environmental dissimilarity were not detected. Instead, a well-known endosymbiotic member of the microbiota- Wolbachia- disproportionately dominated composition. Wolbachia relative abundance did covary with host phylogeny and environment. For my fifth chapter I expand upon my previous Green Salamander system to explore microbiome variation across a substantial proportion of the Green Salamander species range from Alabama to Virginia experiencing wide bioclimatic variation. Where my previous salamander study quantified differentiation over a small spatial scale (~40km), chapter five quantifies differentiation over a much larger scale (~500 km). My findings suggest that host microbiota differentiation across large spatial extents is chiefly influenced by spatial proximity of hosts. I observed that host phylogeny minimally impacted microbiota composition refuting the hypothesis that microbiota community assembly across a species range would be heavily influenced by evolutionary history. While microbiota profiles did differ by host clade, the differences did not recapitulate host phylogeny as expected by phylosymbiosis. Similar to the full microbiota, Chytridinhibitory community composition varied by host clade, but interestingly, richness did not.
Recommended Citation
Malagon, Daniel, "Spatial Variaiton in Host-Associated Microbiota" (2025). All Dissertations. 3945.
https://open.clemson.edu/all_dissertations/3945