Harmonizing traditional and biotechnological approaches to engineer crop microbiomes: enhancing resilience optimization

Plants are constantly confronted with both abiotic and biotic stresses, significantly affecting plant growth, development, and ultimately reducing crop yield. These complex and dynamic stress factors constitute a significant challenge to global food security. Harnessing plant-associated microbiomes represents a key strategy for enhancing agricultural sustainability. In the current era, the field of plant microbiome engineering has acquired significant attention and holds vast potential to revolutionize novel agricultural management practices. Yet, many studies have primarily focused on addressing individual stressors, leaving the intricate interactions largely unexplored. Therefore, this work inquires into the classical and biotechnological and/or ¨omic¨ techniques to engineer plant microbiomes to overcome multiple stressors. Traditional methods such as soil amendments, selective substrates and organic agricultural practices for plant microbiome engineering, are evaluated. Other more direct and advanced multi-omics approaches, such as computational and synthetic biology, host genome manipulation, microbiome breeding and microbiome transplantation, are discussed. The combined effects of pathogen infections and abiotic stresses, with particular emphasis on drought stress, are also reviewed. In addition, the imperative role of plant-growth-promoting microorganisms (PGPM) as part of the resilient plant microbiome is also highlighted. Lastly, this work sheds light on the interplay between different organic agricultural and high-throughput advanced strategies, with the final goal of reshaping the plant microbiome and pave the way for sustainable agricultural practices.