A multi-omics approach to solving problems in plant disease ecology

Abstract

The swift rise of omics-approaches allows for investigating microbial diversity and plant-microbe 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 multi-omics 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.

Fig 1. Multi-omics approaches inform the genotype to phenotype cascade.

Omics approaches from the genotype (top left) to the phenotype (bottom right) inform plant disease ecology in a holistic manner and can shed light on microbial communities above and belowground. Red arrow on plant symbolizes dynamic intra-plant communication in the metabolome affecting the microbial community through released volatiles. Yellow check is light for spectranomics with multiple bands of sensing (below leaf).