Multiple Wolbachia subpopulations co-occur in single Culex pipiens mosquito organs

Abstract Wolbachia is a maternally inherited intracellular bacterium that infects a wide range of arthropods including mosquitoes. The endosymbiont is widely used in biocontrol strategies due to its capacity to modulate arthropod reproduction and limit pathogen transmission. Wolbachia infections are generally assumed to be monoclonal within individual hosts. By reconstructing Wolbachia genomes from naturally-infected single individual Culex pipiens mosquitoes from both ovary and midgut metagenomes, here we show that an ancestral Wolbachia population can evolve to a set of closely related but genetically distinct subpopulations which coexist within the same hosts and are maternally transmitted to host progeny. Our analysis of Wolbachia population genetics within and between organs across individual mosquitoes from Southern France revealed consistent single-nucleotide and single-amino acid variants that we could confirm in egg metagenomes from Northern Africa locations. The striking occurrence of SNVs at identical positions within protein-coding genes in independent and geographically distant samples suggest that the observed Wolbachia genomic variants are potentially important for the biology of the endosymbiont. Overall, the presence of multiple co-existing Wolbachia subpopulations in individual mosquitoes may have critical implications on the use of Wolbachia in fundamental and applied research.