Time-resolved, integrated multi-omic analysis reveals central role of amino acid pathways for defense responses in Arabidopsis thaliana

Plants respond to biotic stresses by altering gene expression and metabolism. However, how fast different tissues respond to microbial presence, and how similar these responses are is mostly unresolved. Here, we treat Arabidopsis thaliana with elicitors and investigate time-resolved changes in shoot, root, and root-derived (exudate) metabolite profiles. We find that root responses precede shoots and that first metabolite changes take place after 1.5 h and persist for 3 d. Exudates respond within 4 h (earliest timepoint available) to elicitor presence. This response diminishes when plants are pulse-treated but persists for continuously treated plants. Defense compounds such as phenylpropanoids increase after 1.5-4 h. Amino acids were iden6fied as central players in defense: they increase after 1.5 h in shoots, roots, and exudates. Transcriptome analysis at 4 h and 1 d and integrated, multi-omic analysis of transcription and metabolome suggest that aromatic and aliphatic amino acids are central players in defense responses. As their transcriptional and metabolite increases are fast and persisting over days for most amino acids, we propose amino acids as early indicators for biotic stress monitoring.