Dictyostelium discoideum microbiome dynamics and genomics of its putative symbionts : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science, College of Sciences, Massey University, Palmerston North, New Zealand. EMBARGOED until 13th March 2027

Abstract

Dictyostelium discoideum, a social amoeba, is an exceptional model for studying host microbe interactions and microbial community dynamics due to its reliance on phagocytosis for nutrition and its associations with diverse bacterial symbionts. Metagenomic analyses were performed on 702 D. discoideum isolates, of which 587 met sequencing depth thresholds and were retained for analysis of associated microbiomes across spatial and temporal scales, revealing substantial variability in microbial diversity and community composition. Core microbiome analyses identified three persistent bacterial taxa that influence community structure, highlighting the dynamic interplay of stochastic and deterministic processes. Additionally, four novel bacterial clones from Staphylococcus, Pseudomonas, and Acinetobacter genera, were identified and characterized. Genomic investigations of these isolates uncovered evidence of antimicrobial resistance genes, virulence factors, and other adaptations such as horizontal gene transfer. Genomic characterization of the frequent and known symbiont, Paraburkholderia agricolaris, provided possible insights into limited genome instability that may indicate ongoing adaptation to a symbiotic lifestyle with D. discoideum. These findings reinforce the value of D. discoideum as a model system for exploring microbiome assembly and symbiotic evolution, while also providing critical insights into the emergence of potential pathogens and their implications for host fitness and microbial diversity.