Terminal Restriction Fragment Length Polymorphism for Soil Microbial Community Fingerprinting

2011 ◽  
Vol 75 (1) ◽  
pp. 102-111 ◽  
Author(s):  
Jane T. Aiken
Keyword(s):  
Microbial Community ◽  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Soil Microbial Community ◽  
Fragment Length Polymorphism ◽  
Soil Microbial ◽  
Community Fingerprinting ◽  
Restriction Fragment Length

scholarly journals Fingerprinting Microbial Assemblages from the Oxic/Anoxic Chemocline of the Black Sea

2003 ◽  
Vol 69 (11) ◽  
pp. 6481-6488 ◽  
Author(s):  
Costantino Vetriani ◽  
Hiep V. Tran ◽  
Lee J. Kerkhof
Keyword(s):  
Microbial Community ◽  
Restriction Fragment Length Polymorphism ◽  
Water Column ◽  
Black Sea ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
The Black Sea ◽  
Restriction Fragment Length

ABSTRACT Biomass samples from the Black Sea collected in 1988 were analyzed for SSU genes from Bacteria and Archaea after 10 years of storage at −80°C. Both clonal libraries and direct fingerprinting by terminal restriction fragment length polymorphism (T-RFLP) analyses were used to assess the microbial community. Uniform and discrete depth distributions of different SSU phylotypes were observed. However, most recombinant clones were not restricted to a specific depth in the water column, and many of the major T-RFLP peaks remain uncharacterized. Of the clones obtained, an ε-Proteobacteria and a Pseudoalteromonas-like clone accounted for major peaks in the fingerprint, while deeply branching lineages of α- and γ-Proteobacteria were associated with smaller peaks. Additionally, members were found among both the δ-Proteobacteria related to sulfate reducers and the Archaea related to phylotypes from the ANME groups that anaerobically oxidize methane.

scholarly journals Methodological Aspects of Multiplex Terminal Restriction Fragment Length Polymorphism-Technique to Describe the Genetic Diversity of Soil Bacteria, Archaea and Fungi

Sensors ◽  
2020 ◽  
Vol 20 (11) ◽  
pp. 3292 ◽  
Author(s):  
Agata Gryta ◽  
Magdalena Frąc
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Microbial Diversity ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Soil Microbial Diversity ◽  
Soil Dna ◽  
Soil Microbial ◽  
Restriction Fragment Length

The molecular fingerprinting methods used to evaluate soil microbial diversity could also be used as effective biosensors for the purposes of monitoring ecological soil status. The biodiversity of microorganisms is a relevant index of soil activity and there is a necessity to develop tools to generate reliable results for an emerging approach in the field of environmental control using microbial diversity biosensors. This work reports a method under development for determining soil microbial diversity using high efficiency Multiplex PCR-Terminal Restriction Fragment Length Polymorphism (M-T-RFLP) for the simultaneous detection of bacteria, archaea and fungi. Three different primer sets were used in the reaction and the analytical conditions were optimized. Optimal analytical conditions were achieved using 0.5 µM of primer for bacteria and 1 µM for archaea and fungi, 4 ng of soil DNA template, and HaeIII restriction enzyme. Comparative tests using the proposed analytical approach and a single analysis of each microorganism group were carried out to indicate that both genetic profiles were similar. The Jaccard similarity coefficient between single and multiplexing approach ranged from 0.773 to 0.850 for bacteria and fungi, and 0.208 to 0.905 for archaea. In conclusion, the multiplexing and pooling approaches significantly reduced the costs and time required to perform the analyses, while maintaining a proper effectiveness.

scholarly journals Terminal Restriction Fragment Length Polymorphism Analysis Program, a Web-Based Research Tool for Microbial Community Analysis

2000 ◽  
Vol 66 (8) ◽  
pp. 3616-3620 ◽  
Author(s):  
Terence L. Marsh ◽  
Paul Saxman ◽  
James Cole ◽  
James Tiedje
Keyword(s):  
Microbial Community ◽  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Web Based ◽  
Restriction Fragment Length

ABSTRACT Rapid analysis of microbial communities has proven to be a difficult task. This is due, in part, to both the tremendous diversity of the microbial world and the high complexity of many microbial communities. Several techniques for community analysis have emerged over the past decade, and most take advantage of the molecular phylogeny derived from 16S rRNA comparative sequence analysis. We describe a web-based research tool located at the Ribosomal Database Project web site (http://www.cme.msu.edu/RDP/html/analyses.html ) that facilitates microbial community analysis using terminal restriction fragment length polymorphism of 16S ribosomal DNA. The analysis function (designated TAP T-RFLP) permits the user to perform in silico restriction digestions of the entire 16S sequence database and derive terminal restriction fragment sizes, measured in base pairs, from the 5′ terminus of the user-specified primer to the 3′ terminus of the restriction endonuclease target site. The output can be sorted and viewed either phylogenetically or by size. It is anticipated that the site will guide experimental design as well as provide insight into interpreting results of community analysis with terminal restriction fragment length polymorphisms.

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