Microbial diversity in polluted harbor sediments II: Sulfate-reducing bacterial community assessment using terminal restriction fragment length polymorphism and clone library of dsrAB gene

2008 ◽  
Vol 76 (3) ◽  
pp. 682-691 ◽  
Author(s):  
Wen Zhang ◽  
Lin-sheng Song ◽  
Jang-Seu Ki ◽  
Chun-Kwan Lau ◽  
Xiang-Dong Li ◽  
...  
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Bacterial Community ◽  
Microbial Diversity ◽  
Clone Library ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Sulfate Reducing ◽  
Dsrab Gene ◽  
Restriction Fragment Length

scholarly journals Improved dsrA-Based Terminal Restriction Fragment Length Polymorphism Analysis of Sulfate-Reducing Bacteria

2010 ◽  
Vol 76 (15) ◽  
pp. 5308-5311 ◽  
Author(s):  
Daniel Santillano ◽  
Antje Boetius ◽  
Alban Ramette
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Sulfate Reducing Bacteria ◽  
Polymorphism Analysis ◽  
Sulfate Reducing ◽  
Reducing Bacteria ◽  
Restriction Fragment Length

ABSTRACT To better describe the community structure of sulfate-reducing bacteria in environmental systems, we compared several dissimilatory sulfite reductase (dsr) primer sets for terminal restriction fragment length polymorphism application. A new reverse primer that increased allelic diversity estimates up to 5-fold was applied to hydrocarbon seep samples to examine the relationship between guild activity and diversity.

scholarly journals Detection and Characterization of a Dehalogenating Microorganism by Terminal Restriction Fragment Length Polymorphism Fingerprinting of 16S rRNA in a Sulfidogenic, 2-Bromophenol-Utilizing Enrichment

2004 ◽  
Vol 70 (2) ◽  
pp. 1169-1175 ◽  
Author(s):  
Donna E. Fennell ◽  
Sung-Keun Rhee ◽  
Young-Beom Ahn ◽  
Max M. Häggblom ◽  
Lee J. Kerkhof
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
16S Rrna ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Reductive Dehalogenation ◽  
Polymorphism Analysis ◽  
Sulfate Reducing ◽  
Restriction Fragment Length

ABSTRACT Terminal restriction fragment length polymorphism analysis of reverse-transcribed 16S rRNA during periods of community flux was used as a tool to delineate the roles of the members of a 2-bromophenol-degrading, sulfate-reducing consortium. Starved, washed cultures were amended with 2-bromophenol plus sulfate, 2-bromophenol plus hydrogen, phenol plus sulfate, or phenol with no electron acceptor and were monitored for substrate use. In the presence of sulfate, 2-bromophenol and phenol were completely degraded. In the absence of sulfate, 2-bromophenol was dehalogenated and phenol accumulated. Direct terminal restriction fragment length polymorphism fingerprinting of the 16S rRNA in the various subcultures indicated that phylotype 2BP-48 (a Desulfovibrio-like sequence) was responsible for the dehalogenation of 2-bromophenol. A stable coculture was established which contained predominantly 2BP-48 and a second Desulfovibrio-like bacterium (designated BP212 based on terminal restriction fragment length polymorphism fingerprinting) that was capable of dehalogenating 2-bromophenol to phenol. Strain 2BP-48 in the coculture could couple reductive dehalogenation to growth with 2-bromophenol, 2,6-dibromophenol, or 2-iodophenol and lactate or formate as the electron donor. In addition to halophenols, strain 2BP-48 appears to use sulfate, sulfite, and thiosulfate as electron acceptors and is capable of simultaneous sulfidogenesis and reductive dehalogenation in the presence of sulfate.

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.

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