Date of Award

2022

Degree Type

Dissertation

Degree Name

Doctor of Philosophy in Biological and Environmental Sciences

Specialization

Cell and Molecular Biology

Department

Cell & Molecular Biology

First Advisor

Ying Zhang

Abstract

In temperate coastal ecosystems, there are a variety of potential environmental niches and lifestyles for bacteria to occupy, along with constantly changing environmental conditions. Residing in such a diverse environment with broad habitats, bacterial adaptation can be observed at both the community and genome level. For example, an individual strain may acquire new mutations or genes to respond to varying conditions or occupy a new niche. In addition, the taxonomic composition of bacterial communities can shift, resulting in higher abundances of strains specialized for a new condition. In this dissertation, community and genome-level adaptations to varying lifestyles and environmental change in a temperate coastal ecosystem were investigated.

In Manuscript I, free-living (FL) and particle-associated (PA) communities of bacteria were profiled in the surface waters at the Narragansett Bay Long-Term Plankton Time Series for one year. While differences in the taxonomic composition of these communities were observed, similar relationships with changing environmental parameters were detected. A historically large winter-spring algal bloom allowed for fine-scale comparisons between the responses of FL and PA communities to change. While decreased alpha diversity was observed in both communities towards the end of the bloom, similar and unique bacteria were associated with the bloom across the two communities.

In Manuscript II, host-associated bacterial communities were profiled in the ecologically and economically important eastern oyster, Crassostrea virginica. At the community level, differences were observed between tissue types based on alpha and beta diversity analyses. Further, detection of genomic-level adaptations to life in the eastern oyster gut were enabled for the class Mollicutes through a metabolic reconstruction of a metagenome-assembled genome. Overall, a chitin degradation and an arginine deiminase pathway were present in the oyster-associated Mollicutes MAG but not in closely related Mollicutes genomes isolated from other marine and freshwater hosts.

In Manuscript III, a process of horizontal gene transfer called natural transformation, which can be associated with the acquisition of new functions in bacterial genomes, was investigated. Natural transformation involves the incorporation of exogenous DNA into host genomes. The process of DNA transport is facilitated by the ComEC protein. Despite few bacterial species being experimentally confirmed to be capable of the process, ComEC was identified in 89% of a set of proteomes derived from all complete bacterial genomes, including isolates from the marine environment. In addition, a universal, central Competence protein domain was identified with varying presence/absence of two flanking domains DUF4131 and Lactamase_B. Ancestral state reconstruction across the bacterial tree of life suggested an origin of a Competence-only domain profile, with multiple gains and losses of the DUF4131 and Lactamase_B throughout.

Overall, these studies advanced our understanding of community and genome-level dynamics of bacteria in temperate coastal ecosystems. Analysis of free-living, particle-associated, and host-associated bacterial lifestyles in the coastal waters of Rhode Island revealed differences in the taxonomic composition of these communities, identified environmental and host factors that may shape them, and revealed potential genome-level adaptations that contribute to the ability to thrive in a particular lifestyle. Beyond the coastal waters of Rhode Island, a broader analysis of bacterial genomes highlighted the near-universal presence of a gene essential to a process important for changing and adapting bacterial genomes.

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