Fish Out of Water: Understanding the Impacts of Regional Species Pool Variation on Local Community Assembly in a Host-Microbiome Model System
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Date
2024-08-07
Authors
Evens, Kayla
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Publisher
University of Oregon
Abstract
The host-microbiome is essential to many aspects of host health and function, and acts as a useful model system in which to investigate broader questions of community assembly. Since the composition of host-microbiomes is, in part, determined by the input of microbes from the surrounding environment, it is integral to understand how variation in the environmental microbiome may influence host-microbiome assembly. For my dissertation research, I used a species pool conceptual framework to investigate drivers of variation in the microbiomes of aquaculture research facilities and the fish they house. Zebrafish (Danio rerio) are used extensively as model organisms in scientific research, especially in studies investigating host-microbiome dynamics. For in-vitro experimentation utilizing model organisms, we rely on the reproducibility of results to make broadly applicable conclusions about the host-microbiome. However, evidence suggests that inter-facility variation may influence zebrafish gut microbiome composition via acquisition of microbes from the environment, potentially leading to phenotypic differences among fish housed at different aquaculture facilities.
To investigate the relationship between aquaculture facility water and fish gut microbiomes, I first characterized spatial and temporal variation across multiple aquaculture facilities on the University of Oregon campus. Facility water microbiota not only varied over time, but patterns of spatial variation in each facility were consistent despite differences in host species. I then used this information to guide an expanded, intensive sampling of water and fish across four zebrafish facilities in Oregon and Norway. I observed significant variation in microbiome composition both within and between facility water systems and zebrafish gut samples. Further, there was evidence that variation in the water microbiome was a source of variation in zebrafish gut microbiomes. Finally, as differences in facility management and technical specifications can make directly linking microbiome variation in the water to variation in fish difficult, I attempted to isolate the effects by experimentally manipulating the water microbiome in a laboratory study using germ-free larval fish. My results indicate that microbial inputs from live feed overwhelmed any potential influence of water microbiome variation in early-life microbiome assembly.
Overall, this dissertation provides a comprehensive look at the drivers of environmental microbiome variation and how these may mediate aspects of host-associated microbiota. My results have implications for fish microbiome research and suggest that research conducted with zebrafish sourced from a single facility may be heavily influenced by facility-specific effects.
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Keywords
aquaculture, community ecology, host-microbiome, zebrafish