Novel Chlamydiae andAmoebophilusendosymbionts are prevalent in wild isolates of the model social amoebaDictyostelium discoideum

Abstract

Amoebae interact with bacteria in diverse and 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 (pathogenic or mutualistic). Indeed, amoebae are often infected with bacterial endosymbionts. Acanthamoeba and Hartmannella harbor symbionts from five distinct lineages within the Proteobacteria, Bacteroidetes, and Chlamydiae. Here, we PCR-screened an extensive collection of Dictyostelium discoideum wild isolates for the presence of bacterial symbionts. For the first time we found that obligate symbionts are surprisingly common in this highly-studied amoeba species, identified in 42% of screened isolates (N=730). Members of the environmental Chlamydiae are particularly prevalent. These strains are novel and phylogenetically distinct. We also found Amoebophilus symbionts in 8% of screened isolates (N=730). Under laboratory conditions, antibiotic-cured amoebae behave similarly to their endosymbiont-infected counterparts, suggesting that endosymbionts do not significantly impact host fitness, at least in the laboratory. We found several natural isolates were co-infected with different endosymbionts. 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.

Characterization of the bacterial microbiomes of social amoebae and exploration of the roles of host and environment on microbiome composition

“…(2020), and the three most frequent Procabacter ASVs grouped with the novel Procabacter endosymbiont of D. discoideum identified by Haselkorn et al . (2020) with high bootstrap support.…”

“…We therefore took all amoeba associated Chlamydiae ASVs (12 total, with 26/39 amoeba samples containing one or more of these ASVs) and added them to the Chlamydiae tree created by Haselkorn et al . (2020) (Supporting Information Fig. S5).…”

“…We also inserted our Amoebophilus and Procabacter ASVs into the full‐length 16S rRNA phylogenies created by Haselkorn et al . (2020) (Supporting Information Figs. S7 and S8).…”

“…Chlamydiae, Amoebophilus , and Procabacter phylogenies were created by aligning ASVs to the full‐length 16S rRNA alignments from Haselkorn et al . (2020). Another phylogeny was created by aligning ASVs assigned to genus Burkholderia‐Caballeronia‐Paraburkholderia with 16S rRNA sequences from the three known D. discoideum endosymbionts P. agricolaris , P. bonniea , and P. hayleyella .…”

“…Further work has identified 32 operational taxonomic units (OTUs) from the phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria in the culturable bacterial microbiome of D. discoideum fruiting bodies (Brock et al ., 2018). Most recently, screening of wild D. discoideum populations for known endosymbionts of other amoebae using PCR has revealed the presence of novel unculturable Amoebophilus , Procabacter , and Chlamydiae species (Haselkorn et al ., 2020). However, the full unculturable microbiome of wild D. discoideum has yet to be characterized, which is a first step in extending the usefulness of D. discoideum as a model organism to include microbiome dynamics.…”