A QUALITATIVE EVALUATION OF THE PUBLISHED OLIGONUCLEOTIDES SPECIFIC FOR THE 16S RIBOSOMAL-RNA GENE-SEQUENCES OF THE AMMONIA-OXIDIZING BACTERIA

Over the past few years, there has been an increasing interest in maki ng oligonucleotides specific for ammonia-oxidizing bacteria (AOB), in order to detect and monitor these slow growing bacteria in environment al samples, in enrichment cultures and in wastewater treatment plants. Based on 16S rDNA sequences. a broad selection of oligonucleotides ha ve been designed, either encompassing all known AOB in the beta-subgro up of the Proteobacteria (beta AOB), or subclasses within beta AOB. Th irty different oligonucleotides have so far been published, with varyi ng specificity. The first AOB-specific oligonucleotides published were obtained as a result of an alignment of only eleven 16S rDNA sequence s from ROB. Including the present study, there are now ferry nearly fu ll length 16S rDNA sequences available from these bacteria, in additio n to a number of partial sequences, so that an improved evaluation of the published oligonucleotides can be done. Two new 16S rRNA gene sequ ences from Nitrosospira are presented here, in a phylogenetic analysis containing every 16S rRNA gene sequences (>1 kb) available from AOB. On the basis of ail alignment of all these sequences, combined with se arches in the nucleotide sequence databases, an evaluation of the thir ty published oligonucleotides is presented. The analysis expose the st rength and weakness of each oligonucleotide and discuss the use of oli gonucleotides specific for 16S rRNA genes in future studies of AOB. Th e present work also identifies one new, broad range primer, specific f or the AOB in the beta-subgroup of the Proteobacteria.