Rhizosphere analysis of auxin producers harboring the indole-3-pyruvate decarboxylase pathway

3-indole acetic acid (IAA) produced by microorganisms in the rhizosphere modulates root growth and physiology, but the analysis of these microorganisms relies on isolation of culturable IAA producers as molecular tools are lacking. Microbial biosynthesis of IAA may involve several pathways and especially the phenylpyruvate decarboxylase pathway (using the ppdC gene), present in many phytobeneficial microorganisms. Here, we developed PCR primers to quantify ppdC+ microorganisms and assess ppdC allele diversity in rhizosphere and bulk soil. Effective ppdC primers were obtained and validated in silico and using individual ppdC+ strains. By qPCR, they enabled to evidence high abundance of ppdC+ microorganisms in different types of bulk and rhizosphere soils, up to 8 log of ppdC copies per g of soil. OTUs obtained with Illumina sequencing of bulk and rhizosphere soil samples clustered in numerous clades encompassing almost all the known ppdC diversity in soil environments, and pointing to soil type and plant species as factors potentially shaping ppdC allelic diversity. In conclusion, these new primers enabled the first culture-independent analysis of the ppdC+ functional group of IAA producers in environmental samples.