In this study, we show that noncoding sequences from amplified fragment length polymorphisms (AFLPs) can provide robust and sensitive genetic markers suitable for PCR-based discrimination of closely related strains of Bacillus and Paenibacillus, and quantitative PCR (qPCR)-based tracking of the strains in complex natural systems like soil. Quantitative PCR was accurate in the ∼1 × 109 to ∼1 × 104 colony forming units (CFU)/g soil range. The detection limit was improved to ∼1 × 102 CFU/g when amplicons were analyzed by gel electrophoresis. Studies with laboratory-contained intact soil-core microcosms indicated that environmental persistence trends vary among different strains. For example, Bacillus circulans ATCC 9500, Bacillus amyloliquefaciens DSL 13563-0, Bacillus licheniformis ATCC 12713, Paenibacillus polymyxa NRRL B-4317, and 3 Bacillus subtilisstrains (ATCC 6051A, ATCC 55405, and NRRL B-941) died down to below the 1 × 10 2 CFU/g detection limit by days 28-105. In contrast, over a 105-day period, B. licheniformis ATCC 55406, Bacillus megaterium NRRL B-14308, and P. polymyxa strains ATCC 55407 and DSL 13540-4 died down but persisted at levels just above the detection limit, whereas Bacillus thuringiensis ATCC 13367 experienced a less than 10-fold decrease in cell numbers.

Additional Metadata
Keywords Bacillus thuringiensis environmental persistence, Bacterial persistence, qPCR, Tracking microbe strains in the environment
Persistent URL dx.doi.org/10.1139/W09-071
Journal Canadian Journal of Microbiology
Citation
Providenti, M.A. (Miguel A.), Begin, M. (Melissa), Hynes, S. (Samielle), Lamarche, C. (Christine), Chitty, D. (David), Hahn, J. (Jessica), … Smith, M. (2009). Identification and application of AFLP-derived genetic markers for quantitative PCR-based tracking of Bacillus and Paenibacillus spp. released in soil. Canadian Journal of Microbiology, 55(10), 1166–1175. doi:10.1139/W09-071