DIVERSITY OF CULTURABLE DENITRIFYING BACTERIA - LIMITS OF RDNA RFLP ANALYSIS AND PROBES FOR THE FUNCTIONAL GENE, NITRITE REDUCTASE

Sequence divergence in the ribosomal genes of known strains and isolat es of aquatic denitrifying bacteria was investigated using restriction fragment length polymorphism (RFLP) analysis. The same cultures were characterized for their homology with antibody and gene probes for nit rite reductase (NiR), a key enzyme in the denitrification pathway, and for amplification with a set of polymerase chain reaction primers des igned to amplify a portion of the NiR gene. The NiR probes were develo ped from Pseudomonas stutzeri (ATCC 14405) and several P. stutzeri str ains were included in the analyses. The RFLP analysis clustered most o f the P. stutzeri strains together, but detected considerable diversit y within this group. Isolates from three aquatic environments exhibite d within - and among - habitat diversity by RFLP. Hybridization with t he NiR probes and amplification with the NiR primers were not correlat ed with the clustering of strains by rDNA RFLP analysis. The relations hips among strains deduced from ribosomal DNA RFLP reflect heterogenei ty within the P. stutzeri group and among other pseudomonads, and the patterns differ from those inferred from specificity of the NIR probes .