Phylogenetic Diversity of Natural Populations of Ammonia Oxidizers Investigated by Specific PCR Amplification

The species composition of ammonia-oxidizing bacteria in aquatic environments was investigated using PCR primers for 16S rRNA genes to amplify specific subsets of the total ammonia-oxidizer population. The specificity of the amplification reactions was determined using total genomic DNA from known n...

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Bibliographic Details
Published in:Microbial ecology 1997-03, Vol.33 (2), p.87-96
Main Authors: Ward, B. B., Voytek, M. A., K.-P. Witzel
Format: Article
Language:English
Subjects:
Ammonia
Animal, plant and microbial ecology
Bacteria
Biological and medical sciences
Cultural enrichment
DNA
Fluorescent antibody techniques
Freshwater
Fundamental and applied biological sciences. Psychology
Marine
Microbial ecology
Nitrosococcus mobilis
Nitrosococcus oceanus
Nitrosomonas
Nitrosomonas europaea
Nitrosomonas eutropha
Nitrosospira briensis
Nitrosospira multiformis
Nitrosospira tenuis
Oxidizers
Polymerase chain reaction
Product category rules
Various environments (extraatmospheric space, air, water)
Water samples
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Summary:The species composition of ammonia-oxidizing bacteria in aquatic environments was investigated using PCR primers for 16S rRNA genes to amplify specific subsets of the total ammonia-oxidizer population. The specificity of the amplification reactions was determined using total genomic DNA from known nitrifying strains and non-nitrifying strains identified as having similar rDNA sequences. Specificity of amplification was determined both for direct amplification, using the nitrifier specific primers, and with nested amplification, in which the nitrifier primers were used to reamplify a fragment obtained from direct amplification with Eubacterial universal primers. The present level of specificity allows the distinction between Nitrosomonas europaea, Nitrosomonas sp. (marine) and the other known ammonia-oxidizers in the beta subclass of the Proteobacteria. Using total DNA extracted from natural samples, we used direct amplification to determine presence/absence of different species groups. Species composition was found to differ among depths in vertical profiles of lake samples and among samples and enrichments from various other aquatic environments. Nested PCR yielded several more positive reactions, which implies that nitrifier DNA was present in most samples, but often at very low levels.
ISSN:0095-3628
1432-184X
DOI:10.1007/s002489900011