Soutenance de thèse de Gianluca Grasso, doctorant ISYEB

(If you are interested you can follow the presentation using the following zoom link: )

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  https://cnrs.zoom.us/j/93248433635?pwd=5i8c2HpEQVxutsoQZwa2AoybA9C68W.1
  
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Résumé de la thèse en anglais - (Here a abstract of my thesis) 

The current biodiversity crisis has been essentially documented for plants and animals, thanks to the availability of historical data their populations and communities, in some cases dating back several centuries. What about microorganisms, and more specifically soil microorganisms? In the absence of archives from the past, the only available data on the impacts of current environmental changes on microbial diversity come mainly from short-term impact studies comparing soils subjected to different management practices.

We observed that plant roots preserved in herbariums are occasionally surrounded by a sheath of rhizospheric soil that may have preserved traces of past microbial communities. In this thesis, we investigated which plants are best suited for preserving soil in herbarium collections and how these can be used to study past microbiomes and understand the effects of climate change and the intensification of agricultural practices that have occurred over the past two centuries.

Through a citizen science project (Les Herbonautes), we created a curated database of herbarium specimens of major crop plants (more than 3000 specimens in 14 species) cultivated in France. It contains information on the presence or absence of roots and soil in herbaria. It revealed that several species, particularly in the Poaceae, are better suited to preserve soil compared to plants with simpler root systems (like Fabaceae) or large plants (like Zea mays or Cannabis). DNA extraction performed on 30 herbarium soil samples associated to Triticum and Hordeum plants (collected between 1820 and 1980) allowed us to identify chemical and physical soil parameters that seem to affect soil DNA preservation.

Thus using herbarium soils, we developed a molecular paleomicrobiological approach to study the diversity of ancient soil microbial communities. It is based on the extraction of ancient DNA from this material and on its systematic sequencing. Annotation of the resulting sequences illustrated the taxonomic of past rhizospheric microbial communities associated to several crop species (Avena, Secale, Triticum, Lactuca). Our results do suggest that herbarium soil seem to preserve traces of their original soil microbiome, which are very similar (in composition, identity of the most abundant taxa, alpha and beta diversity) to modern soil microbiomes. This approach should thus allow us to assess the long-term impact of global changes on these communities such as the intensification of farming practices and climate change.