Phylogenetic differences between particle-associated and planktonic ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria inthe northwestern Mediterranean Sea

The aim of this study was to determine if there were differences between th e types of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria associated with particulate material and planktonic samples obtained from the northwestern Mediterranean Sea. A nested PCR procedure pe rformed with ammonia oxidizer-selective primers was used to amplify 16S rKN A genes from extracted DNA. The results of partial and full-length sequence analyses of 16S rRNA genes suggested that different groups of ammonia-oxid izing bacteria were associated with the two sample types. The particle-asso ciated sequences were predominantly related to Nitrosomonas eutropha, while the sequences obtained from the planktonic samples were related to a novel marine Nitrosospira group (cluster 1) for which there is no cultured repre sentative yet. A number of oligonucleotide probes specific for different gr oups of ammonia oxidizers were used to estimate the relative abundance of s equence types in samples of clone libraries. The planktonic libraries conta ined lower proportions of ammonia oxidizer clones (0 to 26%) than the parti culate material libraries (9 to 83%). Samples of the planktonic and particl e-associated libraries showed that there were depth-related differences in the ammonia oxidizer populations, with the highest number of positive clone s in the particle-associated sample occurring at a depth of 700 m. The grea test difference between planktonic and particle-associated populations occu rred at a depth of 400 m, where only 4% of the clones in the planktonic lib rary were identified as Nitrosomonas clones, while 96% of these clones were identified as clones that were related to the marine Nitrosospira species. Conversely, all ammonia oxidizer-positive clones obtained from the particl e-associated library were members of the Nitrosomonas group. This is the fi rst indication that Nitrosomonas species and Nitrosospira species may occup y at least two distinct environmental niches in marine environments. The oc currence of these groups in different niches may result from differences in physiological properties and, coupled with the different environmental con ditions associated with these niches, may lead to significant differences i n the nature and rates of nitrogen cycling in these environments.