MIBIREM approach for microbiome analysis and bioremediation application development

As conventional soil remediation is often too expensive and inefficient, MIBIREM uses biotechnological remediation and employs the use of living organisms, mostly bacteria, in the removal of contaminants from the environment.

Biological methods using bacteria for degradation of organic contaminants are an under-exploited alternative: they are slower but more cost effective and eco-friendly compared to other remediation methods: they do not extract net water (no water footprint), do not produce waste and do not need an extensive on-site treatment plant or transport to and treatment by an off-site soil cleaner (CO2-footprint).

However microbial degradation in the environment depends on a network of microbes providing complementary degradation pathways and accessory functions. Microbial consortia are more efficient and faster in degradation compared to individual strains, characterisation and isolation of whole microbiomes active in degradation of organic contaminants can hugely boost bioremediation. MIBIREM combines expertise from site remediation with microbiological know-how and bioinformatics to get a deeper understanding of microbiomes that are active in degradation and develop them all the way to apply them in field test.

To implement this the unique ‘MIBIREM approach’ has been designed, detailing all necessary steps as depicted in the graphic. This graphic shows material flows and order of activities. Consecutive activities overlap – respective tasks have a longer run-time.

Samples from contaminated sites will be taken to analyse the microbiome (metagenome) together with standard physico-chemical site assessment. Microbiomes active in degradation will be identified (degradation tests in microcosms, enrichment cultures, bac-traps, stable isotope probing-SIP). Single bacterial strains will be isolated from active microbiomes, sequenced to better characterise them, and deposited together with some microbiomes. In parallel degrading microbiomes will be further improved by laboratory evolution and selected strains combined in artificial microbiomes. An informatics prediction-tool will be developed based on the combined hydrogeological, chemical, geophysical and biological data to better understand and guide bioremediation. This tool will then be used together with the most promising microbiomes for upscaling and field tests. The services, resources and protocols developed and applied will be combined in the innovative MIBIREM TOOLBOX.

Most of the MIBIREM approach and TOOLBOX are relevant for related biotechnology / bio-economy areas, where they can be used shortly post-project. MIBIREM is focusing on industrial or other non-agricultural land where contaminations are local, but highly concentrated.