The complexities of inferring symbiont function: Paraburkholderia symbiont dynamics in social amoeba populations and its impact on the amoeba microbiome

The relationship between the social amoeba Dictyostelium discoideum and its endosymbiotic bacteria Paraburkholderia provides a model system for studying the development of symbiotic relationships. Laboratory experiments have shown that any of three species of Paraburkholderia symbiont allow D. discoideum food bacteria to persist through the amoeba lifecycle and survive in amoeba spores, rather than being fully digested. This phenomenon is termed "farming", as it potentially allows spores dispersed to food poor locations to grow their own. The occurrence and impact of farming in natural populations, however, has been a challenge to measure. Here, we surveyed natural D. discoideum populations and found that only one of the three symbiont species, P. agricolaris, remained prevalent. We then explored the effect of Paraburkholdia on the amoeba microbiome, expecting that by facilitating bacterial food carriage it would diversify the microbiome. Contrary to our expectations, Paraburkholderia tended to infectiously dominate the D. discoideum microbiome, in some cases decreasing diversity. Similarly, we found little evidence for Paraburkholderia facilitating the carriage of particular food bacteria. These findings change our understanding of farming and suggest the possibility that Paraburkholderia could be playing multiple roles for its host, as inferred metagenomic analysis indicates a potential role of P. agricolaris in toxin degradation.