Open AccessDevelopment of Amplified Fragment Length Polymorphism-Derived Functional Strain-Specific Markers To Assess the Persistence of 10 Bacterial Strains in Soil Microcosms
Author(s) -
Shurong Xiang,
Marcia Cook,
Stacey Saucier,
Portia M. Gillespie,
Raymond D. Socha,
Richard P. Scroggins,
Lee A. Beaudette
Publication year - 2010
Publication title -
applied and environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.552
H-Index - 324
eISSN - 1070-6291
pISSN - 0099-2240
DOI - 10.1128/aem.00574-10
Subject(s) - biology , microbiology and biotechnology , strain (injury) , soil microbiology , amplified fragment length polymorphism , persistence (discontinuity) , escherichia coli , microorganism , microcosm , population , pseudomonas , dna profiling , bacteria , genetics , dna , ecology , gene , genetic diversity , demography , geotechnical engineering , sociology , anatomy , engineering
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 byPseudomonas stutzeri (ATCC 17587) andPseudomonas denitrificans (ATCC 13867) strains. In the second pattern, represented byBacillus subtilis (ATCC 6051) andEscherichia 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.