Lessons from Plant–Microbe Interactions: Concepts for Improving Plant Nutrition and Stress Tolerance

Plant-associated microorganisms, particularly plant growth-promoting bacteria (PGPB), enhance plant nutrition and stress tolerance and offer potential complementary approaches to conventional fertilization and crop protection. However, inconsistent field performance, ecological concerns associated with introducing non-native bacterial strains, and the need for formulations tailored to specific plant genotypes and soil conditions limit their agricultural application. These challenges have stimulated research into complementary strategies for promoting plant growth under favorable and stressful conditions. Here, we review advances and limitations of PGPB-based biofertilizers, focusing on multi-strain consortia, endophytic versus epiphytic microorganisms, and precision agriculture approaches integrating soil microbiome dynamics with plant-genotype-specific formulations. We also examine molecular mechanisms through which PGPB influence plant gene expression, stress signaling, nutrient acquisition, and rhizosphere communication. Building on these insights, we discuss strategies for using beneficial microbial mechanisms to improve abiotic stress tolerance and nutrient uptake. Integrating microbiome-informed biofertilizer development with genetic engineering, crop breeding, and precision agriculture could improve plant resilience. However, successful application requires functional validation and field testing under variable environmental conditions. Such approaches may reduce dependence on external agricultural inputs while improving crop productivity and sustainability. Together, these complementary strategies provide a framework for harnessing plant–microbe interactions to support climate-resilient agriculture and future food security worldwide.