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

Volumn 55, Issue 10, 2009, Pages 1166-1175

  Providenti, Miguel A ^a,b   Begin, Melissa ^a   Hynes, Samielle ^a   Lamarche, Christine ^a   Chitty, David ^a   Hahn, Jessica ^b   Beaudette, Lee A ^b   Scroggins, Rick ^b   Smith, Myron L ^b  

^a CARLETON UNIVERSITY   (Canada)

^b ENVIRONMENT CANADA   (Canada)

Author keywords

Bacillus thuringiensis environmental persistence; Bacterial persistence; qPCR; Tracking microbe strains in the environment

Indexed keywords

AMPLICONS; AMPLIFIED FRAGMENT LENGTH POLYMORPHISMS; BACILLUS AMYLOLIQUEFACIENS; BACILLUS CIRCULANS; BACILLUS LICHENIFORMIS; BACILLUS MEGATERIUM; BACILLUS THURINGIENSIS; BACILLUS THURINGIENSIS ENVIRONMENTAL PERSISTENCE; BACTERIAL PERSISTENCE; COLONY FORMING UNITS; DETECTION LIMITS; GEL ELECTROPHORESIS; GENETIC MARKERS; IN-CELL; NATURAL SYSTEMS; NON-CODING SEQUENCES; PAENIBACILLUS POLYMYXA; QPCR; QUANTITATIVE PCR; TRACKING MICROBE STRAINS IN THE ENVIRONMENT;

CELL MEMBRANES; DSL; ELECTROPHORESIS; MODEMS; SOILS; TELECOMMUNICATION LINES;

BACTERIOLOGY;

BACTERIUM; ELECTROKINESIS; GENETIC MARKER; IDENTIFICATION METHOD; MICROCOSM; POLYMERASE CHAIN REACTION; SOIL MICROORGANISM;

ACCURACY; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; BACILLUS; BACTERIUM DETECTION; COLONY FORMING UNIT; ENVIRONMENTAL IMPACT; GEL ELECTROPHORESIS; GENETIC MARKER; MICROCOSM; NONHUMAN; NUCLEOTIDE SEQUENCE; PAENIBACILLUS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SOIL; SOIL MICROFLORA; STRAIN DIFFERENCE;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; BACILLUS; BASE SEQUENCE; COLONY COUNT, MICROBIAL; DNA PRIMERS; DNA, BACTERIAL; ECOSYSTEM; GENETIC MARKERS; MOLECULAR SEQUENCE DATA; PAENIBACILLUS; SOIL MICROBIOLOGY; SPECIES SPECIFICITY;

BACILLUS (BACTERIUM); BACILLUS AMYLOLIQUEFACIENS; BACILLUS CIRCULANS; BACILLUS LICHENIFORMIS; BACILLUS MEGATERIUM; BACILLUS THURINGIENSIS; BACTERIA (MICROORGANISMS); PAENIBACILLUS; PAENIBACILLUS POLYMYXA;

EID: 70350219120     PISSN: 00084166     EISSN: None     Source Type: Journal    
DOI: 10.1139/W09-071     Document Type: Article

