Eco-Evolutionary Dynamics of Plant Microbiomes: From the Friend–Foe Continuum to Sustainable Disease Management

Plant microbiomes are a hidden frontier in the effort to secure global food production, offering a route to shift agriculture away from chemical-intensive practices toward more sustainable, biologically driven solutions. The microbial communities inhabiting seeds, the rhizosphere, and the phyllosphere form a dynamic “bio-barrier” that can suppress pathogens through competitive exclusion, the production of antagonistic metabolites, and the modulation of host immune responses.These interactions, however, are not fixed. Microbial lifestyles shift along a “friend–foe continuum”, moving between mutualistic and pathogenic states depending on genetic, environmental, and ecological context. This plasticity is the outcome of a deep evolutionary history in which the coevolution of plants and their microbes over millions of years has shaped the rules governing these critical lifestyle transitions. Understanding these eco-evolutionary dynamics is therefore a prerequisite, not merely an academic exercise, for designing robust and reliable microbiome-based biocontrol strategies. By moving beyond descriptive surveys toward a predictive, evolution-informed framework, we can learn to manage the plant holobiont, build disease-suppressive soils, and strengthen crop resilience against mounting biotic and abiotic stresses.This Research Topic aims to bridge ecology, evolution, and plant pathology to elucidate the assembly, function, and evolution of plant microbiomes in the context of disease suppression. We particularly welcome integrative, systems-level studies that connect molecular mechanisms to community and ecosystem dynamics, and that translate this understanding into practical applications. We invite Original Research, Reviews, Methods, Hypothesis and Theory, and Perspective articles addressing, but not limited to:- Assembly and recruitment: how plants assemble a protective microbiome through root exudate signalling and immune modulation, and how this plant-driven selection shapes functional potential for disease suppression.- The coevolutionary framework: how coevolution and the “friend–foe continuum” inform lifestyle transitions in plant-associated microbes, and whether this can yield “evolutionary design rules” for engineering stable microbial consortia.- Mechanisms of suppression: the molecular and ecological mechanisms, including competition, antibiosis, and induced systemic resistance (ISR), that underpin durable, climate-resilient disease control.- Trait-based prediction: moving beyond taxonomy to trait-based frameworks that predict interaction outcomes from functional traits such as enzyme production, nutrient acquisition, and resource-use strategy.- Environmental and climate perturbation: how climate change and agricultural intensification (the “domestication syndrome”) destabilise beneficial plant–microbiome alliances and erode disease suppression, and how microbiomes might be “rewilded” to restore these functions.- By integrating ecological and evolutionary theory with mechanistic and applied research, this collection seeks to establish a predictive foundation for microbiome-based biological control and sustainable disease management. Topic editors: Ayesha Ahmed, Shahzad Munir, Qaiser Shakeel Source: https://www.frontiersin.org/research-topics/83892/eco-evolutionary-dynamics-of-plant-microbiomes-from-the-friend-foe-continuum-to-sustainable-disease-management