Characterization and high-throughput screening of bacterial communities in the soil: mechanisms of antibiotic resistance
Soil is a formidable reservoir of microbial biodiversity and existing antibiotics are principally secondary metabolites produced by soil microorganisms, or semisynthetic derivatives thereof. In nature, these compounds serve as weapons in the competition between genotypes, and their evolution and dissemination are intimately coupled with the evolution and dissemination of antibiotic resistance. This project aims i) to investigate the functional diversity (genes and metabolic pathways) of soil microbial communities involved in antibiotic production, and corresponding resistomes, ii) to develop a better understanding of ecological and evolutionary processes in the soil communities involved in antibiotic production, and as a consequence, to their associated resistomes.  To this end, we will analyze soil samples from the RMQS, selected to cover the largest soil diversity possible, in terms of environmental parameters (land-use, physico-chemical characteristics and spatial descriptors). These soil samples originated from the second campaign of a national soil survey called the French Soil Quality Monitoring Network (or RMQS). This national survey is the most extensive and without a priori soil sampling survey available to date, developed by the: “Groupement d'Intérêt Scientifique (GIS)” Sol. The multiplicity of genetic diversity associated with antibiotic production and antibiotic resistance will be functionally characterized using a global metagenomic approach and dedicated bioinformatic tools. All these analyses have been funded by the Agence Nationale de Recherche (ANR) with the ANR MicroFlu4AMR project (ANR-20-PAMR-0004).
Soil is a formidable reservoir of microbial biodiversity and existing antibiotics are principally secondary metabolites produced by soil microorganisms, or semisynthetic derivatives thereof. In nature, these compounds serve as weapons in the competition between genotypes, and their evolution and dissemination are intimately coupled with the evolution and dissemination of antibiotic resistance. This project aims i) to investigate the functional diversity (genes and metabolic pathways) of soil microbial communities involved in antibiotic production, and corresponding resistomes, ii) to develop a better understanding of ecological and evolutionary processes in the soil communities involved in antibiotic production, and as a consequence, to their associated resistomes.  To this end, we will analyze soil samples from the RMQS, selected to cover the largest soil diversity possible, in terms of environmental parameters (land-use, physico-chemical characteristics and spatial descriptors). These soil samples originated from the second campaign of a national soil survey called the French Soil Quality Monitoring Network (or RMQS). This national survey is the most extensive and without a priori soil sampling survey available to date, developed by the: “Groupement d'Intérêt Scientifique (GIS)” Sol. The multiplicity of genetic diversity associated with antibiotic production and antibiotic resistance will be functionally characterized using a global metagenomic approach and dedicated bioinformatic tools. All these analyses have been funded by the Agence Nationale de Recherche (ANR) with the ANR MicroFlu4AMR project (ANR-20-PAMR-0004).