Multi-Omics and Bioinformatics for Plant–Microbiome Interactions and Crop Stress Resilience

Plants respond to drought, salinity, nutrient limitation, pathogens, and temperature stress through coordinated changes in gene regulation, metabolism, root development, and interactions with microbial communities. The rhizosphere, endosphere, and phyllosphere contain bacteria and fungi that can influence nutrient acquisition, hormone signalling, defence, and tolerance to environmental stress. Understanding these interactions is increasingly important for developing sustainable strategies that protect crop productivity under changing environmental conditions.Genomics, metagenomics, transcriptomics, metabolomics, proteomics, and high-throughput phenotyping now make it possible to study plant–microbiome systems in far greater detail. However, these data are often analysed separately. This makes it difficult to identify the microbial functions, plant regulatory pathways, and environmental conditions that jointly determine beneficial or harmful outcomes. Progress requires computational approaches that integrate heterogeneous datasets across plant genotypes, microbial communities, tissues, developmental stages, and field environments.This Research Topic will bring together bioinformatics, multi-omics, and systems-level studies of plant–microbiome interactions that shape crop resilience. It welcomes work that develops or applies robust computational methods to connect microbial composition and function with plant molecular responses, physiological traits, and agronomic performance. The goal is to produce interpretable and reusable insights that support sustainable crop management, microbial biostimulant development, and climate-resilient agriculture.We welcome contributions addressing, but not limited to, the following themes:• Integration of plant genomics, transcriptomics, metabolomics, proteomics, metagenomics, and microbiome data• Computational analysis of plant–microbiome signalling, regulatory networks, and host–microbe interactions• Microbial functions associated with drought, salinity, nutrient stress, temperature stress, and pathogen resistance• Bioinformatics approaches for studying rhizosphere, endosphere, phyllosphere, seed, and soil microbiomes• Multi-omics evaluation of beneficial microbes, microbial consortia, biostimulants, and biofertilisers• Machine learning, network modelling, causal inference, and predictive approaches for crop resilience• Longitudinal, spatial, and field-scale analysis of plant–microbiome dynamics• Open databases, reproducible workflows, benchmarks, metadata standards, and interoperable resources for plant–microbiome research• Translation of multi-omics findings into sustainable crop management, soil health, and resilient agricultural systemsWe welcome Original Research, Methods, Technology and Code, Reviews, Mini Reviews, Perspectives, and Data Reports. Topic editors: Eduardo Larriba, David Alors, Lourdes Cardozo Téllez Source: https://www.frontiersin.org/research-topics/87314/multi-omics-and-bioinformatics-for-plant-microbiome-interactions-and-crop-stress-resilience