Nitrogen cycling and community structure of proteobacterial beta-subgroup ammonia-oxidizing bacteria within polluted marine fish farm sediments

A multidisciplinary approach was used to study the effects of pollution fro m a marine fish farm on nitrification rates and on the community structure of ammonia-oxidizing bacteria in the underlying sediment. Organic content, ammonium concentrations, nitrification rates, and ammonia oxidizer most-pro bable-number counts were determined in samples of sediment collected from b eneath a fish cage and on a transect at 20 and 40 m from the cage. The data suggest that nitrogen cycling was significantly disrupted directly beneath the fish cage, with inhibition of nitrification and denitrification. Altho ugh visual examination indicated some slight changes in sediment appearance at 20 m, all other measurements were similar to those obtained at 40 m, wh ere the sediment was considered pristine. The community structures of prote obacterial beta-subgroup ammonia-oxidizing bacteria at the sampling sites w ere compared by PCR amplification of 16S ribosomal DNA (rDNA), using primer s which target this group. PCR products were analyzed by denaturing gradien t gel electrophoresis (DGGE) and with oligonucleotide hybridization probes specific for different ammonia oxidizers. A DGGE doublet observed in PCR pr oducts from the highly polluted fish cage sediment sample was present at a lower intensity in the 20-m sample but was absent from the pristine 40-m sa mple station. Band migration, hybridization, and sequencing demonstrated th at the doublet corresponded to a marine Nitrosomonas group which was origin ally observed in 16S rDNA clone libraries prepared from the same sediment s amples but with different PCR primers. Our data suggest that this novel Nit rosomonas subgroup was selected for within polluted fish farm sediments and that the relative abundance of this group was influenced by the extent of pollution.