Soil mycobiota in agroecosystem: influence of land use and management

The present work investigated the biodiversity of soil fungi of agricultural areas differently managed by means of new generation sequencing technologies – NGS. The main object of this research was the analysis of the fungal biota in the Colombian soils, especially that of the upper Andean agro-environment. The study area was located in the region of Boyacá between 2800 and 3200 m asl. and characterized by different form of soil appropriation (apple and peach orchards, 10-year-old wood, and uncultivated grass field). Moreover, a case study has been analysed in Italy where metagenomic of soil micobiota was pictured in a production farm, in three plots differently managed in terms of fertilization, pesticide and tillage application: conventional, organic, no-tillage. Chapter I represents the general introduction of the thesis. Chapter II focuses on the practices of soil appropriation in the indigenous and urban Colombian contexts, both from biologically and socio-culturally point of view. The southern region of Colombian Amazon was taken into consideration, since this region constitutes an important model for the traditional utilization of natural resources and a fundamental basis for the definition of strategies for ecosystem management. In Chapter III the focus is on the mycological knowledge of Colombian soils based on data published in scientific research papers. Published data on diversity of native soil microfungi reported for the different natural regions of Colombia were analysed and compared. Some of the most relevant aspects of the country's mycological diversity are discussed and the most frequently registered species and genera, as well as the references for each of them, are presented. In Chapter IV the soil mycobiota in the Colombian High-Andean agro-environment is assessed through high-throughput sequencing technology. The chapter depicts the entire soil fungal community from qualitative and quantitative point of view in areas with different land use. The bootstrap-based clustering analysis highlighted that different land use strongly influences the soil mycobiota: the uncultivated and cultivated areas are characterized by abundant presence of some exclusive species. Differences in fungal species composition is consistent with the clustering analysis on higher taxonomic hierarchical level composition. Chapter V reports data collected in a case study planned in the Italian agro-environment context. The results showed that various agricultural management practices and seasonality influence the composition of the soil mycological community in agroecosystems, through a metagenomic picture. Metagenomic analyses show that the highest richness indices correspond to soils under organic production systems, while the non-tillage system showed the most divergent communities, with their own composition, prevalence and seasonal trends. Finally, the Chapter VI represents a sort of perspective for those areas subjected to conventional management and strongly polluted by pesticides that could be remediated and led towards a sustainable agriculture. The usefulness of soil fungi as key tools for the sustainable bioremediation of chemical pesticides in the soil is discussed as a strategy for the recovery of the quality of degraded agricultural soils. The results of this study provide insight into the complexity of micobiota of managed soils under different farming systems, with the ultimate goal of better understanding the multiple mechanisms governing soil quality and to develop an environmentally sound management that improves production, allowing the maintenance of ecosystem diversity and the wellness of human communities linked