scholarly journals Development of Amplified Fragment Length Polymorphism-Derived Functional Strain-Specific Markers To Assess the Persistence of 10 Bacterial Strains in Soil Microcosms

2010 ◽  
Vol 76 (21) ◽  
pp. 7126-7135 ◽  
Author(s):  
S.-R. Xiang ◽  
M. Cook ◽  
S. Saucier ◽  
P. Gillespie ◽  
R. Socha ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Dna Markers ◽  
Fragment Length Polymorphism ◽  
Detection Threshold ◽  
Amplified Fragment Length Polymorphism ◽  
High Specificity ◽  
Strain Level ◽  
Bacterial Strains ◽  
Functional Strain

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.

Assessment of genetic variation withinBrassica campestris cultivars using amplified fragment length polymorphism and random amplification of polymorphic DNA markers

1999 ◽  
Vol 24 (4) ◽  
pp. 433-440 ◽  
Author(s):  
Sandip Das ◽  
Jyothi Rajagopal ◽  
Sabhyata Bhatia ◽  
P. S. Srivastava ◽  
Malathi Lakshmikumaran
Keyword(s):  
Genetic Variation ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Dna Markers ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Random Amplification

scholarly journals Characterization and Determination of Origin of Lactic Acid Bacteria from a Sorghum-Based Fermented Weaning Food by Analysis of Soluble Proteins and Amplified Fragment Length Polymorphism Fingerprinting

2000 ◽  
Vol 66 (3) ◽  
pp. 1084-1092 ◽  
Author(s):  
Nokuthula F. Kunene ◽  
Ifigenia Geornaras ◽  
Alexander von Holy ◽  
John W. Hastings
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Soluble Proteins ◽  
Bacterial Strains ◽  
Lactobacillus Curvatus ◽  
Lactobacillus Sake

ABSTRACT The group that includes the lactic acid bacteria is one of the most diverse groups of bacteria known, and these organisms have been characterized extensively by using different techniques. In this study, 180 lactic acid bacterial strains isolated from sorghum powder (44 strains) and from corresponding fermented (93 strains) and cooked fermented (43 strains) porridge samples that were prepared in 15 households were characterized by using biochemical and physiological methods, as well as by analyzing the electrophoretic profiles of total soluble proteins. A total of 58 of the 180 strains wereLactobacillus plantarum strains, 47 were Leuconostoc mesenteroides strains, 25 were Lactobacillus sake-Lactobacillus curvatus strains, 17 were Pediococcus pentosaceus strains, 13 were Pediococcus acidilacticistrains, and 7 were Lactococcus lactis strains. L. plantarum and L. mesenteroides strains were the dominant strains during the fermentation process and were recovered from 87 and 73% of the households, respectively. The potential origins of these groups of lactic acid bacteria were assessed by amplified fragment length polymorphism fingerprint analysis.

scholarly journals Gene Action and Linkage of Avirulence Genes to DNA Markers in the Rust Fungus Puccinia graminis

2000 ◽  
Vol 90 (8) ◽  
pp. 819-826 ◽  
Author(s):  
P. J. Zambino ◽  
A. R. Kubelik ◽  
L. J. Szabo
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Stem Rust ◽  
Dna Markers ◽  
Fragment Length Polymorphism ◽  
Rust Fungus ◽  
Amplified Fragment Length Polymorphism ◽  
Puccinia Graminis ◽  
Avirulence Genes ◽  
Wheat Stem Rust

Two strains of the wheat stem rust fungus, Puccinia graminis f. sp. tritici, were crossed on barberry, and a single F1 progeny strain was selfed. The parents, F1, and 81 F2 progeny were examined for virulence phenotypes on wheat differential cultivars carrying stem rust resistance (Sr) genes. For eight Sr differentials, phenotypic ratios are suggestive of single dominant avirulence genes AvrT6, AvrT8a, AvrT9a, AvrT10, AvrT21, AvrT28, AvrT30, and AvrTU. Avirulence on the Sr; (Sr ‘fleck’) differential showed phenotypic ratios of approximately 15:1, indicating epistatic interaction of two genes dominant for avirulence. Avirulence on Sr9d favored a 3:13 over a 1:3 ratio, possibly indicating two segregating genes-one dominant for avirulence and one dominant for avirulence inhibition. Linkage analysis of eight single dominant avirulence genes and 970 DNA markers identified DNA markers linked to each of these avirulence genes. The closest linkages between AvrT genes and DNA markers were between AvrT6 and the random amplified polymorphic DNA marker crl34-155 (6 centimorgans [cM]) AvrT8a and the amplified fragment length polymorphism marker eAC/mCT-197 (6 cM) and between AvrT9a and the amplified fragment length polymorphism marker eAC/mCT-184 (6 cM). AvrT10 and AvrTU are linked at distance of 9 cM.

Genetic diversity of the endangered Chinese endemic herb Primulina tabacum (Gesneriaceae) revealed by amplified fragment length polymorphism (AFLP)

Genetica ◽  
2006 ◽  
Vol 127 (1-3) ◽  
pp. 177-183 ◽  
Author(s):  
Xiaowei Ni ◽  
Yelin Huang ◽  
Lin Wu ◽  
Renchao Zhou ◽  
Shulin Deng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Primulina Tabacum

Amplified Fragment Length Polymorphism in a Selected Sample of Soft Red Winter Wheat

2001 ◽  
Vol 29 (3-4) ◽  
pp. 251-258 ◽  
Author(s):  
Anne M. Grünberg ◽  
José M. Costa ◽  
Robert J. Kratochvil
Keyword(s):  
Winter Wheat ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Soft Red Winter Wheat ◽  
Red Winter Wheat
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