Crispr loci-pcr as tool for tracking azospirillum sp. Strain b510

Joaquin I. Rilling, Fumito Maruyama, Michael J. Sadowsky, Jacquelinne J. Acuña, Milko A. Jorquera

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


Azospirillum-based plant and soil inoculants are widely used in agriculture. The inoculated Azospirillum 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 Azospirillum species. Here, we investigated the use of CRISPR loci to track specific Azospirillum strains in soils systems by PCR. Primer sets for Azospirillum sp. strain B510 were designed and eval-uated by colony and endpoint PCR. The CRISPRloci-PCR approach was standardized for Azospiril-lum sp. strain B510, and its specificity was observed by testing against 9 different Azospirillum strains, and 38 strains of diverse bacterial genera isolated from wheat plants. The CRISPRloci-PCR approach was validated in assays with substrate and wheat seedlings. Azospirillum 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 CRISPRloci-PCR approach was found to be a useful molecular tool for specific tracking of Azospirillum 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.

Original languageEnglish (US)
Article number1351
Issue number7
StatePublished - Jun 22 2021

Bibliographical note

Funding Information:
This study was funded by the National Fund for Scientific and Technological Development (FONDECYT) project no. 1201386 (J.J.A. and M.A.J.) and 1181050 (J.J.A. and M.A.J.).

Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.


  • Azospirillum
  • CRISPRloci-PCR
  • Microbial inoculants
  • Strain tracking methods

PubMed: MeSH publication types

  • Journal Article


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