Date of Award

2021

Degree Type

Dissertation

Degree Name

Doctor of Philosophy in Oceanography

Department

Oceanography

First Advisor

Tatiana Rynearson

Abstract

Interactions between diatoms and bacteria impact global-scale biogeochemical cycling, through regulating the biological pump, impacting productivity of the marine food web, and regulating fluxes of chemicals. The most intimate of these interactions occur in the diatom’s phycosphere, akin to the mammal’s microbiome or rhizosphere. Research into terrestrial systems has shown intimate connections between an organism’s microbiome or rhizosphere and the genetic structure of the host organism’s species. However, little research has been done to elucidate these interactions in the diatom’s phycosphere. The goal of this work is to explore how diatom population structure impacts the phycosphere microbiome, by surveying the diatoms’ microbiome around the world, testing the specificity of diatom-bacteria interactions in the field, and examining the functional capacity of the phycosphere microbiome.

We examined diatom-bacteria interactions using the diatom host Thalassiosira rotula, a cosmopolitan diatom with global dispersal and whose population structure is not limited by biogeographical patterns. We collected and characterized the microbiome using 16S rDNA of 81 single cell isolates T. rotula collected from 11 different sample sites, three ocean basins, and eight genetically distinct populations. While no single bacterial phylotype was shared across all genotypes, we found strong genotypic influence of T. rotula, with microbiomes associating more strongly with host genetic population than with environmental factors. Microbiome association with host genetic population persisted across different ocean basins, suggesting that microbiomes may be associated with host populations for decades.

To isolate the impact of host genotype on microbiomes, a common garden experiment using eight genotypes from three distinct host populations again found that host genotype influenced microbial community composition, suggesting that a process we describe as genotypic filtering, analogous to environmental filtering, shapes phytoplankton microbiomes. In both the environmental and laboratory studies, microbiome variation between genotypes suggests other factors influenced microbiome composition but did not swamp the dominant signal of host genetic background. The long-term association of microbiomes with specific host genotypes reveals a possible mechanism explaining the evolution and maintenance of complex phytoplankton-bacteria chemical exchanges.

Our previous work has shown that different diatom populations host taxonomically distinct phycosphere microbiomes. However, recent work has shown that taxonomically divergent bacterial assemblages can be functional redundant. Therefore, we performed a functional comparison of 39 bacterial metagenomes from two different diatom populations. We found that the diatom microbiomes possess a set of core functional genes that expanded the diatom host’s metabolic potential. However, each of the population’s microbiomes possessed different metabolic pathways. These findings raise the question as to whether differences in metabolic pathways represent different physiological capabilities of the diatom host or adaptation to new environments through their microbiome.

Available for download on Sunday, August 13, 2023

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