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Modern meta7/30/2023 ![]() Soil is the most complex natural physicochemical matrix and the most structured one on our planet. Link Between Soil as a Support for Food Production and a Habitat for Living Organisms These are essential for objective and robust diagnosis, to help actors and stakeholders improve soil management, with a view to or to contribute to combining the food and environmental quality of next-generation farming systems in the context of the agroecological transition. As regards prospects, we outline the importance of building up repositories of soil quality indicators. Our review shows that despite the recent huge advances, some meta-omics approaches (e.g., metatranscriptomics or meta-proteomics) still need developments to be operational for environmental bio-monitoring. The development of metabarcoding approaches in the last 20 years has led to a collection of microbial indicators that are now operational and available for the farming sector. Each meta-omics approach is described in its general principles, methodologies, specificities, strengths and drawbacks, and illustrated with concrete applications for soil monitoring. We reviewed how meta-omics approaches replaced traditional methods and allowed developing modern microbial indicators of the soil biological quality. This revolution has substantially filled the knowledge gap about soil microbial diversity regulation and ecology, but also provided new and robust indicators of agricultural soil quality. The emergence of meta-omics approaches based on recent advances in high-throughput sequencing and bioinformatics has remarkably improved our ability to characterize microbial diversity and its potential functions. Microbial communities are also sensitive to various environmental drivers and to management practices as a result, they are ideal candidates for monitoring soil quality assessment. Within the soil biodiversity reservoir, microbial diversity including Archaea, Bacteria, Fungi and protists is essential for ecosystem functioning and resilience. In the face of the numerous causes of soil degradation such as unsustainable soil management practices, pollution, waste disposal, or the increasing number of extreme weather events, it has become clear that (i) preserving the soil biodiversity is key to food security, and (ii) biodiversity-based solutions for environmental monitoring have to be developed. They represent the keystone of the food value chain because they harbor a large fraction of biodiversity-the backbone of the regulation of ecosystem services and “soil health” maintenance. Soils are fundamental resources for agricultural production and play an essential role in food security. ![]() 1Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France.Christophe Djemiel 1 †, Samuel Dequiedt 1, Battle Karimi 1,2 †, Aurélien Cottin 1 †, Walid Horrigue 1 †, Arthur Bailly 1, Ali Boutaleb 1, Sophie Sadet-Bourgeteau 1 †, Pierre-Alain Maron 1 †, Nicolas Chemidlin Prévost-Bouré 1 †, Lionel Ranjard 1 † * and Sébastien Terrat 1 † *
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