ORCID

0000-0002-0434-6178

Date of Award

5-8-2024

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Evolution, Ecology & Population Biology)

Degree Name

Doctor of Philosophy (PhD)

Degree Type

Dissertation

Abstract

Analyzing microbial community responses across systems, particularly in coordinated ways, is critical to informing meaningful community ecology patterns. In Chapter 1, I provide historical contexts to the field of microbial community ecology. In Chapter 2 I have investigated a specific opportunistic pathogen, Staphyloccocus pseudintermedius, by utilizing whole genome sequencing to understand the genomic architecture that contributes to the community structures of S. pseudintermedius found in different environmental niches. We found that unlike other Staphylococcal pathogens, S. pseudintermedius niches are indistinguishable by core and accessory gene architecture. Rather, niches are resolved through the encoding of antimicrobial resistances such as those isolates found in clinical settings. Additional we find that colonizing isolates from the same household harbor similar CRISPR defense systems, likely reflecting common household phage exposures. Together, we observed niche-specific bolstering of S. pseudintermedius defense mechanisms through gene acquisition or mutation. In Chapter 3, I investigated the microbial community structure of a man-made environment. I utilized metagenomic short-read sequencing and functional metagenomics to investigate how manure storage and fertilizer usage from dairy farms structure the microbial communities of manure and fertilized soil. We observed that there is a microbial community structure transition from fresh manure to manure pits. Including decreases in alpha diversity and shifts in antimicrobial resistant gene abundances. Alternatively, we did not observe significant community changes between manure and fertilized field soil, suggesting that soil communities remained resilient to manure-induced perturbations. Overall, we observed that manure experiences composition restructuring during storage. In Chapter 4, I then investigate the effects of a man-made environment on living hosts. I utilized 16S rRNA sequencing, metagenomic short-read sequencing, functional metagenomics, and metagenomic-assembled genomes to understand how the gut and nasal microbiome of dairy farm workers is influenced by their occupational environment. We show that dairy farm microbiomes are associated with dairy cow microbiomes. Specifically, we observed that dairy farm workers harbor a richer and more diverse nasal community than non-farmers. Further, microbial lineage analyses of microbes in the gut microbiome revealed that microbial lineages are shared between cows and farmers from the same farm environment, Together, we characterize the interconnectedness of the dairy farm microbiome. In Chapter 5, I investigate how living hosts can shape their environment. I utilized transgenic antimicrobial-producing Arabidopsis, MtDef4, to understand how the host as an environment can shape its microbial community composition and structure. In summary, we found that the production and localization of Def4 defensins in Arabidopsis plants indicate a growth benefit while influencing the microbial community structure and composition. Our findings indicate that Def4 mutants have a promising usage to improve plant growth while not significantly altering the bacterial richness of plant compartments, increasing rhizosphere fungal richness, and exhibiting enrichment of rhizosphere bacterial taxa families that are correlated with increased growth in wild-type plants. Lastly, in Chapter 6, I conclude the dissertation with an overarching summary of my projects and discuss future directions. Together, this thesis incorporates community ecology, microbiology, and genetics via a multi-omics approach to elucidate community assembly and functional composition across diverse, yet highly relevant environmental systems.

Language

English (en)

Chair and Committee

Gautam Dantas

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