Decoding functional biodiversity in soils: environmental DNA insights into microbial and eukaryotic communities in differently managed agroecosystems

Agricultural practices are among the most impactful human activities on the environment, largely due to the shift in management strategies initiated during the “Green Revolution”. Conventional agriculture relies heavily on synthetic phytochemicals and intensive soil tillage, leading to the depletion of natural balancing factors and a decline in biodiversity, which is essential for ecosystem services. Growing evidence supports the adoption of sustainable farming practices to mitigate these environmental pressures, a perspective reinforced by international policy frameworks. This PhD thesis aims to empirically assess the impact of different agricultural practices on soil biodiversity and evaluate the effectiveness of sustainable approaches. Soil biodiversity, a key reservoir of biological activity, remains poorly understood in agroecosystems. The study integrates environmental DNA (eDNA) analysis with ecological and agricultural parameters to characterise soil organism communities. The research is divided into two main sections. The first part provides a comprehensive review of agroecosystem functioning, ecosystem services, and the environmental impact of agricultural practices, followed by an overview of soil biodiversity and eDNA methodologies. The second part presents experimental studies across three chapters. Chapter 1 investigates how different agricultural practices influence protist and metazoan diversity in rice paddies, revealing higher diversity in sustainably managed fields. Chapter 2 and 3 examine cross-kingdom biostimulants in tomato crops, demonstrating their role in microbial community shifts, increased beneficial bacteria, and improved crop yield. Overall, this research underscores the importance of sustainable agriculture in preserving soil biodiversity and highlights the need for further studies to understand the drivers of microbial and eukaryotes functional diversity in agroecosystems.