Root Microbiome and Metabolome Traits Associated with Improved Post-Harvest Root Storage for Sugar Beet Breeding Lines Under Southern Idaho Conditions

Post-harvest storage loss in sugar beets due to root rot and respiration can cause >20% sugar loss. Breeding strategies focused on factors contributing to improved post-harvest storage quality are of great importance to prevent losses. Using 16S rRNA and ITS sequencing and sugar beet mutational breeding lines with high disease resistance (R), along with a susceptible (S) commercial cultivar, the role of root microbiome and metabolome in storage performance was investigated. The R lines in general showed higher abundances of bacterial phyla, <i>Patescibacteria</i> at the M time point, and <i>Cyanobacteria</i> and <i>Desulfobacterota</i> at the L time point. Amongst fungal phyla, <i>Basidiomycota</i> (including <i>Athelia</i>) and <i>Ascomycota</i> were predominant in diseased samples. Linear discriminant analysis Effect Size (LEfSe) identified bacterial taxa such as <i>Micrococcales</i>, <i>Micrococcaceae</i>, <i>Bacilli</i>, <i>Glutamicibacter, Nesterenkonia</i>, and <i>Paenarthrobacter</i> as putative biomarkers associated with resistance in the R lines. Further functional enrichment analysis showed a higher abundance of bacteria, such as those related to the super pathway of pyrimidine deoxyribonucleoside degradation, L-tryptophan biosynthesis at M and L, and fungi, such as those associated with the biosynthesis of L-iditol 2-dehydrogenase at L in the R lines. Metabolome analysis of the roots revealed higher enrichment of pathways associated with arginine, proline, alanine, aspartate, and glutamate metabolism at M, in addition to beta-alanine and butanoate metabolism at L in the R lines. Correlation analysis between the microbiome and metabolites indicated that the root's biochemical composition, such as the presence of nitrogen-containing secondary metabolites, may regulate relative abundances of key microbial candidates contributing to better post-harvest storage.