Harnessing Multi-Omics Approaches to Unravel Plant–Microbe Interactions in Cultivated Plants: Implications for Climate Resilience and Sustainable Agriculture

Dear Colleagues,

The study of plant–microbe interactions has long been essential for understanding plant health and growth, particularly in the context of agricultural sustainability. Historically, research in this field focused on symbiotic and pathogenic relationships using classical microbiological methods. However, the rise of multi-omics approaches provides an invaluable toolkit to explore the molecular mechanisms that govern plant resilience in the face of climate change. As environmental stressors become increasingly unpredictable, understanding how cultivated plants interact with their microbiomes and respond to stress is crucial for developing strategies to ensure agricultural sustainability. The plant microbiota plays a pivotal role in plant health, influencing critical processes such as nutrient uptake, disease resistance, and growth under stress conditions.

Recent advances in integrated omics technologies—including genomics, transcriptomics, proteomics, metabolomics, epigenomics, phenomics, interactomics, and ionomics—are enabling a detailed dissection of plant–microbe interactions at multiple molecular levels. These technologies allow researchers to uncover complex regulatory networks, microbial community dynamics, and metabolic pathways involved in plant–microbe interactions. Phenomics, for instance, helps to characterize the phenotypic responses of plants to microbial communities, while epigenomics uncovers how microbial interactions can influence gene expression and stress adaptation. Interactomics is shedding light on the molecular interactions between plants and microbes, helping to map the signaling pathways and networks that govern these associations. Ionomics provides insights into how plants and microbes interact in nutrient exchange processes, which are crucial to plant growth and resilience in the face of environmental challenges.

This Special Issue aims at highlighting the methods, technologies, and cutting-edge research that harness these multi-omics approaches to explore the molecular underpinnings of plant resilience to climate change. By focusing on plant–microbe interactions in cultivated plants, we seek to bring together studies that identify and characterize key molecular markers, pathways, and interactions that enhance plant growth, health, and stress tolerance in changing environmental conditions.

We invite original research articles, reviews, and short communications that explore the following topics:

• Multi-omics methods to identify and understand plant resilience and adaptation mechanisms.
• The role of plant–microbe interactions in supporting resilience to climate stressors.
• Technologies enabling the integration of multi-omics data to reveal molecular networks of resilience.
• Practical applications of these methods for enhancing crop productivity and sustainability under climate change.

Dr. Samathmika Ravi
Dr. Maria Cristina Della Lucia
Dr. Piergiorgio Stevanato
Guest Editors

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• multi-omics
• plant–microbe interactions
• climate resilience
• agricultural sustainability
• microbial dynamics