PHYLOGENETIC DIVERSITY OF NATURAL-POPULATIONS OF AMMONIA OXIDIZERS INVESTIGATED BY SPECIFIC PCR AMPLIFICATION

The species composition of ammonia-oxidizing bacteria in aquatic envir onments was investigated using PCR primers for 16S rRNA genes to ampli fy specific subsets of the total ammonia-oxidizer population. The spec ificity of the amplification reactions was determined using total geno mic DNA from known nitrifying strains and non-nitrifying strains ident ified as having similar rDNA sequences. Specificity of amplification w as determined both for direct amplification, using the nitrifier speci fic primers, and with nested amplification, in which the nitrifier pri mers were used to reamplify a fragment obtained from direct amplificat ion with Eubacterial universal primers. The present level of specifici ty allows the distinction between Nitrosomonas europaea, Nitrosomonas sp. (marine) and the other known ammonia-oxidizers in the beta subclas s of the Proteobacteria. Using total DNA extracted from natural sample s, we used direct amplification to determine presence/absence of diffe rent species groups. Species composition was found to differ among dep ths in vertical profiles of lake samples and among samples and enrichm ents from various other aquatic environments. Nested PCR yielded sever al more positive reactions, which implies that nitrifier DNA was prese nt in most samples, but often at very low levels.