Résumé
The antibiotic 2,4-diacetyphloroglucinol is a major determinant in the biocontrol of plant growth promoting rhizobacteria associated with crops of agronomic relevance. The phlD gene is a useful marker of genetic and phenotypic diversity of 2,4-DAPG-producing rhizobacteria. A two-step amplification procedure was developed in order to assess directly the presence of phlD in environmental DNA, avoiding the tedious procedure of phlD-positive strain screening and isolation. We found a predominance of one or two phlD alleles in wheat fields cultivated in rice–wheat rotations for twenty years, suggesting that continuous rice–wheat cropping would lead to an enrichment of particular phlD genotypes. We also recovered new sequences with no close relative among known phlD sequences, indicating that part of the phlD allelic diversity might have been missed using standard media culture conditions.