Journal Article10.1016/J.MIMET.2006.12.024
Soil microbial community analysis using two-dimensional polyacrylamide gel electrophoresis of the bacterial ribosomal internal transcribed spacer regions.
35
TL;DR: An increase in resolution makes 2D-PAGE of Bacteria ITS fragments from complex microbial communities a viable method for detecting differences between highly similar communities, as well as in streamlining follow-on sequencing efforts by reducing the level of homoplasy often seen in band-based community fingerprinting methods.
read more
About: This article is published in Journal of Microbiological Methods. The article was published on 01 May 2007. The article focuses on the topics: Community Fingerprinting & Temperature gradient gel electrophoresis.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Soil microbial community analysis using terminal restriction fragment length polymorphisms
TL;DR: The T-RFLP method is a user-friendly molecular approach to microbial community analysis that is adding significant information to studies of microbial populations in many environments.
221
Role of root microbiota in plant productivity.
Andrzej Tkacz,Philip S. Poole +1 more
TL;DR: It is essential to understand microbial community structure and their 'metagenome' and how it is influenced by different soil types and crop varieties to be able to modify and better utilize the soil microbiota potential for promoting plant growth.
Transgenic Bt rice does not affect enzyme activities and microbial composition in the rhizosphere during crop development
TL;DR: Seasonal effects of transgenic rice expressing the Cry1Ab insecticidal protein active against lepidoperan pests and the insecticide triazophos on soil enzyme activities and microbial communities were compared under field conditions and suggested that the changes in rhizophere soil microbial community composition associated with the crop growth stage overweighed the application of triazophile.
125
Two-dimensional single strand conformation polymorphism (SSCP) of 16S rRNA gene fragments reveals highly dissimilar bacterial communities in an acidic fen
Achim Schmalenberger,Achim Schmalenberger,Christoph C. Tebbe,Michael A. Kertesz,Harold L. Drake,Kirsten Küsel +5 more
TL;DR: This study reports a two-dimensional SSCP fingerprinting method that has the capability to resolve hundreds of signals in a single fingerprint by using different gel temperatures in the two dimensions of the separation.
17
References
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
TL;DR: A simplified scoring system is proposed that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length.
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
TL;DR: An overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA is provided.
Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
TL;DR: Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment.
12K
MAFFT version 5: improvement in accuracy of multiple sequence alignment
TL;DR: Improvement in accuracy was generally observed for most methods, but remarkably large for the new options of MAFFT proposed here, which showed higher accuracy than currently available methods including TCoffee version 2 and CLUSTAL W in benchmark tests consisting of alignments of >50 sequences.