CRISPR loci-PCR as Tool for Tracking sp. Strain B510.

-based plant and soil inoculants are widely used in agriculture. The inoculated strains are commonly tracked by both culture-dependent and culture-independent methods, which are time-consuming or expensive. In this context, clustered regularly interspaced short palindromic repeats (CRISPR) loci structure is unique in the bacterial genome, including some species. Here, we investigated the use of CRISPR loci to track specific strains in soils systems by PCR. Primer sets for sp. strain B510 were designed and evaluated by colony and endpoint PCR. The CRISPR-PCR approach was standardized for sp. strain B510, and its specificity was observed by testing against 9 different strains, and 38 strains of diverse bacterial genera isolated from wheat plants. The CRISPR-PCR approach was validated in assays with substrate and wheat seedlings. sp. strain B510 was detected after of two weeks of inoculation in both sterile and nonsterile substrates as well as rhizosphere grown in sterile substrate. The CRISPR-PCR approach was found to be a useful molecular tool for specific tracking of at the strain level. This technique can be easily adapted to other microbial inoculants carrying CRISPR loci and can be used to complement other microbiological techniques.