Metabolome and microbiome signatures in the roots of citrus affected by Huanglongbing

Huanglongbing (HLB) is a severe, incurable citrus disease caused by the bacterium Candidatus Liberibacter asiaticus (CLas). Although citrus leaves serve as the site of initial infection, CLas is known to migrate to and colonize the root system, but little is known about the impact of CLas infection on root metabolism and resident microbial communities. Scions of 'Lisbon' lemon and 'Washington Navel' orange grafted onto 'Carrizo' rootstock were grafted with either CLas-infected citrus budwood or uninfected budwood. Roots were obtained from trees 46 weeks post-grafting and analyzed via 1H NMR spectroscopy to identify water-soluble root metabolites, and high-throughput sequencing of 16S rRNA and ITS gene amplicons to determine the relative abundance of bacterial and fungal taxa in the root rhizosphere and endosphere. In both citrus varieties, 27 metabolites were identified of which several were significantly different between CLas(+) and control plants. CLas infection also appeared to alter the microbial community structure near and inside the roots of citrus plants. Non-metric multidimensional scaling (NMDS) and principal coordinate analysis (PCoA) revealed distinct metabolite and microbial profiles, demonstrating that CLas impacts the root metabolome and microbiome in a manner that is variety-specific.