Mycotoxin Research

, Volume 34, Issue 3, pp 187–194 | Cite as

Development of a droplet digital PCR assay for population analysis of aflatoxigenic and atoxigenic Aspergillus flavus mixtures in soil

  • Sui Sheng T. Hua
  • Jeffrey D. Palumbo
  • Dan E. Parfitt
  • Siov Bouy L. Sarreal
  • Teresa L. O’Keeffe
Original Article


Aflatoxin B1 is a potent hepatotoxin and carcinogen that poses a serious safety hazard to both humans and animals. Aspergillus flavus is the most common aflatoxin-producing species on corn, cotton, peanuts, and tree nuts. Application of atoxigenic strains to compete against aflatoxigenic strains of A. flavus has emerged as one of the most practical strategies for ameliorating aflatoxin contamination in food. Genes directly involved in aflatoxin biosynthesis are clustered on an 82-kb region of the genome. Three atoxigenic strains (CA12, M34, and AF123) were each paired with each of four aflatoxigenic strains (CA28, CA42, CA90, and M52), inoculated into soil and incubated at 28 °C for 2 weeks and 1 month. TaqMan probes, omtA-FAM, and norA-HEX were designed for developing a droplet digital PCR (ddPCR) assay to analyze the soil population of mixtures of A. flavus strains. DNA was extracted from each soil sample and used for ddPCR assays. The data indicated that competition between atoxigenic and aflatoxigenic was strain dependent. Variation in competitive ability among different strains of A. flavus influenced the population reduction of the aflatoxigenic strain by the atoxigenic strain. Higher ratios of atoxigenic to aflatoxigenic strains increased soil population of atoxigenic strains. This is the first study to demonstrate the utility of ddPCR to quantify mixtures of both atoxigenic and aflatoxigenic A. flavus strains in soil and allows for rapid and accurate determination of population sizes of atoxigenic and aflatoxigenic strains. This method eliminates the need for isolation and identification of individual fungal isolates from experimental soil samples.


Biocontrol Soil population composition Gene deletion in atoxigenic strain ddPCR assay 



This work is supported by in-house research program funds from the US Department of Agriculture, Agricultural Research Services (Project Number: 5325-42000-039-00). We thank Oscar Castillo and Nicholas Hayter for technical assistance.

Compliance with ethical standards

Conflict of interest


Supplementary material

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Copyright information

© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2018

Authors and Affiliations

  • Sui Sheng T. Hua
    • 1
  • Jeffrey D. Palumbo
    • 1
  • Dan E. Parfitt
    • 2
  • Siov Bouy L. Sarreal
    • 1
  • Teresa L. O’Keeffe
    • 1
  1. 1.U.S. Department of Agriculture, Agricultural Research ServiceWestern Regional Research CenterAlbanyUSA
  2. 2.Department of Plant SciencesUniversity of California, DavisDavisUSA

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