Phylogeny of All Recognized Species of Ammonia Oxidizers Based on Comparative 16S rRNA and amoA Sequence Analysis: Implications for Molecular Diversity Surveys

doi:10.1128/AEM.66.12.5368-5382.2000

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Applied and Environmental Microbiology, December 2000, p. 5368-5382, Vol. 66, No. 12
0099-2240/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

Phylogeny of All Recognized Species of Ammonia Oxidizers Based on Comparative 16S rRNA and amoA Sequence Analysis: Implications for Molecular Diversity Surveys

Ulrike Purkhold,¹ Andreas Pommerening-Röser,² Stefan Juretschko,¹ Markus C. Schmid,¹ Hans-Peter Koops,² and Michael Wagner¹^,^*

Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350 Freising,¹ Institut für allgemeine Botanik, Abteilung Mikrobiologie, Universität Hamburg, D-22609 Hamburg,² Germany

Received 17 July 2000/Accepted 4 October 2000

The current perception of evolutionary relationships and the natural diversity of ammonia-oxidizing bacteria (AOB) is mainlybased on comparative sequence analyses of their genes encodingthe 16S rRNA and the active site polypeptide of the ammonia monooxygenase(AmoA). However, only partial 16S rRNA sequences are availablefor many AOB species and most AOB have not yet been analyzed onthe amoA level. In this study, the 16S rDNA sequence data of 10Nitrosomonas species and Nitrosococcus mobilis were completed.Furthermore, previously unavailable 16S rRNA sequences were determinedfor three Nitrosomonas sp. isolates and for the gamma-subclassproteobacterium Nitrosococcus halophilus. These data were usedto revaluate the specificities of published oligonucleotide primersand probes for AOB. In addition, partial amoA sequences of 17AOB, including the above-mentioned 15 AOB, were obtained. Comparativephylogenetic analyses suggested similar but not identical evolutionaryrelationships of AOB by using 16S rRNA and AmoA as marker molecules,respectively. The presented 16S rRNA and amoA and AmoA sequencedata from all recognized AOB species significantly extend thecurrently used molecular classification schemes for AOB and nowprovide a more robust phylogenetic framework for molecular diversityinventories of AOB. For 16S rRNA-independent evaluation of AOBspecies-level diversity in environmental samples, amoA and AmoAsequence similarity threshold values were determined which canbe used to tentatively identify novel species based on clonedamoA sequences. Subsequently, 122 amoA sequences were obtainedfrom 11 nitrifying wastewater treatment plants. Phylogenetic analysesof the molecular isolates showed that in all but two plants onlynitrosomonads could be detected. Although several of the obtainedamoA sequences were only relatively distantly related to knownAOB, none of these sequences unequivocally suggested the existenceof previously unrecognized species in the wastewater treatmentenvironmentsexamined.

^* Corresponding author. Mailing address: Lehrstuhl für Mikrobiologie, Technische Universität München, Am Hochanger 4, D-85350Freising, Germany. Phone: 49 8161 71 5444. Fax: 49 8161 71 5475.E-mail: wagner{at}mikro.biologie.tu-muenchen.de.

Applied and Environmental Microbiology, December 2000, p. 5368-5382, Vol. 66, No. 12
0099-2240/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

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