Omics-Driven Deciphering of Plant-Microbiome Interactions: Mechanisms, Functional Ecology, and Biotechnological Applications for Sustainable Soil Systems

The interaction between plants and their associated microbiomes is a rapidly advancing field situated at the intersection of molecular biology, microbial ecology, and biotechnology. Recent progress in ‘omics’ technologies - encompassing metagenomics, metatranscriptomics, metabolomics, and culturomics - has transformed our understanding of how plants and microorganisms communicate, adapt, and co-evolve. Studies have shed light on complex signaling networks, microbial recruitment processes in the rhizosphere, and functional diversity within plant-associated microbial communities. Despite these advances, significant gaps remain regarding the integration of multi-omics data to discern causal molecular mechanisms and ecological dynamics. Moreover, the translation of omics-derived insights into scalable applications for soil health and sustainability is still in its infancy, requiring interdisciplinary efforts to connect molecular findings with agronomic and environmental outcomes.This Research Topic aims to elucidate the molecular and ecological basis of plant–microbiome interactions using advanced omics-driven approaches. The main goal is to identify the molecular signals, pathways, and community-level processes that govern beneficial plant–microbe relationships, and to examine how these insights can inform microbiome engineering and targeted biotechnological applications. Central questions include: How do plants selectively recruit microorganisms under different environmental conditions? What omics-based markers can predict plant–microbiome compatibility? How can integrative multi-omics analyses contribute to the design of resilient, sustainable soil systems?To gather further insights into plant-associated microbial processes and their biotechnological potential, we welcome contributions focusing on empirical, theoretical, and applied studies across diverse soil and crop systems. We encourage submissions addressing, but not limited to, the following themes:• multi-omics approaches (metagenomics, metatranscriptomics, metabolomics, culturomics),• molecular mechanisms governing plant–microorganism interactions,• rhizosphere functional ecology,• microbial signaling and recruitment processes,• microbiome engineering,• and biotechnological strategies for sustainable agriculture and environmental restoration. Topic editors: Efren Garcia-Ordiales, Daniel González Reguero, Pedro Antonio Jimenez Gomez, Marina Robas Mora, Pablo Higueras Higueras Source: https://www.frontiersin.org/research-topics/81813/omics-driven-deciphering-of-plant-microbiome-interactions-mechanisms-functional-ecology-and-biotechnological-applications-for-sustainable-soil-systems