Spiroplasma display an intricate continuum of infection heterogeneity and persistence in Myrmica ants

Many bacterial taxa evolved a facultative symbiotic association with insects and spread by maternal transmission though host populations. Infections of these facultative symbionts typically do not persist on the same timescale as host speciation. Here, unstable infection persistence is compensated by horizontal transmission into novel hosts, generating incongruent host-symbiont phylogenies. Spiroplasma bacteria display independent origins of symbiosis with insects, generating a poorly understood continuum in maternal transmission and infection persistence. Here, we examined Spiroplasma symbiosis with Myrmica ants. Exhaustive genotyping of field and experimental colonies of six Myrmica species uncovered previously cryptic co-infections of Ixodetis and Citri Spiroplasma. Ixodetis variants co-segregated with Citri variants, albeit at much lower frequencies, creating complex co-infection patterns. Within Myrmica ruginodis, co-infection of two Citri variants was widespread in queens but workers were mainly characterized by infection of one specific variant. Another Citri variant infected four Myrmica species and was widespread in both queens and workers. We collect phylogenomic and functional genomic support for an exceptionally stable symbiosis, with a predicted infection persistence of seven million years. Our findings reveal that Spiroplasma symbionts can display complex infection heterogeneity in social insects and evolve a stable infection persistence within insect hosts.