Microbiome and Microbiome Engineering in Plant and Soils

The intersection of plant biology, soil science, and microbial ecology has given rise to the fast-growing field of microbiome engineering. Growing evidence highlights the key role that plant- and soil-associated microbial communities play in plant development, nutrient cycling, soil fertility, pathogen suppression, and ecosystem resilience. In recent years, researchers have moved beyond profiling microbial diversity to actively manipulating and engineering microbiome structure and function in order to unlock new levels of agricultural performance and environmental sustainability. However, the complex interactions between host plants, their environment, and associated microbiomes pose significant challenges to the effective design and deployment of engineered solutions.

Innovative technologies such as high-throughput sequencing, metagenomics, genome editing, and synthetic microbial consortia are now enabling the rational design of microbiome interventions aimed at improving plant growth, stress tolerance, and soil health. These advances offer promising opportunities to reduce chemical inputs, restore degraded soils, and address the impacts of climate change, yet practical application remains at an early stage. Key questions persist regarding the principles governing successful microbiome assembly, the stability and persistence of introduced communities, the functional outcomes of engineering interventions, and potential ecological risks. Greater understanding is needed to move from proof-of-concept studies towards robust microbial engineering strategies that are applicable across diverse plant species and agroecosystems.

This Research Topic aims to advance the science and application of microbiome engineering in plant and soil systems. The primary goal is to gather pioneering research and critical perspectives that deepen mechanistic insights, refine engineering approaches, and assess the transformative potential of microbiome manipulation for environmental and agricultural sustainability. We encourage submissions that integrate molecular, ecological, biotechnological, and modelling approaches to drive the field forward.

Given the translational nature of microbiome engineering, we also welcome contributions that address regulatory considerations shaping the development and deployment of engineered microbiomes. Submissions may examine how regulatory frameworks differ across regions, how engineered or introduced microbial products are classified and assessed, and what evidence is required for approval, stewardship, and long-term monitoring. Perspectives that connect regulatory pathways with innovation, field implementation, risk assessment, and stakeholder adoption are particularly encouraged.

The scope of this Research Topic is focused on the design, testing, and implementation of microbiome-based interventions in plant and soil health, while excluding broader topics that do not pertain directly to engineering or manipulation of microbial communities.

To gather further insights in microbiome engineering in plant and soils, we welcome articles addressing, but not limited to, the following themes:

o Synthetic microbial consortia for plant growth promotion and disease suppression

o Genome editing and functional screening of plant- and soil-associated microbes

o Ecological principles underlying microbiome assembly, stability, and resilience after engineering

o Field-scale implementation and monitoring of microbiome interventions in agriculture and restoration

o Computational modelling, predictive analytics, and multi-omics for rational microbiome design

o Environmental and biosafety considerations of microbiome engineering approaches

o Regulatory considerations for engineered or introduced microbiomes, including policy, governance, approval pathways, and compliance for field deployment

o Interaction of engineered microbiomes with plant genetics and soil properties

This Research Topic welcomes the following article types: Original Research, Review, Mini Review, Perspective, Opinion, Methods, Technology Reports, and Brief Research Reports.

Article types and fees

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

• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• 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:

• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Review
• Systematic Review
• Technology and Code

Keywords: Microbiome Engineering, Plant Microbiome, Soil Health, Synthetic Microbial Consortia, Sustainable Agriculture

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.