Literature DB >> 15746378

Application of a newly developed ARB software-integrated tool for in silico terminal restriction fragment length polymorphism analysis reveals the dominance of a novel pmoA cluster in a forest soil.

Peter Ricke1, Steffen Kolb, Gesche Braker.   

Abstract

TRF-CUT, an ARB-implemented tool, was developed to predict in silico the terminal restriction fragments of aligned small-subunit rRNA gene or functional gene sequences. Application of this new tool to perform directed terminal restriction fragment length polymorphism analysis of pmoA products obtained from a forest soil revealed that novel cluster I methanotrophic bacteria were dominant.

Mesh：

Year:  2005        PMID： 15746378      PMCID： PMC1065180          DOI： 10.1128/AEM.71.3.1671-1673.2005

Source DB:  PubMed          Journal:  Appl Environ Microbiol        ISSN： 0099-2240            Impact factor:   4.792


  14 in total

1.  Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes.

Authors:  G Braker; H L Ayala-del-Río; A H Devol; A Fesefeldt; J M Tiedje
Journal:  Appl Environ Microbiol       Date:  2001-04       Impact factor: 4.792

2.  Molecular analyses of novel methanotrophic communities in forest soil that oxidize atmospheric methane.

Authors:  T Henckel; U Jäckel; S Schnell; R Conrad
Journal:  Appl Environ Microbiol       Date:  2000-05       Impact factor: 4.792

3.  Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis.

Authors:  T L Marsh; P Saxman; J Cole; J Tiedje
Journal:  Appl Environ Microbiol       Date:  2000-08       Impact factor: 4.792

4.  Detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoA, mmoX, mxaF, and 16S rRNA and ribosomal DNA, including pmoA-based terminal restriction fragment length polymorphism profiling.

Authors:  H P Horz; M T Yimga; W Liesack
Journal:  Appl Environ Microbiol       Date:  2001-09       Impact factor: 4.792

5.  ARB: a software environment for sequence data.

Authors:  Wolfgang Ludwig; Oliver Strunk; Ralf Westram; Lothar Richter; Harald Meier; Arno Buchner; Tina Lai; Susanne Steppi; Gangolf Jobb; Wolfram Förster; Igor Brettske; Stefan Gerber; Anton W Ginhart; Oliver Gross; Silke Grumann; Stefan Hermann; Ralf Jost; Andreas König; Thomas Liss; Ralph Lüssmann; Michael May; Björn Nonhoff; Boris Reichel; Robert Strehlow; Alexandros Stamatakis; Norbert Stuckmann; Alexander Vilbig; Michael Lenke; Thomas Ludwig; Arndt Bode; Karl-Heinz Schleifer
Journal:  Nucleic Acids Res       Date:  2004-02-25       Impact factor: 16.971

6.  Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related.

Authors:  A J Holmes; A Costello; M E Lidstrom; J C Murrell
Journal:  FEMS Microbiol Lett       Date:  1995-10-15       Impact factor: 2.742

7.  Effect of soil ammonium concentration on N2O release and on the community structure of ammonia oxidizers and denitrifiers.

Authors:  Sharon Avrahami; Ralf Conrad; Gesche Braker
Journal:  Appl Environ Microbiol       Date:  2002-11       Impact factor: 4.792

8.  Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time PCR assays.

Authors:  Steffen Kolb; Claudia Knief; Stephan Stubner; Ralf Conrad
Journal:  Appl Environ Microbiol       Date:  2003-05       Impact factor: 4.792

9.  Formation of pseudo-terminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure.

Authors:  Markus Egert; Michael W Friedrich
Journal:  Appl Environ Microbiol       Date:  2003-05       Impact factor: 4.792

10.  Diazotrophic community structure and function in two successional stages of biological soil crusts from the Colorado Plateau and Chihuahuan Desert.

Authors:  Chris M Yeager; Jennifer L Kornosky; David C Housman; Edmund E Grote; Jayne Belnap; Cheryl R Kuske
Journal:  Appl Environ Microbiol       Date:  2004-02       Impact factor: 4.792
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  26 in total

1.  Effect of inhibition of acetoclastic methanogenesis on growth of archaeal populations in an anoxic model environment.

Authors:  Holger Penning; Ralf Conrad
Journal:  Appl Environ Microbiol       Date:  2006-01       Impact factor: 4.792

2.  Redox fluctuation structures microbial communities in a wet tropical soil.

Authors:  J Pett-Ridge; M K Firestone
Journal:  Appl Environ Microbiol       Date:  2005-11       Impact factor: 4.792

3.  Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.

Authors:  T Z DeSantis; P Hugenholtz; N Larsen; M Rojas; E L Brodie; K Keller; T Huber; D Dalevi; P Hu; G L Andersen
Journal:  Appl Environ Microbiol       Date:  2006-07       Impact factor: 4.792

4.  Fluorescence in situ hybridization-flow cytometry-cell sorting-based method for separation and enrichment of type I and type II methanotroph populations.

Authors:  Marina G Kalyuzhnaya; Rebecca Zabinsky; Sarah Bowerman; David R Baker; Mary E Lidstrom; Ludmila Chistoserdova
Journal:  Appl Environ Microbiol       Date:  2006-06       Impact factor: 4.792

5.  Comparison of two fingerprinting techniques, terminal restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis, for determination of bacterial diversity in aquatic environments.

Authors:  R Danovaro; G M Luna; A Dell'anno; B Pietrangeli
Journal:  Appl Environ Microbiol       Date:  2006-09       Impact factor: 4.792

6.  Interpreting ecological diversity indices applied to terminal restriction fragment length polymorphism data: insights from simulated microbial communities.

Authors:  Christopher B Blackwood; Deborah Hudleston; Donald R Zak; Jeffrey S Buyer
Journal:  Appl Environ Microbiol       Date:  2007-06-29       Impact factor: 4.792

7.  Impact of plant functional group, plant species, and sampling time on the composition of nirK-type denitrifier communities in soil.

Authors:  Christina Bremer; Gesche Braker; Diethart Matthies; Andreas Reuter; Christof Engels; Ralf Conrad
Journal:  Appl Environ Microbiol       Date:  2007-08-31       Impact factor: 4.792

Review 8.  Molecular ecology techniques for the study of aerobic methanotrophs.

Authors:  Ian R McDonald; Levente Bodrossy; Yin Chen; J Colin Murrell
Journal:  Appl Environ Microbiol       Date:  2007-12-28       Impact factor: 4.792

9.  Methanol oxidation by temperate soils and environmental determinants of associated methylotrophs.

Authors:  Astrid Stacheter; Matthias Noll; Charles K Lee; Mirjam Selzer; Beate Glowik; Linda Ebertsch; Ralf Mertel; Daria Schulz; Niclas Lampert; Harold L Drake; Steffen Kolb
Journal:  ISME J       Date:  2012-12-20       Impact factor: 10.302

10.  Effect of carbohydrate composition in barley and oat cultivars on microbial ecophysiology and proliferation of Salmonella enterica in an in vitro model of the porcine gastrointestinal tract.

Authors:  Robert Pieper; Jérôme Bindelle; Brian Rossnagel; Andrew Van Kessel; Pascal Leterme
Journal:  Appl Environ Microbiol       Date:  2009-09-25       Impact factor: 4.792
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