The ability to rapidly identify and quantify a microbial strain in a complex environmental sample has widespread applications in ecology, epidemiology, and industry. In this study, we describe a rapid method to obtain functionally specific genetic markers that can be used in conjunction with standard or real-time polymerase chain reaction (PCR) to determine the abundance of target fungal strains in selected environmental samples. The method involves sequencing of randomly cloned AFLP (amplified fragment length polymorphism) products from the target organism and the design of PCR primers internal to the AFLP fragments. The strain-specific markers were used to determine the fate of three industrially relevant fungi, Aspergillus niger, Aspergillus oryzae, and Chaetomium globosum, during a 4 month soil microcosm experiment. The persistence of each of the three fungal strains inoculated separately into intact soil microcosms was determined by PCR analyses of DNA directly extracted from soil. Presence and absence data based on standard PCR and quantification of the target DNA by real-time PCR showed that all three strains declined after inoculation (-14-, 32-, and 4-fold for A. niger, A. oryzae, and C. globosum, respectively) but remained detectable at the end of the experiment, suggesting that these strains would survive for extended periods if released into nature.

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Keywords Canada domestic substances list (DSL), Canadian Environmental Protection Act (CEPA), Genetically modified organisms (GMO), Quantitative polymerase chain reaction (qPCR)
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Journal Canadian Journal of Microbiology
Hynes, S.S. (S. S.), Chaudhry, O. (O.), Providenti, M.A. (M. A.), & Smith, M. (2006). Development of AFLP-derived, functionally specific markers for environmental persistence studies of fungal strains. Canadian Journal of Microbiology, 52(5), 451–461. doi:10.1139/W05-140