Soil metagenomes and MAGs from vineyards under different fertilization regimes

Climate change, soil degradation, and unsustainable management practices threaten agricultural productivity and sustainability in the Mediterranean region, particularly in traditional viticulture. This study evaluates the long-term impacts of 20 years of continuous application of composted organic residues, mineral fertilizers, and no fertilization on soil functioning. Four years after ceasing fertilization, a comprehensive analysis of soil physicochemical and biological properties, microbial diversity, and functional traits was conducted, employing metagenomic approaches and advanced bioinformatic tools. The results revealed that organic amendments significantly enhanced soil organic matter, fertility, water retention, and microbial activity, contributing to improved soil multifunctionality. The different fertilization regimes had a strong influence on the prokaryotic communities, as 70% of the metagenome-assembled genomes and 86% of the functional traits showed statistically significant differences between treatments. However, organic amendments reduced prokaryotic alpha diversity, fostering the dominance of specific taxa (e.g., ammonia and nitrite oxidizers) adapted to the enriched soil environment. In contrast, mineral fertilization promoted resource acquisition and stress tolerance strategies among prokaryotic communities, potentially linked to long-term resource limitation and soil degradation. This study demonstrates the lasting benefits of organic fertilization in mitigating soil degradation and promoting soil health in viticulture. The results obtained highlight the importance of microbial functional roles over alpha diversity indices in assessing the impact of management practices on soil health. They also emphasise the need for long-term studies and advanced metagenomic tools to unravel complex soil-ecosystem dynamics and their implications for sustainable agriculture.