Microbial diversity of plant pathogens and insect endosymbionts in Reptalus artemisiae

Phloem-sap-feeding planthopper Reptalus artemisiae is an emerging vector of rubbery taproot disease (RTD) and syndrome basses richesses (SBR) in sugar beet, diseases associated with 'Candidatus Phytoplasma solani' and 'Candidatus Arsenophonus phytopathogenicus', respectively. Despite studies on related cixiids, the microbiome of R. artemisiae remains uncharacterized. Using a PCR-free metagenomic long-read shotgun sequencing approach, this study investigates the bacterial diversity associated with R. artemisiae, and provides genomic insight into two plant pathogens 'Ca. P. solani' and 'Ca. A. phytopathogenicus'. Taxonomic assignment revealed six prokaryotic taxa in R. artemisiae: two plant pathogens ('Ca. P. solani' and 'Ca. A. phytopathogenicus') and four insect endosymbionts – three primary endosymbionts ('Candidatus Vidania', 'Candidatus Purcelliella', and 'Candidatus Karelsulcia') and a secondary endosymbiont (Wolbachia). Community profiles showed a consistent presence of all four endosymbionts across five evaluated R. artemisiae individuals. Phylogenetic analyses of 16S rRNA gene sequences of primary endosymbionts confirmed strong congruence with the cytochrome oxidase subunit I phylogeny of the insect host, indicative of long coevolution and vertical transmission. In contrast, plant pathogen presence in R. artemisiae varied, with 'Ca. P. solani' and 'Ca. A. phytopathogenicus' each detected in three individuals. Genome assembly yielded a complete 774 kb circular chromosome for 'Ca. P. solani' with streamlined metabolism featuring limited biosynthetic pathways, but a full arsenal of genes related to host–pathogen interactions and pathogenicity typical for this biotrophs. The draft genome of 'Ca. A. phytopathogenicus' comprising 18 scaffolds totalling 3.11 Mb and two plasmids shows a self-sufficient metabolism with several missing metabolic modules and presence of genomic islands, virulence factors, and a dynamic mobilome indicating a bacterium in transition that is reorganizing its genetic material, possibly in response to host interactions. These findings represent the first in-depth characterization of R. artemisiae microbiome, highlighting a stable endosymbiont consortium and variable pathogen presence that emphasize ecological complexity in vector-pathogen-endosymbiont interactions. The assembled genomes enhance the understanding of microbial ecology, pathogen adaptation and transmission, offering resources for comparative genomics and potential applications in disease management strategies.