Date of Award

5-2012

Degree Type

Dissertation

Degree Name

Doctor of Philosophy

Major

Microbiology

Major Professor

Alison Buchan

Committee Members

Steven W. Wilhelm, Erik Zinser, Mark Radosevich

Abstract

Bacteria of the Roseobacter lineage are dominant bacterioplankton in coastal systems and contribute significantly to secondary production in oceanic environments. Generalities of Roseobacter ecology, diversity, and distributions are known, but the intraspecific differences between species and their dynamics over short temporal periods is not well understood. Bacteriophage that infect Roseobacters (‘roseophage’) have the potential to shunt secondary production into the dissolved carbon pool and through the process of infection alter Roseobacter physiology. Despite their significance, little effort was made prior to the onset of this study to characterize roseophage. Using culture dependent and independent approaches, I describe the diversity and activity of Roseobacters and roseophage from two distinct coastal environments. Chapter 2 describes the development of an alternative method to enumerate viruses using epifluorescence microscopy that not only reduces sample processing costs, but also the total volume of sample required. A novel species of the Roseobacter lineage (Marivita roseacus) is proposed in Chapter 3. M. roseacus is unique in its needle-like morphology, forming long, relatively inflexible chains of cells. The Marivita genus is characterized by a distinct ecology, being closely associated with algae, resistant to grazing, and present in numerous marine and saline environments. Chapter 4 details the use of deep-amplicon sequencing (16S rDNA) to describe bacterial succession patterns during a mesocosm algal bloom, revealing the temporal dynamics of ~100 distinct phylotypes. A multivariate analysis showed that temporal portioning amongst the bacterial community was occurring at both high and low taxonomic levels. Chapter 5 details the isolation and genomic characterization of roseophage and describes their ecology using publically available metagenomic databases collected from throughout the world. Four distinct phage were isolated and sequenced including an N4-like strain, a novel Siphoviridae, and two temperate Podoviridae. The two temperate phage were practically identical at the nucleotide level, except for a 3000 bp putative replication module, which showed no homology between the two. Overall, this dissertation suggests that ecological partitioning within the Roseobacter lineage is occurring at and arguably below traditional species level taxonomic classifications and microdiversity amongst closely related marine bacteria is likely the norm rather than the exception.