- Pseudomonas is a diverse, ubiquitous, and widely studied genus of bacteria. As Pseudomonas species occupy a wide range of niches in the ecosystem, they have made remarkable biological impacts. Better understanding of Pseudomonas biology, genetic diversity, and functional interactions with other organisms and the environment will provide valuable insights into our understanding of their roles in nature, and open doors to developing practical scientific applications involving these bacteria. Chapter 1 of this dissertation provided background information about Pseudomonas spp., and discussed strategies for investigating these and other bacteria in the postgenomic era. The first data chapter of this dissertation, Chapter 2, focused on the genomes of phages that infect Pseudomonas spp. bacteria; phages directly influence the diversity and evolution of their host bacteria, yet remain an understudied component of Pseudomonas biology. The diversity, phage host range evolution, and the evolutionary pressures acting on Pseudomonas phage genes were investigated using whole genome comparative and evolutionary analysis, focusing on 130 complete phage genomes. The results revealed immense genome sequence
variation, evidence that some phage possess potential to shift between host species, and purifying selection as the dominant evolutionary force acting on phage genes. In Chapter 3, a metagenomic approach was applied to detect and characterize phage DNA, including those that infect Pseudomonas spp. and other bacteria, focusing on a set of eight metagenomic data sets associated with two different plant-parasitic nematode species: Globodera pallida (potato cyst nematode) and Heterodera glycines (soybean cyst nematode). Three complementary bioinformatics strategies were deployed to analyze phage DNA in this study. Phage DNA was detected in all of the metagenomes, with varying patterns observed between the different focal nematode species. Strengths and weaknesses of the three different analytical strategies were considered in this chapter. One phage DNA sequence, with fixed length and highly similar DNA sequences and gene annotations, was detected at very high DNA sequence coverage levels in each of the eight metagenomes. Chapter 4 explored the dynamics of Pseudomonas spp. and other bacteria in microbiomes associated with a slug-parasitic nematode, Phasmarhabditis hermaphrodita, before and after nematodes infect slugs in a controlled laboratory setting.16S rRNA amplicon data analysis was conducted to investigate the microbial community composition, infer the microbiome diversity and level of dissimilarity between pre- and post-infection time points. Notable shifts in microbial community composition before and after infection was detected. Four 16S rRNA sequences classified as Pseudomonas expanded in post-infection samples during the assay, and constitute candidate bacterial contributors that might positively interact with P. hermaphrodita nematodes in the slug killing process. Chapter 5 discussed future study directions that will potentially advance the results of
this work. Altogether, this dissertation provides findings that may contribute to the integrated understanding of microbes and their dynamics, with special focus on Pseudomonas spp. and the organisms with which these bacteria interact. The dissertation research delivered new insights, with the potential to contribute to the future development of clinical and industrial applications, and genomic exploratory tools.