Novel Chlamydiae and Amoebophilus endosymbionts are prevalent in wild isolates of the model social amoeba Dictyostelium discoideum

Abstract

Amoebae interact with bacteria in multifaceted ways. Amoeba predation can serve as a selective pressure for the development of bacterial virulence traits. Bacteria may also adapt to life inside amoebae, resulting in symbiotic relationships. Indeed, particular lineages of obligate bacterial endosymbionts have been found in different amoebae. Here, we screened an extensive collection of Dictyostelium discoideum wild isolates for the presence of these bacterial symbionts using endosymbiont specific PCR primers. We find that these symbionts are surprisingly common, identified in 42% of screened isolates (N = 730). Members of the Chlamydiae phylum are particularly prevalent, occurring in 27% of the amoeba isolated. They are novel and phylogenetically distinct from other Chlamydiae. We also found Amoebophilus symbionts in 8% of screened isolates (N = 730). Antibiotic-cured amoebae behave similarly to their Chlamydiae or Amoebophilus-infected counterparts, suggesting that these endosymbionts do not significantly impact host fitness, at least in the laboratory. We found several natural isolates were co-infected with multiple endosymbionts, with no obvious fitness effect of coinfection under laboratory conditions. The high prevalence and novelty of amoeba endosymbiont clades in the model organism D. discoideum opens the door to future research on the significance and mechanisms of amoeba-symbiont interactions.

Reduced and Nonreduced Genomes in Paraburkholderia Symbionts of Social Amoebas

“…While not a direct demonstration of any fitness benefits, P. agricolaris and P. hayleyella show positive chemotaxis toward D. discoideum supernatant ( 17 ). Later, D. discoideum was discovered to also associate with unculturable Chlamydiae and Amoebophilus symbionts but with no obvious fitness effects of infection or clear patterns of coinfection with Paraburkholderia ( 18 ).…”

The complexities of inferring symbiont function: Paraburkholderia symbiont dynamics in social amoeba populations and their impacts on the amoeba microbiota

“…Like Paraburkholderia, we found that Chlamydiae is highly prevalent in natural populations, though the reasons for this are less clear. Laboratory studies of Chlamydiae in D. discoideum found no fitness cost of infection (Haselkorn et al, 2021), but potential benefits have yet to be explored. Like Paraburkholderia, Chlamydiae was overabundant in the microbiota that it occupied, resulting in compositional uniformity.…”

“…We re-sampled natural D. discoideum populations in the Virginia Mountain Lake area (Haselkorn et al, 2019(Haselkorn et al, , 2021. Soil, sampled from below the leaf litter layer of the forest floor or below rotting logs, was collected from ten different sites at each of four separate locations (Supplemental Table 1) and was plated on hay agar within 96 hours (Supplemental Table 2).…”

“…To identify the current prevalence of D. discoideum endosymbionts, we screened 244 D. discoideum isolates collected from the Mountain Lake area in 2019 for Paraburkholderia, Chlamydiae, and Amoebophilus. We then compared the prevalence of each endosymbiont in 2019 to that of a previous collection in 2000 (Haselkorn et al, 2019(Haselkorn et al, , 2021. P. agricolaris exhibited a prevalence of 35.1%, up from a 14.9% prevalence in 2000.…”

“…In natural populations of D. discoideum, the most widespread and persistent bacterial symbionts are Paraburkholderia, Chlamydiae, and Amoebophilus (Haselkorn et al, 2021). Although the functions of these symbionts in natural populations are largely unknown, the Paraburkholderia farming symbionts have been the best characterized.…”