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Unraveling Effects of the Microbiome on Host Fitness in the Keystone Zooplankton Daphnia magna

Reilly O Cooper, University of Nebraska - Lincoln


The microorganisms living on and in hosts, collectively known as the microbiome, significantly impact host life history through a wide range of functions. While it is often assumed that abundant taxa contribute more functional benefits to their hosts, rare keystone taxa can also have significant impacts on host fitness. In my research, I sought to understand the functional roles of abundant and rare taxa in the microbiome of the model zooplankton species Daphnia magna, as its simple microbiome and experimental tractability readily allowed for microbiome manipulation and characterization of functionally relevant taxa. To unravel the functions of Daphnia magna-associated bacteria, I first address how we understand transmission of beneficial host-associated taxa from colonized hosts to naïve hosts in Chapter 1, as transmission is a critical component of functional relationships among hosts and microbes. I then ask what species and functions were present in the Daphnia magna microbiome, using short-read metagenome sequencing to assemble and profile metagenome-assembled genomes of abundant and rare species (Chapter 2). Next, I manipulate the Daphnia magna microbiome with antibiotics to suppress different classes of the microbiome and measured host fitness outcomes (Chapter 3). In Chapter 4, I explore the impacts of 5 generations of antibiotic exposure and isolation on microbiome composition and host fitness. Finally, I expand the effect of isolation discovered in Chapter 4 to a 15-generation experiment in Chapter 5, asking what functions are lost as rare taxa and how host fitness is impacted by this loss. Overall, I find evidence of host-microbe and microbe-microbe interactions, with abundant species exerting beneficial effects on host fitness. I also find that rare taxa are likely beneficial in stressful contexts. Furthermore, I discovered 13 distinct metagenome-assembled genomes, revealing strain-level diversity in the Daphnia magna microbiome. My research demonstrates the tractability of Daphnia magna as a model organism for microbiome research and lays the groundwork for future research using multi-omics methods to understand multispecies interactions in this model system.

Subject Area


Recommended Citation

Cooper, Reilly O, "Unraveling Effects of the Microbiome on Host Fitness in the Keystone Zooplankton Daphnia magna" (2021). ETD collection for University of Nebraska-Lincoln. AAI28652592.