Periodic Reporting for period 1 - MicroTRIAS (Learning from nature: Microbiome training towards improving agricultural sustainability)
Periodo di rendicontazione: 2023-10-01 al 2025-09-30
Climate change and environmental degradation increasingly threaten agricultural productivity across Europe, particularly in Mediterranean regions where elevated temperatures, drought, salinity are intensifying together with increased pressure of pathogens. The microTRIAS project was conceived in response to the urgent need for sustainable strategies that improve crop resilience to abiotic stress while reducing dependence on chemical inputs. Conventional microbial inoculants, often based on one or few strains, rarely perform as expected in the field because they fail to establish and interact effectively within native soil microbiomes. This inefficiency underscores the need to understand and manipulate microbial communities as functional wholes rather than as isolated agents.
microTRIAS aimed to pioneer and provide a proof of concept of an approach of Microbiome Training of soil microbiomes aiming to Increase their plant-beneficial potential. Instead of introducing nonresident inoculants, the project sought to “train” native microbiomes by selectively enriching microbial consortia capable of promoting plant growth, nutrient uptake, and tolerance to salinity and drought stress. The approach was designed around two model crops, Triticum aestivum (wheat) and Solanum lycopersicum (tomato), both economically relevant and highly affected by environmental stressors in southern Europe.
The overarching objectives were to:
1. Deliver a proof of concept for microbiome functional training as a scalable, sustainable agricultural biotechnology.
2. Develop and optimize tools for microbial community training directed toward beneficial functions.
3. Produce Trained Microbial Communities (TMCs) exhibiting improved functional traits in vitro and in planta.
4. Characterize the mechanisms underpinning TMC performance using multi-omics approaches.
Within the broader political and strategic context of the European Green Deal and the “Farm to Fork” strategy, microTRIAS contributes to the transition toward climate-resilient agriculture and reduced agrochemical dependence. The expected long-term impact lies in enabling circular, microbiome-based crop management systems that harness the potential of native microbiomes rather than adding new elements or replacing it.
microTRIAS aimed to pioneer and provide a proof of concept of an approach of Microbiome Training of soil microbiomes aiming to Increase their plant-beneficial potential. Instead of introducing nonresident inoculants, the project sought to “train” native microbiomes by selectively enriching microbial consortia capable of promoting plant growth, nutrient uptake, and tolerance to salinity and drought stress. The approach was designed around two model crops, Triticum aestivum (wheat) and Solanum lycopersicum (tomato), both economically relevant and highly affected by environmental stressors in southern Europe.
The overarching objectives were to:
1. Deliver a proof of concept for microbiome functional training as a scalable, sustainable agricultural biotechnology.
2. Develop and optimize tools for microbial community training directed toward beneficial functions.
3. Produce Trained Microbial Communities (TMCs) exhibiting improved functional traits in vitro and in planta.
4. Characterize the mechanisms underpinning TMC performance using multi-omics approaches.
Within the broader political and strategic context of the European Green Deal and the “Farm to Fork” strategy, microTRIAS contributes to the transition toward climate-resilient agriculture and reduced agrochemical dependence. The expected long-term impact lies in enabling circular, microbiome-based crop management systems that harness the potential of native microbiomes rather than adding new elements or replacing it.
The project was implemented at the Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM-UMA-CSIC) in Malaga, Spain. Three work packages (WPs 1–3) covered experimental and analytical work, while WPs 4–6 addressed training, dissemination, and management.
WP1 – Local Insight and Materials
Field surveys were carried out in Andalusia to select representative soils and crop varieties. Soils from wheat and tomato farms from different types of cultivation (open and greenhouse) were characterized for physical and chemical properties, and their native microbiomes were isolated as the experimental starting point. Based on the initial analysis 4 soils were selected for further testing.
WP2 – Microbial Community training
Custom media based on plant root exudates and cultivation conditions were designed to promote microbial consortia performing four target functions: phosphorus solubilization, iron bioavailability, tolerance to salinity and drought, and antagonism toward fungal pathogens (Fusarium oxysporum and Rhizoctonia solani AG2 and AG8).
Functional training was carried out over several cycles of enrichment, increasing the intensity of the stressor. During the preliminary experiments the trained communities alleviating abiotic stresses, drought and salinity in tomato were prioritized presenting the most coherent and promising results. In the prioritized training directions DNA samples were preserved during the cultures cultivation and plant growing (rhizosphere) to follow the communities functional and taxonomic dynamics.
WP3 – Comprehensive analysis of selected TMCs
The best-performing TMCs were evaluated in controlled greenhouse assays. Because of the prioritization at this moment the project focused on the trained microbial communities developed to alleviate the abiotic stresses in tomato. Trained consortia showed improved physiological performance under salinity and drought stress relative to controls, confirming the proof of concept.
