Profilazione avanzata del DNA del suolo mediante la tecnologia Next-Generation Sequencing (NGS)

The establishment of soil science can be traced back to the 19th century. However, the study of soil, whose origins are intertwined with human history, began with the development of sedentary agriculture. Despite advancements in soil management techniques, recent estimations depict an alarming situation in which more than 60% of European soils are deemed unhealthy. The prevailing degradation processes appear to be linked to the loss of organic carbon (48%), the loss of biodiversity (37.5%), and the loss of solid phase due to erosion (32%). Hence, there is an urgent need for a multidisciplinary approach, employing the latest scientific techniques, to comprehend soil health. The microbiome, with its ability to influence nearly all soil processes, stands as one of the most crucial affecting the health of terrestrial ecosystems, albeit it is one of the most recent key players considered for soil evaluation. The overarching goal of this thesis was to delve into the role of soil microbiomes within ecosystem services. A combination of physiochemical and molecular techniques has been employed to enhance the sustainability of current management practices. From a biodiversity conservation perspective, comprehending the structure and function of microbial communities influencing soil properties is crucial. In this work, the exploitation of contemporary molecular and bioinformatic techniques enabled taxonomical and functional classification of the bacterial species. The objective was the translation of the "soil microbial biodiversity" concept into practical, recognizable terms, associating it with taxonomic compositions that provide uniqueness and distinctive identification. The first contribution included in this thesis presents a study focused on changes in the structure and functionality of the soil microbiome concerning the severe degradation of the matrix due to the use of the area as a municipal solid waste landfill and its subsequent restoration using a patented method aimed at rebuilding soil structure. The study reveals that, although soil restoration contributed to ecological diversity indices improvement, only prolonged observations over time could definitively ascertain whether the new microbial community structure stability and its functionality can be considered stable and permanent. The second contribution presents a study that proposes molecular markers, including bacterial genera well known for their role as sugar beet (Beta vulgaris L.) growth promoters, to distinguish the effects of organic versus conventional soil management. The study reveals that the two managements do not significantly affect the overall microbiome structure. However, organic management is characterized by higher quantities of total soil DNA and copies of 16S ribosomal RNA genes. Moreover, functional genes related to carbon and nitrogen biogeochemical cycles and bacterial growth-promoting genera are more abundant. Therefore, it can be inferred that organic management appears to favor the functionality of the agroecosystem. The third contribution presents a study of microbial communities characterizing the active layer and permafrost along a chronosequence composed of three beaches in the Canadian High Arctic (Devon Island, Nunavut). These beaches are subjected to the same climatic and environmental factors but have emerged at different times between 2,360 and 8,410 years before the present (YBP). The results, in line with other scientific studies, identify specific chemical parameters, such as pH, organic carbon, and available phosphorus, as driving factors in shaping the structure of microbial communities. In detail, changes in chemical parameters along the soil profile correspond to variations in ecological diversity indices and the microbial community structure. However, it also emerges that the bacterial taxa composing the shared fraction of the microbial community across all horizons are also present in soils located in distinct ecosystems equ