Microbiomes have high potential to improve biobased processes. For example, in soil and groundwater they can degrade organic contaminants, a process called bioremediation. In Europe about 324,000 severely contaminated sites exist, which pose a risk to humans and the environment. Conventional remediation technologies to clean them are often too expensive and technically Microbiomes have a high potential to improve processes in the bio-based industry. Like the microbiome in the gut, that supports the body in the digestion of food, microbiomes in environmental compartments like soil and groundwater can produce enzymes that can degrade organic contaminants caused by human activities. In MIBIREM we will develop a TOOLBOX that helps to better develop applications for microbiomes. The TOOLBOX includes molecular methods for a better understand and monitoring, isolation and cultivation techniques as well as quality criteria for deposition of whole microbiomes and last, but not least methods that are applied to improve specific functions of microbiomes like microbiome evolution and enrichment cultures and microcosm tests. The TOOLBOX is developed for the environmental applications of microbiomes for ‘bioremediation’. For that purpose, three use-cases were selected. In these three use-cases the degradation of organic contaminants in soil and groundwater by active microbiomes is investigated and developed. The three groups of contaminants are cyanides, hexachlorocyclohexane (HCH) and petroleum hydrocarbons (PHC). The project starts with sampling of contaminated sites to isolate microbiomes active in degradation and to gain data for the development of a prediction tool that helps guide bioremediation. Isolated microbiomes and degrading strains will be deposited and will also be improved via laboratory evolution. Finally, the performance of the isolated microbiomes will be tested based on the gained knowledge about degrading microbiomes in pilot tests under real field conditions.
Project ID
Funding period
1 October 2022 - 31 March 2027Total budget
EU contribution
Funding programme
Call for proposals
Type of action
Type of stakeholder
Project contribution to Mission Soil’s:
Specific objectives
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1. Reduce land degradation relating to desertification
Not targeted -
2. Conserve and increase soil organic carbon stocks
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3. No net soil sealing and increase the reuse of urban soils
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4. Reduce soil pollution and enhance restoration
Targeted -
5. Prevent erosion
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6. Improve soil structure to enhance habitat quality for soil biota and crops
Partially targeted -
7. Reduce the EU global footprint on soils
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8. Increase soil literacy in society across Member States
Not targeted
Operational objectives
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1. Build capacities and the knowledge base for soil stewardship
Partially targeted
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2. Co-create and upscale place-based innovations to improve soil health in all places
Partially targeted
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3. Develop an integrated EU soil monitoring system and track progress towards soil health
Partially targeted
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4. Engage with the soil user community and society at large
Partially targeted
Innovation hotspots
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1. Carbon farming
Not targeted
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2. Soil pollution and restoration
Targeted
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3. Soil biodiversity including the microbiome
Targeted
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4. Circular economy solutions
Not targeted
Cross-cutting dimensions
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1. Business
Not targeted
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2. Digital
Targeted
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3. Territorial
Not targeted
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4. International
Not targeted
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