Microbiome and metabolome analysis identify keystone groups putatively associated with resistance in a sugar beet mutant line resistant to rhizomania

Authors: Majumdar, Rajtilak; Long, Evan; Rogers, Christopher; STRAUSBAUGH, CARL - Retired ARS Employee; Pokhrel, Suresh

Submitted to: Journal of Agriculture and Food Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/29/2026
Publication Date: 4/30/2026
Citation: Majumdar, R., Long, E.M., Rogers, C.W., Strausbaugh, C., Pokhrel, S. 2026. Microbiome and metabolome analysis identify keystone groups putatively associated with resistance in a sugar beet mutant line resistant to rhizomania. Journal of Agriculture and Food Research. https://doi.org/10.1016/j.jafr.2026.102971.
DOI: https://doi.org/10.1016/j.jafr.2026.102971

Interpretive Summary: Sugar beet rhizomania disease reduces root yield and sugar content globally. Resistance to rhizomania in commercial cultivars is primarily dependent upon the use of Rz1 and Rz2 resistant genes. Other approaches, namely chemical control and management practices, are unable to control rhizomania at the commercial level. The role of beneficial bacteria in the rhizosphere in disease suppression against soil borne pathogens has been studied in crop plants. It is unknown how rhizosphere and root associated bacteria may contribute to sugar beet rhizomania resistance. In this study we have identified key rhizosphere bacteria and their association with specific root metabolites that may have beneficial roles in rhizomania disease suppression in sugar beet. The information provided here opens future opportunities to investigate cover crops that can provide these key metabolites identified in this study and promote rhizomania suppressive bacteria in the soil to improve sugar beet resistance to this disease.

Technical Abstract: Rhizomania in sugar beet caused by beet necrotic yellow vein virus (BNYVV) and vectored by Polymyxa betae, significantly reduces root yield and sugar production. Resistance in commercial cultivars is primarily dependent upon the use of Rz1 and Rz2 resistant genes. The role of the root microbiome, and metabolites in resistance in non-Rz resistant background is not fully understood. Using an EMS mutant resistant (R) line and susceptible (S) lines, natural infection in the field, 16S sequencing, and metabolome analysis, putative roles of bacteriome and metabolites against rhizomania disease severity were investigated. The rhizosphere of R line (vs. S) showed higher abundance of bacterial genera such as Enterobacter, Chryseobacterium, Stenotrophomonas, and Pseudomonas at pre-symptomatic stage and Nocardioides, Arthrobacter at symptomatic stage. Metabolome analysis of the rhizosphere exhibited enrichment of pathways and metabolites associated with sesquiterpenoid and triterpenoid at pre-symptomatic, and linoleic acid metabolism at symptomatic stages that were higher in the R vs. S lines. Higher abundance of genera such as Nocardioides, Ramlibacter, Caulobacteraceae in the rhizosphere of R line at symptomatic stage showed strong positive correlations with L-methionine, isoleucine, and lauric acid respectively in the roots that were higher in the R line. Our results indicate that root metabolites may play a role in restructuring rhizosphere bacteriome thereby contributing to the suppression of rhizomania symptoms.