Graduate Thesis Or Dissertation


Bacterial Predation in Host Microbiomes Public Deposited

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  • In host-associated microbiomes, the mechanisms that regulate community composition or the principles that govern dynamics remain far from clear. However, understanding how the structure of microbial communities shift as the system moves away from a healthy state is critical to assessing disease progression and to formulate any potential mitigation strategy. In this dissertation, I targeted a relatively understudied genus of predatory bacteria, Halobacteriovorax, capable of preying on known pathogens, and aimed to determine the ecological role of these unusual predators in the microbiome of their coral host. Halobacteriovorax are a genus of delta proteobacteria which exhibit a biphasic lifestyle. In attack phase they are small (1 to 2 μm in length and 0.35μm in width), highly motile, single flagellated vibriod shaped bacteria that must attach to other bacteria before penetrating their periplasm where they undergo filamentous growth and genome replication without competition. As nutrients become exhausted from the prey cell, the elongated Halobacteriovorax filament divides into multiple attack phase progeny that lyse the bdelloplast. The ecological role of these predators is still relatively understudied, but given their predatory lifestyle, high grazing rates, and broad prey range, Halobacteriovorax could play a major role in structuring microbial communities. In order to study how cell-cell interactions impact microbial community structure and function, I employed a wide range of methods and technologies utilizing culture dependent and independent techniques. Using high throughput sequencing I detailed shifts in community structure of the microbiome of the mucosal surface layer of multiple coral species in their natural environment by repeatedly sampling individuals over a two-year time scale. Halobacteriovorax were a core microbiome component detected in over 78 percent of the 198 samples. Using network analysis I was able to obtain the temporal and spatial dynamics of Halobacteriovorax, and show that despite their predatory nature they predominately co-occur with their potential prey in our networks. I also isolated and cultured novel Halobacteriovorax strains from multiple coral species, and characterized these coral-associated predatory bacterial isolates using full-length 16S rRNA sequencing of cultures, phylogenetic analysis of the full length reads, prey range evaluation, and microscopic documentation of unique predatory lifecycle stages. In order to study cell-cell interactions I employed microfluidic devices and high-resolution video microscopy, image analysis, and cell tracking to observe individual predator-prey interactions utilizing predatory Halobacteriovorax and a common pathogen to a variety of aquatic host organisms, Vibrio coralliilyticus, as the prey. In this co-culture system, I captured striking microscale observations that demonstrate Halobacteriovorax’s ability to effectively prey on and reduce pathogenic V. coralliilyticus populations. To illuminate the role of Halobacteriovorax on the host microbiome, I challenged specimens of the important reef-building coral Montastraea cavernosa with V. coralliilyticus pathogens in the presence or absence of Halobacteriovorax predators, and then detailed the changes in the microbial communities over time using 16S rRNA amplicon sequencing. The pathogen challenge reshaped coral microbiomes by increasing richness and reducing stability (increased beta-diversity) of the rest of the microbiome, suggesting strong secondary effects of pathogen invasion on commensal and mutualistic coral bacteria. The addition of Halobacteriovorax alone had only minor effects on the microbiome, and no infiltration of Halobacteriovorax into coral tissues was detected in amplicon libraries. Simultaneous challenges with both pathogen and predator eliminated detectable V. coralliilyticus infiltration into coral tissue samples, ameliorated changes to the rest of the coral microbiome, and prevented secondary blooms of opportunistic bacteria. All together my results suggest predation by Halobacteriovorax may act as a mechanism to regulate population size of a wide range of opportunistic pathogens and illustrates the powerful role of these predatory bacteria in the marine microbiome.
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