title: Development of amplified fragment length polymorphism-derived functional strain-specific markers to assess the persistence of 10 bacterial strains in soil microcosms.
abstract: To augment the information on commercial microbial products, we investigated the persistence patterns of high-priority bacterial strains from the Canadian Domestic Substance List (DSL). Specific DNA markers for each of the 10 DSL bacterial strains were developed using the amplified fragment length polymorphism (AFLP) technique, and the fates of DSL strains introduced in soil were assessed by real-time quantitative PCR (qPCR). The results indicated that all DNA markers had high specificity at the functional strain level and that detection of the target microorganisms was sensitive at a detection limitation range from 1.3 × 10² to 3.25 × 10⁵ CFU/g of dry soil. The results indicated that all introduced strains showed a trend toward a declining persistence in soil and could be categorized into three pattern types. The first type was long-term persistence exemplified by Pseudomonas stutzeri (ATCC 17587) and Pseudomonas denitrificans (ATCC 13867) strains. In the second pattern, represented by Bacillus subtilis (ATCC 6051) and Escherichia hermannii (ATCC 700368), the inoculated strain populations dropped dramatically below the detection threshold after 10 to 21 days, while in the third pattern there was a gradual decrease, with the population falling below the detectable level within the 180-day incubation period. These patterns indicate a selection effect of a microbial community related to the ecological function of microbial strains introduced in soil. As a key finding, the DSL strains can be quantitatively tracked in soil with high sensitivity and specificity at the functional strain level. This provides the basic evidence for further risk assessment of the priority DSL strains.
authors.affiliation: Biological Assessment and Standardization Section, Science and Technology Branch, Environment Canada, Ottawa, Ontario K1A 0H3, Canada.
authors.forename: S-R
authors.initials: SR
authors.lastname: Xiang
authors.forename: M
authors.initials: M
authors.lastname: Cook
authors.forename: S
authors.initials: S
authors.lastname: Saucier
authors.forename: P
authors.initials: P
authors.lastname: Gillespie
authors.forename: R
authors.initials: R
authors.lastname: Socha
authors.forename: R
authors.initials: R
authors.lastname: Scroggins
authors.forename: L A
authors.initials: LA
authors.lastname: Beaudette
mesh_terms: D054458:Amplified Fragment Length Polymorphism Analysis / Q000379:methods*; D001412:Bacillus subtilis / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D004925:Escherichia / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics*; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods; D011549:Pseudomonas / Q000235:genetics; D044223:Pseudomonas stutzeri / Q000235:genetics; D012680:Sensitivity and Specificity; D012987:Soil / Q000032:analysis; D012988:Soil Microbiology
chemical_list: D004269:DNA, Bacterial; D005819:Genetic Markers; D012987:Soil
references.citation: Biochem Biophys Res Commun. 1979 Mar 15;87(1):140-5
references.pmid: 454392
references.citation: Nucleic Acids Res. 1995 Nov 11;23(21):4407-14
references.pmid: 7501463
references.citation: Eur J Biochem. 1986 Mar 17;155(3):659-69
references.pmid: 2420587
references.citation: Appl Environ Microbiol. 1995 Apr;61(4):1341-7
references.pmid: 7747955
references.citation: J Biol Chem. 1993 Dec 15;268(35):26162-70
references.pmid: 8253735
references.citation: Nature. 1992 Jan 23;355(6358):318-25
references.pmid: 1731246
references.citation: J Microbiol Methods. 2006 Jan;64(1):1-8
references.pmid: 15932774
references.citation: Appl Environ Microbiol. 2000 Feb;66(2):678-83
references.pmid: 10653735
references.citation: Appl Environ Microbiol. 2003 Apr;69(4):2166-71
references.pmid: 12676697
references.citation: Microbiol Mol Biol Rev. 1997 Jun;61(2):121-35
references.pmid: 9184007
references.citation: Appl Microbiol Biotechnol. 1991 Jun;35(3):416-9
references.pmid: 1367541
references.citation: Avian Pathol. 1989 Jan;18(1):135-46
references.pmid: 18679844
references.citation: Gene. 1990 Sep 1;93(1):139-42
references.pmid: 2172086
references.citation: J Microbiol Methods. 2000 Feb;39(3):205-11
references.pmid: 10670767
references.citation: Can J Microbiol. 2006 May;52(5):451-61
references.pmid: 16699570
references.citation: Emerg Infect Dis. 2008 Jun;14(6):941-3
references.pmid: 18507908
references.citation: Carbohydr Res. 2005 Mar 21;340(4):651-6
references.pmid: 15721336
references.citation: Trends Microbiol. 1996 Dec;4(12):495-503
references.pmid: 9004408
references.citation: Sci China C Life Sci. 2005 Dec;48(6):585-92
references.pmid: 16483137
references.citation: J Microbiol Methods. 2000 May;40(3):241-54
references.pmid: 10802141
references.citation: Curr Opin Biotechnol. 2001 Jun;12(3):289-95
references.pmid: 11404107
references.citation: J Clin Microbiol. 1981 Mar;13(3):456-8
references.pmid: 6787067
references.citation: J Microbiol Methods. 2002 Jul;50(2):215-23
references.pmid: 11997172
references.citation: Sci Total Environ. 2007 Aug 15;382(1):121-9
references.pmid: 17462712
references.citation: Can J Microbiol. 2004 Aug;50(8):623-31
references.pmid: 15467788
references.citation: Microbiology (Reading). 2006 Dec;152(Pt 12):3535-3542
references.pmid: 17159205
references.citation: Genome Res. 2009 Jan;19(1):12-23
references.pmid: 19047519
references.citation: Genes Dev. 1990 Sep;4(9):1623-36
references.pmid: 2253882
references.citation: J Hered. 2004 Jan-Feb;95(1):53-61
references.pmid: 14757730
references.citation: Chem Biol Interact. 2008 Jan 30;171(2):236-49
references.pmid: 17434157
references.citation: Appl Environ Microbiol. 2007 Oct;73(20):6557-65
references.pmid: 17720820
references.citation: Appl Environ Microbiol. 1997 Jul;63(7):2863-9
references.pmid: 9212434
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3751-4
references.pmid: 12824410
references.citation: Curr Opin Biotechnol. 1995 Jun;6(3):275-83
references.pmid: 7780181
references.citation: J Microbiol Methods. 2004 Oct;59(1):141-6
references.pmid: 15325762
references.citation: Appl Environ Microbiol. 1994 Apr;60(4):1059-67
references.pmid: 7912498
references.citation: Can J Microbiol. 2009 Oct;55(10):1166-75
references.pmid: 19935889
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Environ Sci Pollut Res Int. 2001;8(2):120-6
references.pmid: 11400637
references.citation: Appl Environ Microbiol. 1998 Apr;64(4):1203-9
references.pmid: 9546154
references.citation: Can J Microbiol. 2002 Mar;48(3):256-61
references.pmid: 11989770