At the end of the project the taxonomic characterization of abiotic stress alleviating microbial communities pointed into the enrichment of the taxonomic groups of Bacillus and Actinomycetota. Those results will be further expanded with additional data based on metagenomic and metabolomics analysis.
Overall, the microTRIAS project demonstrated the feasibility of steering native microbiomes toward abiotic stress alleviation ecological functions, representing the first experimental validation of this concept in an agricultural context. The objectives of mechanistic understanding of the functional changes in the trained microbiomes were not reached within the timeline of the project but the continuation of the work is currently continued within a newly founded project financed by Spanish Ministry of Science and Innovation and co-financed by the European Union.
WP1 – Local Insight and Materials
Field surveys were carried out in Andalusia to select representative soils and crop varieties. Soils from wheat and tomato farms from different types of cultivation (open and greenhouse) were characterized for physical and chemical properties, and their native microbiomes were isolated as the experimental starting point. Based on the initial analysis 4 soils were selected for further testing.
WP2 – Microbial Community training
Custom media based on plant root exudates and cultivation conditions were designed to promote microbial consortia performing four target functions: phosphorus solubilization, iron bioavailability, tolerance to salinity and drought, and antagonism toward fungal pathogens (Fusarium oxysporum and Rhizoctonia solani AG2 and AG8).
Functional training was carried out over several cycles of enrichment, increasing the intensity of the stressor. During the preliminary experiments the trained communities alleviating abiotic stresses, drought and salinity in tomato were prioritized presenting the most coherent and promising results. In the prioritized training directions DNA samples were preserved during the cultures cultivation and plant growing (rhizosphere) to follow the communities functional and taxonomic dynamics.
WP3 – Comprehensive analysis of selected TMCs
The best-performing TMCs were evaluated in controlled greenhouse assays. Because of the prioritization at this moment the project focused on the trained microbial communities developed to alleviate the abiotic stresses in tomato. Trained consortia showed improved physiological performance under salinity and drought stress relative to controls, confirming the proof of concept.
At the end of the project the taxonomic characterization of abiotic stress alleviating microbial communities pointed into the enrichment of the taxonomic groups of Bacillus and Actinomycetota. Those results will be further expanded with additional data based on metagenomic and metabolomics analysis.
Overall, the microTRIAS project demonstrated the feasibility of steering native microbiomes toward abiotic stress alleviation ecological functions, representing the first experimental validation of this concept in an agricultural context. The objectives of mechanistic understanding of the functional changes in the trained microbiomes were not reached within the timeline of the project but the continuation of the work is currently continued within a newly founded project financed by Spanish Ministry of Science and Innovation and co-financed by the European Union.
microTRIAS project brought a new perspective into crop beneficial bioinoculants. It provided a proof of concept of an individualized improvement of soil microbiome based on self-assembled microbial communities without introduction of new species or single strain isolation.
This project exceeded the paradigm of universal biological solutions by introducing a top-down community training strategy—a systemic approach enabling native microbiomes to self-organize under selective pressures and express plant-beneficial traits.
The main advances beyond the state of the art include: a) Novel methodological framework: Development of optimized enrichment media and experimental workflows for directed microbiome functional evolution, applicable to multiple crops and stress conditions and b)Demonstration of microbiome plasticity: Empirical evidence that native soil communities can be selectively reshaped toward desired functional outcomes, with measurable benefits for plants under abiotic stress.
Having in mind all the limitations of the project including limited scale of the performed experiments microTRIAS sets the foundation for next-generation individualized microbial technologies. The approach offers a pathway toward designing ecologically adapted microbial communities that can be implemented directly in regional soils, bridging laboratory innovation and field applicability.
The expected impact extends beyond scientific advancement: the methods can foster new bio-based products, strengthen Europe’s agri-biotech sector, and contribute to achieving the United Nations Sustainable Development Goals on zero hunger and climate action.
This project exceeded the paradigm of universal biological solutions by introducing a top-down community training strategy—a systemic approach enabling native microbiomes to self-organize under selective pressures and express plant-beneficial traits.
The main advances beyond the state of the art include: a) Novel methodological framework: Development of optimized enrichment media and experimental workflows for directed microbiome functional evolution, applicable to multiple crops and stress conditions and b)Demonstration of microbiome plasticity: Empirical evidence that native soil communities can be selectively reshaped toward desired functional outcomes, with measurable benefits for plants under abiotic stress.
Having in mind all the limitations of the project including limited scale of the performed experiments microTRIAS sets the foundation for next-generation individualized microbial technologies. The approach offers a pathway toward designing ecologically adapted microbial communities that can be implemented directly in regional soils, bridging laboratory innovation and field applicability.
The expected impact extends beyond scientific advancement: the methods can foster new bio-based products, strengthen Europe’s agri-biotech sector, and contribute to achieving the United Nations Sustainable Development Goals on zero hunger and climate action.