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

Authors: PADHI, EMILY - University Of California, Davis; MAHARAJ, NILESH - University Of California, Davis; LIN, SHIN-LI - University Of California, Davis; MISHCHUK, DARYA - University Of California, Davis; CHIN, ELIZABETH - University Of California, Davis; GODFREY, KRIS - University Of California, Davis; FOSTER, ELIZABETH - University Of California, Davis; Polek, Marylou; LEVEAU, JOHAN - University Of California, Davis; SLUPSKY, CAROLYN - University Of California, Davis

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/4/2019
Publication Date: 11/8/2019
Citation: Padhi, E.M., Maharaj, N., Lin, S., Mishchuk, D.O., Chin, E., Godfrey, K., Foster, E., Polek, M., Leveau, J.H., Slupsky, C. 2019. Metabolome and microbiome signatures in the roots of citrus affected by Huanglongbing. Phytopathology, 109 (12). https://doi.org/10.1094/PHYTO-03-19-0103-R.
DOI: https://doi.org/10.1094/PHYTO-03-19-0103-R

Interpretive Summary: In order to investigate the impact of Candidatus Liberibacter asiaticus (CLas), the associated pathogen of Huanglongbing (HLB) in roots of citrus trees, 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 collected from trees 46 weeks post-grafting and analyzed via 1H NMR spectroscopy to identify water-soluble root metabolites. High-throughput sequencing was performed on 16S rRNA and ITS gene amplicons to determine the relative abundance of bacterial and fungal taxa on the root surface and in the root tissue. Metabolite profiles of non-inoculated lemon and Washington navel root tissue were not significantly different, however the microbial populations within the root endosphere were different. The metabolome of lemon changed significantly when inoculated with CLas; sugars such as glucose, maltose, and sucrose and amino acids including alanine, asparagine, proline, threonine, and valine decreased. In navel orange roots, glucose, maltose, and proline were the metabolites most greatly affected by CLas infection. The rhizosphere of healthy navel trees contained primarily Enterobacteriaceae, however populations were significantly reduced with CLas infection. Shifts in microbial communities in navel roots were characterized by large increases in Burkholderiaceae and Burkholderia in both the endosphere and rhizosphere, a dramatic drop in Enterobacteriacae in the rhizosphere, and an increase in the fungus Aspergillus ochraceus in both the endosphere and rhizosphere with CLas infection. Burkholderiaceae (represented mostly by Burkholderia) accounted for the largest proportion of bacteria in the lemon endosphere and rhizosphere. In lemon roots of CLas positive trees, there was an increase of Xanthomonadaceae in both the endosphere and rhizosphere, a dramatic drop in Exophiala pisciphila, and an increase in Hypocrea. As expected, the root mass of both lemons and navel orange was greatly reduced in inoculated trees versus healthy controls.

Technical Abstract: 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 on the root surface and in the root tissue. In both citrus varieties, 27 metabolites were identified of which several were significantly different between control plants, and between CLas(+) and control plants. Scion and CLas infection also appeared to alter the microbial community structure on and in the roots of infected plants. Non- metric multidimensional scaling (NMDS) and principal coordinate analysis (PCoA) revealed distinct metabolite and microbial profiles, demonstrating that the citrus root metabolome and microbiome are have unique features that are similarly affected by CLas.