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<div>Microbiomes can bolster host productivity by providing protection against pathogens, among other mechanisms. To investigate associations between citrus microbiome function and Huanglongbing (HLB) disease progression, microbial communities of leaves and roots from citrus trees (n=70) that varied in HLB symptom severity were characterized with 16S Illumina sequencing and metagenomes were predicted with PICRUSt. The taxonomically rich communities contained abundant core members, some over-represented site-specific members, and a diverse set of low-abundance variable taxa. The microbiota and the metagenomes were strongly associated with the presence of HLB symptoms. Substantial variation between the functional potential of healthy and diseased microbiomes was explained by abundances of genes encoding KEGG pathways for ribosomes, DNA repair proteins, ABC transporters, two-component systems, secretion systems, and various forms of metabolism. Genes involved in nucleotide and energy metabolism were crucial to the health-state of leaves, while those associated with carbohydrate, lipid, xenobiotic, and cofactor metabolism were crucial to that of roots. Interestingly, the rank abundances of KEGG pathways in the respective microbiomes were still highly conserved. This may have been due to the core members encoding core functions and/or to functional redundancies across certain variable taxa. Key microbiome functions that were identified may be important for citrus health.</div>