Holobiont-Mediated Adaptation Strategies in Plants Under Habitat-Imposed Stress

Plants function as holobionts—integrated systems composed of the host and its associated microbiome—that together shape the ability to cope with habitat-imposed stress. In both natural and managed environments, plants routinely face abiotic challenges such as drought, salinity, temperature extremes, and nutrient deficiencies, many of which are intensifying under climate change. Growing evidence shows that plant-associated microbial communities in the rhizosphere, endosphere, and phyllosphere shape these adaptive responses through selective recruitment and dynamic assembly, communicating with the host via signaling pathways that modulate phytohormones, osmotic balance, antioxidant activity, and nutrient uptake. This dynamic partnership allows plants to maintain phenotypic flexibility and resilience under adverse conditions.

Conventional strategies based on plant genetic improvement and chemical inputs alone are often insufficient to sustain crop productivity under increasingly variable environmental conditions. A critical gap remains in understanding how plants recruit, stabilize, and functionally integrate beneficial microbial partners under field-level stress. Recent advances in multi-omics, microbiome engineering, and synthetic microbial consortia are opening new ways to study these plant–microbiome relationships, while AI-driven analytics are improving prediction of plant stress phenotypes and plant–microbiome outcomes across environmental conditions.

This Research Topic aims to advance understanding of how plants adapt to habitat-imposed stress through their associated microbiome, with a focus on the symbiotic relationship itself—how it forms, functions, and can be harnessed. We invite contributions exploring microbiome recruitment and assembly, plant–microbe signaling mechanisms, and the functional roles of rhizosphere, endophytic, and phyllosphere communities in supporting plant resilience.

To gather further insights in this area, we welcome articles addressing, but not limited to, the following themes:

-Mechanisms of plant-driven recruitment and assembly of rhizosphere, endophytic, and phyllosphere microbial communities under abiotic stress
-Plant–microbe signaling pathways underlying holobiont-mediated stress adaptation
-Functional contribution of plant-associated microbiomes to drought, salinity, heat, and nutrient stress tolerance
-Multi-omics approaches to decoding plant–microbiome interactions under stress conditions
-Synthetic microbial consortia and microbiome engineering to enhance plant resilience
-AI-enabled and predictive modeling approaches for plant stress phenotypes and plant–microbiome responses
-Translational applications of bioinoculants and biostimulants for climate-resilient crop performance
-Field-level validation and scalability of microbiome-based interventions in agricultural systems

We welcome original research articles, reviews, mini-reviews, perspectives, and methods papers. Interdisciplinary studies bridging microbiology, ecology, and agricultural technology are encouraged, provided the plant–microbiome relationship remains the central focus.

Article types and fees

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Editorial
• FAIR² Data
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• ... View all formats

Articles that are accepted for publication by our external editors following rigorous peer review incur a publishing fee charged to Authors, institutions, or funders.

Article types

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Editorial
• FAIR² Data
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Policy and Practice Reviews
• Review
• Systematic Review
• Technology and Code

Keywords: Plant holobiont, Microbiome-assisted adaptation, Abiotic stress tolerance, Rhizosphere microbiome, Climate resilience

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.