Early Life Assembly of Zebrafish (Danio rerio) Microbiomes
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Date
2025-02-24
Authors
Smith, Caitlin
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Publisher
University of Oregon
Abstract
Microbiomes can influence fish health and development and may play a role in fish evolution. How fish acquire their microbes, especially early in life, remains a fundamental question in microbial ecology. Here, I address this question using the model organism, zebrafish (Danio rerio). Zebrafish are a useful model vertebrate with which to uncover the relationships between a host and its resident microbes, and explore questions related to community assembly of the microbiome. Zebrafish develop quickly, hatching by 3 days post fertilization, and reaching sexual maturity by 75 days post fertilization. Zebrafish eggs can be sterilized to derive axenic larvae. Axenic larvae are a boon for microbiome research, since they allow researchers to study how a lack of microbiome influences larval health, or how individual members of the microbiome modulate different host responses. However, rendering these fish axenic removes the microbes that naturally colonize the eggs surfaces, erasing any contribution of the parents or the environment as source pools of microbes to the offspring. These microbes may be critical for egg survivability and larval development.
In this dissertation, I explore the early-life microbiome assembly of zebrafish, beginning with the egg. In chapter 2, I review current literature on early-life assembly in fishes, drawing from research performed in other species, such as Atlantic salmon (Salmo salmar), brown trout (Salmo trutta), and lake sturgeon (Acipenser fulvescens), to inform my hypotheses regarding how the egg microbiome might be influenced by parental genetics, transmission, and developmental stage of the embryo. In chapter 3, I characterize the egg microbiome of zebrafish reared in the UO Huestis Zebrafish Facility, and address the role of parentage and embryonic development on microbiome composition. Finally, in chapter 4, I explore the roles of the parental microbiome and the environmental microbiome as sources to the egg and larval gut microbiome.
The egg microbiome of zebrafish is dynamic, and composition rapidly changes between fertilization and hatching. I find that parentage and developmental stage are important drivers for microbiome assembly on zebrafish eggs. Post-hatching, the egg microbiome is also an important source to the larval gut microbiome, therefore its contributions to larval health and development cannot be ignored. I observed that the skin microbiome was a major source of microbes for both eggs and larvae, as was water collected from the crossing tanks in which the eggs were fertilized. This suggests that water may be an important medium of transmission of microbiota from parent to egg.
Overall, this dissertation presents novel research characterizing the egg microbiome of zebrafish. Currently, this is an underexplored life stage with respect to microbiome assembly in this important model organism. These results have implications for future research on host-microbiome assembly and host-microbe interactions using zebrafish as a model.
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Keywords
eggs, larvae, microbiome assembly, zebrafish