Genome-resolved metagenomics reveals conserved, flexible and emerging symbioses across global leafhoppers

Abstract

Leafhoppers are major vectors of plant pathogens that depend on microbial symbionts to exploit nutrient-poor diets. However, most studies of leafhopper-associated microbiota have focused on a limited number of taxa leaving the genomic diversity, and ecological organization of these microbial communities poorly understood. Here, we generated a genome-resolved global leafhopper microbiome resource by integrating genome-resolved metagenomics from 171 leafhopper species across 11 subfamilies and 13 countries, including the first microbiomes characterized from Arctic leafhoppers. De novo assembly and genome reconstruction generated 272 non-redundant microbial genomes and 18.6 million non-redundant genes, substantially expanding the known microbial diversity associated with Cicadellidae, including several previously undescribed bacterial lineages. Comparative analyses revealed a recurrent modular microbiome architecture composed of: (i) a conserved core of obligate nutritional symbionts; (ii) a heterogeneous layer of secondary symbionts; and (iii) a dynamic pool of environmentally acquired bacteria. While obligate symbionts remained highly conserved across divergent hosts, secondary and environmental taxa varied substantially among species and regions, suggesting repeated acquisition shaped by ecological filtering rather than host phylogeny alone. Comparative analyses between the specialist corn leafhopper and the polyphagous aster leafhopper further showed that closely related vectors can maintain conserved ancestral symbionts while harboring distinct accessory microbiomes. Arctic populations contained unique microbial assemblages with annotated functions associated with cold tolerance, oxidative stress, and reproductive manipulation. This work establishes a genome-resolved framework for understanding microbiome evolution in insect vectors and provides a resource for testing the potential roles of microbiome variation in host adaptation, pathogen ecology, and sustainable pest management.