In partial fulfillment of the requirements for the degree of

Doctor of Philosophy in Biology

In the

School of Biological Sciences

Ana Clavere-Graciette

Will defend her dissertation

Community assembly in host-associated and environmental microbes

Thursday, April 22nd, 2021

12:30 PM

https://bluejeans.com/796741975

Meeting ID: 796 741 975

Thesis Advisor:

Dr. Frank Stewart

School of Biological Sciences

Georgia Institute of Technology

Committee Members:

Dr. Brian Hammer

School of Biological Sciences

Georgia Institute of Technology

Dr. Joel Kostka

School of Biological Sciences

Georgia Institute of Technology

Dr. Martial Taillefert

School of earth and Atmospheric Sciences

Georgia Institute of Technology

Dr.Lisa Hoopes

                                         Director of Research, Conservation and Nutritiond Biomedical Sciences

Georgia Aquarium

ABSTRACT

Microbes play ecological and biogeochemical roles in all environments, including in host-associated systems. They are central providers of ecosystem services, notably by transforming matter and energy (Kowalchuk, Jones et al. 2008). They also engage in social interactions that directly affect the health, development, and behavior of animals and plants (Das, Lyla et al. 2006, Van Der Heijden, Bardgett et al. 2008, Steffan, Chikaraishi et al. 2015). Identifying the factors that influence community taxonomic assembly in microbiomes - i.e., which microbes are present and in what abundance - is necessary to predict how microbiomes might influence an ecosystem’s diversity, functional services, and overall health.

Many studies have investigated the factors shaping microbial distributions and community diversity.  Despite a wealth of data on the topic, it has been challenging to identify universal principles of microbiome assembly across diverse systems.  For host-associated microbiomes, for instance, it is often hard to quantify the relative contributions of host physiology versus environmental conditions in shaping microbiomes. This dissertation explores these challenges in both host-associated and free-living microbiomes that are subjected to distinct organizing factors. In Chapter 2, I sample across a diverse set of host-associated niches to understand how the microbiome of wild spotted eagle rays (Aetobatus narinari) differs from that of individuals housed at Georgia Aquarium.  In Chapter 3, I provide the first assessment of the microbiomes of African penguins (Spheniscus demersus), focusing the analysis on the variation among body site niches and one of the first characterizations of the oral microbiome of birds. Finally, in a collaborative study that couples electrochemical measurements of redox substrates with analysis of both bacterial and archaeal microbiomes, I explore the role of environmental substrate availability in shaping community assembly.