Abstract
The overarching aim of this PhD Thesis was to unravel the impact of soil characteristics, biogeography, and legacy effects of agronomic practices on the soil biodiversity. Understanding the huge amount of biodiversity in terms of soil communities' taxonomic composition, functionality, and ecological interactions is still far from becoming clear. This information is urgent to find suitable soil quality indices that include biodiversity. The first study aims at investigating the effect of integrated agricultural management on soil microbial diversity within a vineyard with 20 years of exposure to fertilisers and pesticides. Soil samples were collected from three sites: row, inter-row (space between vines rows) and headland. Row and inter-row soils were chemically and microbiologically different from the headland soils, with the latter displaying a lower heavy metal content. This soil heterogeneity, including heavy metal content, played an important role in soil microbial beta-diversity. Conversely, alpha-diversity did not vary. The sole variation of the beta-diversity could indicate a possible turnover of soil microbial communities suggesting how this biodiversity metric can be a more valuable indicator of soil quality in agricultural systems rather than the sole alpha-diversity. The constant values of soil microbial-alpha-diversity conducted us to the second study performing a meta-analysis on the response of soil microbial alpha-diversity to the experimental addition of cadmium (Cd) and copper (Cu). The work highlighted a negative metal-dependent (for Cu but not Cd) and pH-dependent bacterial response to additions exceeding 29.6 mg kg−1 (first loss of -0.06 % at 30 mg kg−1) and reaching -13.89 % maximal decrease at 3837 mg kg−1. The work confirmed that the alpha-diversity of soil bacteria is not a valuable index for investigating the impact of heavy metals on soil quality. Indeed, bacterial communities behave differently depending on the metal, being also relatively resistant to soil heavy metals pollution. Alpha-diversity responses’ inconsistency could depend on the structure and composition of soil-inhabiting communities that vary across soils (i.e., beta-diversity). Accordingly, the third study investigated the variability of bacterial and fungal communities in 18 apple orchard soils (n = 270) subjected to organic or conventional farming and located in 3 valleys over a 550 m elevational gradient. Agronomic management significantly influenced soil composition and communities’ alpha- and beta-diversity. However, this influence was outweighed by the effect of geographic distance among samples, and by the effect of latitude and elevation at which samples were collected. These results suggest that in agricultural fields the edaphic variability and climate influence translate into direct effects of the geographic location, and this influence on the soil biodiversity cannot be neglected. In addition, soil comprises a complex web of inter and intra- kingdoms species interactions. These interactions were tested for possibly revealing biological soil legacy effects of past cultivation history in an agricultural field in South Tyrol. Three neighbouring plots enclosed in the same field gradually converted from grapevine to apple cultivation in 2016, 1970, and 1922 were considered. Soil characteristics (e.g., texture, Cu content) and biodiversity inherited strong legacy effects from the conversion time. Indeed, the plots were edaphically and biologically distinguishable based on the conversion time. Co-occurrence ecological network analysis patterns confirmed the beta diversity results. Ecological Interactions gradually rearranged after the conversion and keystone species resulted in driving the rearrangements around the core microbiome, suggesting community stabilisation. These results indicate that soil ecological interactions can be evaluated as interesting indicators of agricultural practices and for telling the past agricultural history of fields. Overall, this thesis led to new insights on the suitability to extend soil quality indices to account for soil biodiversity, showing that soil biodiversity is highly sensitive to multiple agricultural pressures. This will help in understanding the sustainability of common agricultural practices and will be useful for testing new ones.