Journal ArticleDOI
Phylogenetic Analysis of Seven New Isolates of Ammonia-Oxidizing Bacteria Based on 16S rRNA Gene Sequences
TLDR
The results of this phylogenetic analysis confirm the previously proposed emendation of the genus classification within these bacteria, and suggest that the morphological traits have evolved recently, and that 16S ribosomal RNA analysis alone is not sufficient to determine the evolutionary relationship between them.About:
This article is published in Systematic and Applied Microbiology.The article was published on 1995-01-01. It has received 103 citations till now. The article focuses on the topics: Ribosomal DNA & Phylogenetic tree.read more
Citations
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Journal ArticleDOI
Ammonia-Oxidizing Bacteria: A Model for Molecular Microbial Ecology
TL;DR: This chapter reviews recent progress in knowledge of Chemolitho-autotrophic ammonia-oxidizing bacteria of the beta-subclass Proteobacteria, and examines their distribution, diversity, and ecology.
Journal ArticleDOI
Phylogeny of All Recognized Species of Ammonia Oxidizers Based on Comparative 16S rRNA and amoA Sequence Analysis: Implications for Molecular Diversity Surveys
Ulrike Purkhold,Andreas Pommerening-Röser,Stefan Juretschko,Markus Schmid,Hans-Peter Koops,Michael Wagner +5 more
TL;DR: The presented 16S rRNA and amoA and AmoA sequence data from all recognized AOB species significantly extend the currently used molecular classification schemes for AOB and now provide a more robust phylogenetic framework for molecular diversity inventories of AOB.
Journal ArticleDOI
Combined Molecular and Conventional Analyses of Nitrifying Bacterium Diversity in Activated Sludge: Nitrosococcus mobilis and Nitrospira-Like Bacteria as Dominant Populations
Stefan Juretschko,Gabriele Timmermann,Markus Schmid,Karl-Heinz Schleifer,Andreas Pommerening-Röser,Hans-Peter Koops,Michael Wagner +6 more
TL;DR: The rRNA approach was used to investigate the abundance of other well-known nitrite-oxidizing bacterial genera and found that Nitrospira-like bacteria were present in significant numbers and frequently occurred in coaggregated microcolonies with N. mobilis.
Journal ArticleDOI
Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments.
George A. Kowalchuk,John R. Stephen,W.F. de Boer,James I. Prosser,T M Embley,J.W. Woldendorp +5 more
TL;DR: DGGE evaluated the identification of ammonia oxidizers of the beta subdivision of the Proteobacteria based on the mobility of PCR-amplified 16S rDNA fragments and for the analysis of mixtures of PCR products from this group generated by selective PCR of DNA extracted from coastal sand dunes.
Journal ArticleDOI
Microbial Evolution, Diversity, and Ecology: A Decade of Ribosomal RNA Analysis of Uncultivated Microorganisms
TL;DR: This review provides an outline of the main methods used in molecular microbial ecology, and their limitations, with reference to morphologically distinctive, uncultivated bacteria; an important biotechnological process (wastewater treatment); and symbiotic relationships between Bacteria, Archaea and Eukarya.
References
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Journal ArticleDOI
DNA sequencing with chain-terminating inhibitors
TL;DR: A new method for determining nucleotide sequences in DNA is described, which makes use of the 2',3'-dideoxy and arabinon nucleoside analogues of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase.
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The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
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Confidence limits on phylogenies: an approach using the bootstrap.
TL;DR: The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
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A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
TL;DR: Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
Journal ArticleDOI
Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase
Randall Keichi Saiki,David H. Gelfand,Susanne Stoffel,Stephen J. Scharf,Russell Higuchi,Glenn Thomas Horn,Kary B. Mullis,Henry A. Erlich +7 more
TL;DR: A thermostable DNA polymerase was used in an in vitro DNA amplification procedure, the polymerase chain reaction, which significantly improves the specificity, yield, sensitivity, and length of products that can be amplified.