Optimization of a protocol for soil analysis through mass spectrometry-based proteomics and taxonomic and functional analysis of microbial communities to assess soil health status

Soil microbial communities are crucial indicators of soil health and are deeply influenced by agricultural practices. This thesis, developed within an Erasmus traineeship at the University of Greifswald (Germany), aimed to optimize a protocol for soil protein extraction to support mass spectrometry-based metaproteomic analyses. Different extraction protocols were tested and compared on agricultural soil samples to maximize protein yield and identification reliability. Taxonomic and functional analyses, particularly focusing on antibiotic resistance genes (ARGs), were carried out to assess microbial community composition and soil health. Results demonstrate that protocols B and B2 provided the best performance in terms of reproducibility and depth of proteome coverage. The findings contribute to the methodological advancement of soil metaproteomics and provide useful tools for future studies on soil quality assessment.