Unlocking the Potential of Plant Microbiomes Within Ecological Contexts

The exploration of plant microbiomes has fundamentally reshaped our understanding of plant performance, highlighting its dependence on a complex mesh of interactions between plants, associated microbes, and environmental conditions. Plants function as metaorganisms, with their growth, productivity, stress tolerance, and ecological roles emerging from intricate, multi-scale connections with microbial communities inhabiting the rhizosphere, endosphere, and phyllosphere. Across both managed agricultural lands and natural ecosystems, there is a growing drive to harness plant-associated microbiomes as living resources for boosting plant vigor, resilience to abiotic and biotic stressors, and a spectrum of ecosystem services. However, realizing the full biotechnological potential of these microbiomes remains difficult due to persistent uncertainties regarding the ecological mechanisms that control microbial community assembly, persistence, function, and their integrated effects on plant health. Current research highlights key challenges such as the context-dependence of microbiome interventions, inconsistencies in reproducibility across contrasting environments, ambiguities in the functional roles of specific microbial taxa, and the long-term stability and scalability of introduced or manipulated communities. While advanced multi-omics and high-throughput experimentation have deepened our insight into microbiome structure and function, a cohesive ecological framework is still needed to guide microbiome-based applications toward robust and sustainable outcomes across varying environmental and management contexts.This Research Topic aims to unite and advance the understanding of the ecological principles that underpin the biotechnological application of plant microbiomes. The main goal is to resolve how ecological dynamics—including community assembly rules, environmental filtering, host-microbe and microbe-microbe interactions—govern the capacity of plant microbiomes to promote plant performance, ecological fitness, and ecosystem multifunctionality. Critical questions to address include: Which microbial taxa and traits are consistently associated with improved plant outcomes? How do abiotic and biotic variables shape the composition, persistence, and function of beneficial microbiomes? Can key microbial functions be preserved or enhanced under laboratory and field conditions through isolation or synthetic community design? Furthermore, it is imperative to explore whether reintroduced individual strains or synthetic consortia can establish stable associations and sustain targeted functions over time within native microbial assemblages. By fostering contributions that interrogate both functionally characterized isolates and in situ manipulations, this Topic seeks to bridge knowledge gaps regarding the feasibility and long-term consequences of microbiome-based interventions across diverse environments.The scope of this Research Topic encompasses interdisciplinary approaches that integrate ecological theory, functional microbiology, plant physiology, and systems biology, focusing on the rational and ecologically grounded design of microbiome strategies for plant and ecosystem improvement. Studies that merely describe microbial diversity without functional or ecological context are outside the boundary of this Topic. To gather further insights in this area, we welcome articles addressing, but not limited to, the following themes:• Mechanistic studies of microbiome assembly and functional dynamics across environmental gradients and land-use systems• Identification and validation of key microbial taxa and traits that underpin plant productivity, stress tolerance, and ecological fitness• Development and testing of synthetic communities and their interactions with native microbiomes in controlled and field conditions• Strategies for in situ microbiome manipulation through ecological steering, soil amendments, or innovative management practices• Integrated applications of multi-omics, high-throughput phenotyping, ecological network analysis, and predictive modelling to link microbiome change with plant and ecosystem outcomes• Contributions addressing the role of microbiomes in mediating ecosystem services, including soil carbon sequestration, nutrient cycling, soil structure, water regulation, and ecosystem restoration Topic editors: Helena Santiago Lima, Júnia Schultz, Adam Ossowicki, Letusa Momesso Source: https://www.frontiersin.org/research-topics/79377/unlocking-the-potential-of-plant-microbiomes-within-ecological-contexts