Date of Graduation

5-2023

Document Type

Dissertation

Degree Name

Doctor of Philosophy in Biology (PhD)

Degree Level

Graduate

Department

Biological Sciences

Advisor/Mentor

Alverson, Andrew J.

Committee Member

Lewis, Jeffrey A.

Second Committee Member

Beaulieu, Jeremy M.

Third Committee Member

Amin, Shady

Keywords

Algae; beta diversity; Coevolution; HGT; Microbiome; Phycosphere

Abstract

Although photosynthetic macro-eukaryotes (i.e., plants) make up the majority of organic biomass on earth, bacteria are the second largest taxonomic group, by biomass. Bacteria are ubiquitous in our environment, living on, and within, man-made surfaces, natural environments, and eukaryotes themselves. The relationship between bacteria and eukaryotes has existed from the very beginning of eukaryotic life in the form of bacterial endosymbioses that resulted in mitochondria and plastids. Other eukaryote–bacteria relationships have evolved since then, ranging from the beneficial (e.g., mutualistic) to harmful (e.g., parasitic or pathogenic). Understanding these eukaryote–bacteria relationships is key to understanding both the evolution of important ecosystem processes and how these interactions affect human endeavors such as agriculture. To better understand how bacterial communities affect and interact with their eukaryotic partners, we have utilized the genomes and transcriptomes of the ubiquitous micro-eukaryotes known as diatoms to analyze their co-occurring bacteria. This dissertation explores the composition, dynamics, and interactions between diatoms and their bacterial partners. We first sequenced the genome and transcriptome of the araphid pennate diatom Psammoneis japonica and examined its associated bacterial metagenome. Repetitive element content in P. japonica, and other existing diatom genomes, were found to have a positive relationship with genome size. The partial metagenome of P. japonica revealed a diverse microbial community of at least 25 associated bacterial taxa, including four near-complete genomes for novel species of Planctomycetota, ɑ-proteobacteria, and Bacteroidota. The P. japonica genome was found to contain genes and intergenic open reading frame sequences which were transferred to the P. japonica lineage from members of the lineages of several cohabiting bacteria. Several of these HGT candidate proteins are located in regions with transposon densities higher than the average for the genic and intergenic regions of the P. japonica genome. Subsequently, we mapped and extracted bacterial 16S sequences from existing transcriptome reads of diatoms. Transcriptomes were sourced from the Alverson Lab and the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) to investigate bacterial diversity, community phylogenetics, and cophylogenetic concordance between diatom-bacteria associations across cultured diatom strains. There was a high degree of dissimilarity in phylogenetic beta-diversity between diatom bacterial communities at all taxonomic levels of the diatom tree of life. Ordination analysis of phylogenetic beta-diversity demonstrated distinct groupings of diatom microbiomes by salinity. Significant cophylogenetic concordance was found between diatoms of the genus Chaetoceros and their bacterial partners. These results support that diatom phycosphere communities are more similar within salinity levels, while still maintaining high diversity within and across genera. Lastly, this research demonstrates that incidentally collected sequence data can be utilized to investigate microbiomes. These experiments highlight that incidentally collected sequence data can be utilized to investigate the algal phycosphere by using bioinformatics methods to extract bacterial sequences from xenic algal cultures, as well as how normally discarded data can be used to examine community dynamics that would otherwise be overlooked. These findings also suggest that diatom–bacteria relationships are stable over evolutionary timescales and can lead to recurrent horizontal gene transfer events from symbiont to host, as well as cophylogenetic concordance between diatoms and their bacterial partners.

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