The swift rise of omics-approaches allows for investigating microbial diversity and plantmicrobe interactions across diverse ecological communities and spatio-temporal scales. The environment, however, is rapidly changing. The introduction of invasive species and the effects of climate change have particular impact on emerging plant diseases and managing current epidemics. It is critical, therefore, to take a holistic approach to understand how and why pathogenesis occurs in order to effectively manage for diseases given the synergies of changing environmental conditions. A multi-omics approach allows for a detailed picture of plant-microbial interactions and can ultimately allow us to build predictive models for how microbes and plants will respond to stress under environmental change. This article is designed as a primer for those interested in integrating-omic approaches into their plant disease research. We review-omics technologies salient to pathology including metabolomics, genomics, metagenomics, volatilomics, and spectranomics, and present cases where multiomics have been successfully used for plant disease ecology. We then discuss additional limitations and pitfalls to be wary of prior to conducting an integrated research project as well as provide information about promising future directions.

Plant defense research is facilitated by the use of genome-sequenced inbred lines; however, a foundational knowledge of interactions in commercial hybrids remains relevant to understanding mechanisms present in crops. Using an array of commercial maize hybrids, we quantified the accumulation patterns of defense-related metabolites and phytohormones in tissues challenged with diverse fungal pathogens. Across hybrids, Southern leaf blight (Cochliobolus heterostrophus) strongly elicited specific sesqui- and diterpenoid defenses, namely zealexin A4 (ZA4) and kauralexin diacids, compared with the stalk-rotting agents Fusarium graminearum and Colletotrichum graminicola. With respect to biological activity, ZA4 and kauralexin diacids demonstrated potent antimicrobial action against F. graminearum. Unexpectedly, ZA4 displayed an opposite effect on C. graminicola by promoting growth. Overall, a negative correlation was observed between total analyzed terpenoids and fungal growth. Statistical analyses highlighted kauralexin A3 and abscisic acid as metabolites most associated with fungal suppression. As an empirical test, mutants of the ent-copalyl diphosphate synthase Anther ear 2 (An2) lacking kauralexin biosynthetic capacity displayed increased susceptibility to C. heterostrophus and Fusarium verticillioides. Our results highlight a widely occurring defensive function of acidic terpenoids in commercial hybrids and the complex nature of elicited pathway products that display selective activities on fungal pathogen species.

The salicylic acid pathway is one of the primary plant defense pathways, is ubiquitous in vascular plants, and plays a role in rapid adaptions to dynamic abiotic and biotic stress. Its prominence and ubiquity make it uniquely suited for understanding how biochemistry within plants can mediate ecological consequences. Induction of the salicylic acid pathway has primary effects on the plant in which it is induced resulting in genetic, metabolomic, and physiologic changes as the plant adapts to challenges. These primary effects can in turn have secondary consequences for herbivores and pathogens attacking the plant. These secondary effects can both directly influence plant attackers and mediate indirect interactions between herbivores and pathogens. Additionally, stimulation of salicylic acid related defenses can affect natural enemies, predators and parasitoids, which can recruit to plant signals with consequences for herbivore populations and plant herbivory aboveground and belowground. These primary, secondary, and tertiary ecological consequences of salicylic acid signaling hold great promise for application in agricultural systems in developing sustainable high-yielding management practices that adapt to changing abiotic and biotic environments.