Multiple Wolbachia subpopulations co-occur in single Culex pipiens mosquitoes

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 the arthropod reproduction and to limit pathogen transmission. While most studies assume that Wolbachia infections are mono-clonal within individual hosts, we show here that an ancestral Wolbachia 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. To this aim, we reconstructed Wolbachia Metagenome-Assembled Genomes in naturally-infected single individual Culex pipiens mosquitoes from both ovary and midgut metagenomes for the first time and afforded Wolbachia population genomic analyses within and between single individuals. We observed consistent single nucleotide and amnio acid variations across samples that we also confirmed in egg metagenomes from geographical distant locations. This study reveals the presence of multiple Wolbachia populations co-existing in individual mosquitoes that could have critical importance for the good use of Wolbachia in basic and applied research.