References (20)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215(3): 403-410. PMID:2231712.
2. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., and Struhl, K. (Editors). 1999. Short protocols in molecular biology. 4th ed. John Wiley & Sons, New York.
3. CEPA. 1999. Canadian Environmental Protection Act, 1999 [online]. Department of Justice Canada. Available from http://laws. justice.gc.ca/en/C-15. 31/text.html [accessed December 2002].
4. Ecker, D.J., Sampath, R., Massire, C., Blyn, L.B., Hall, T.A., Eshoo, M.W., and Hofstadler, S.A. 2008. Ibis T5000: a universal biosensor approach for microbiology. Nat. Rev. Microbiol. 6(7): 553-558. doi:10.1038/nrmicro1918. PMID:18521073.
5. Environment Canada. 2008a. Screening assessment of living organisms on the Domestic Substances List [online]. Environment Canada, CEPA Registry. Available from http://www.ec.gc.ca/ substances/nsb/eng/bio-screening-e.shtml [accessed December 2008].
6. Environment Canada. 2008b. Chemicals management plan [online]. Government of Canada. Available from http://www. chemicalsubstanceschimiques.gc.ca/plan/ index-e.html [accessed December 2008].
7. Hendriksen, N.B., and Hansen, B.M. 2002. Long-term survival and germination of Bacillus thuringiensis var. kurstaki in a field trial. Can. J. Microbiol. 48(3): 256-261. doi:10.1139/w02-009. PMID:11989770.
8. Hynes, S.S., Chaudhry, O., Providenti, M.A., and Smith, M.L. 2006. Development of AFLP-derived, functionally specific markers for environmental persistence studies of fungal strains. Can. J. Microbiol. 52(5): 451-461. doi:10.1139/W05-140. PMID: 16699570.
9. Jansson, J.K. 1995. Tracking genetically engineered microorganisms in nature. Curr. Opin. Biotechnol. 6(3): 275-283. doi:10. 1016/0958-1669(95)80048- 80054 PMID:7780181.
10. Mechanda, S.M., Baum, B.R., Johnson, D.A., and Arnason, J.T. 2004. Sequence assessment of comigrating AFLPTM bands in Echinacea - implications for comparative biological studies. Genome, 47(1): 15-25. doi:10.1139/g03-094. PMID:15060598.
11. Panning, M., Kramme, S., Petersen, N., and Drosten, C. 2007. High throughput screening for spores and vegetative forms of pathogenic B. anthracis by an internally controlled real-time PCR assay with automated DNA preparation. Med. Microbiol. Immunol. (Berl.), 196(1): 41-50. doi:10.1007/s00430-006-0029-7. PMID: 17093976.
12. Pedersen, J.C., Hansen, B.M., Damgaard, P.H., and Eilenberg, J. 1995. Dispersal of Bacillus thuringiensis var. kurstaki in an experimental cabbage field. Can. J. Microbiol. 41: 118-125. doi:10.1139/m95-016.
13. Providenti, M.A., Mautner, S.I., Chaudhry, O., Bombardier, M., Scroggins, R., Gregorich, E., and Smith, M.L. 2004. Determining the environmental fate of a filamentous fungus, Trichoderma reesei, in laboratory-contained intact soil-core microcosms using competitive PCR and viability plating. Can. J. Microbiol. 50(8): 623-631. doi:10.1139/w04-053. PMID:15467788.
14. Saikaly, P.E., Barlaz, M.A., and de Los Reyes, F.L., 3rd. 2007. Development of quantitative real-time PCR assays for detection and quantification of surrogate biological warfare agents in building debris and leachate. Appl. Environ. Microbiol. 73(20): 6557-6565. doi:10.1128/AEM.00779-07. PMID:17720820.
15. Sambrook, J., and Russell, D.W. 2001. Molecular cloning: a laboratory manual. 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
16. Sneath, P.H.A. 1962. Longevity of micro-organisms. Nature, 195(4842): 643-646. doi:10.1038/195643a0. PMID:13914562.
17. Trevors, J.T., van Elsas, J.D., van Overbeek, L.S., and Starodub, M.E. 1990. Transport of a genetically engineered Pseudomonas fluorescens strain through a soil microcosm. Appl. Environ. Microbiol. 56(2): 401-408. PMID:2106286.
18. Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T., Hornes, M., et al. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23(21): 4407-4414. doi:10. 1093/nar/23.21.4407. PMID:7501463.
19. Weir, S.C., Dupuis, S.P., Providenti, M.A., Lee, H., and Trevors, J.T. 1995. Nutrient-enhanced survival of and phenanthrene mineralization by alginate-encapsulated and free Pseudomonas sp. UG14Lr cells in creosote-contaminated soil slurries. Appl. Microbiol. Biotechnol. 43(5): 946-951. doi:10.1007/ BF02431932. PMID:7576562.
20. Wong, A., Forbes, M.R., and Smith, M.L. 2001. Characterization of AFLP markers in damselflies: prevalence of codominant markers and implications for population genetic applications. Genome, 44(4): 677-684. doi:10.1139/gen-44-4- 677. PMID: 11550904. (Pubitemid 32773644)