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Scientific result | Environment | Proteomics | Mass spectrometry | Bacteria

Metaproteomics and data science for an eco-health diagnosis of soil microbiota

​Researchers from Li2D (SPI/DMTS, Marcoule) and LSCE have developed an innovative methodology for analyzing soil microbiota based on an optimal computational interpretation of metaproteomic databases, which should lead to a better understanding of the impact of pollutants on soil quality and to the prediction of their restoration potential.

Published on 7 October 2021

​Probing the structure of soil microbial communities, analyzing their functioning, and correlating the biological information collected with the presence of pollutants (metals, pesticides, antibiotics, etc.) are the objectives of the GEOMICS project proposed by biologists from Li2D in Marcoule and environmental chemists from LSCE. The immense diversity of environmental microbiota, the multitude of biological compounds they contain, as well as the diversity of chemical molecules that may be present in soils, make these tasks particularly challenging. To carry out these studies, the researchers developed a new methodology for acquiring and processing biological data, which was applied to a specific case study: the sediments of the Seine, downstream from Paris, for which the GEDI team of the LSCE has a detailed knowledge of current and past contamination.

Using high-resolution mass spectrometry, the researchers recorded millions of elemental masses for each soil sample and identified tens of thousands of proteins. They then applied a metaproteomic methodology called "phylopeptidomics", i.e. a computational interpretation of the data, designed at Li2D, that links proteins to the organisms that produce them. By comparing the millions of recorded signals to giant databases containing billions of peptide combinations, they were able to identify the microorganisms present in the sample and their function. The combination of database searching, processing of genomic sample data, successive "cascades" of searches, and a new approach to false-positive evaluation, allowed the researchers to achieve exceptional results by interpreting five times more mass spectra than before. A revolution in environmental metaproteomics ....

This new strategy will be potentially applicable to other fields of study such as microbiota and pollens transported by atmospheric particles or trapped in permafrost, or microbiota present in river and marine sediments or in groundwater.

Contacts : Jean Armengaud (; Sophie Ayrault (

Screenshot of the video presentation of Virginie Jouffret's thesis illustrating soil pollution ©CEA

Video : "Probing soil microbial life: a new eco-health diagnostic" by Virginie Jouffret, PhD student at Li2D, Marcoule, presented at the Global Young Scientists Summit GYSS in January 2021.

See also the associated video/abstract edited by the journal

- The GEOMICS project was initiated through the DRF-Impulsion program in October 2016 and has received thesis funding from October 2018 to study a sediment archive collected from a floodplain downstream of Paris, and representing a hundred-year history of the contamination of the Seine River (thesis of Virginie Jouffret, Joliot/LSCE).
- LSCE: Laboratoire des Sciences du Climat et de l'Environnement
- GEDI: GÉochimie Des Impacts team
- Li2D: Laboratoire Innovations technologiques pour la Détection et le Diagnostic, SPI/Marcoule

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