Characterization of the nitrifying bacteria in aquaria and Mono Lake, California, using molecular methods

Oligonucleotide probes were developed and tested with (i) ammonia-oxidizing bacteria (AOB) of the beta subdivision of the class Proteobacteria , (ii) nitrite-oxidizing bacteria (NOB) of the alpha subdivision of the class Proteobacteria, and, (iii) nitrite-oxidizing bacteria belong to the Nitrospira group. One probe (NITROSO4E) targets the majority of known sequences for AOB in the beta subdivision, while the second probe (NSM1B) is specific for the Nitrosomonas subgroup of AOB in the beta subdivision. The probe for the alpha subdivision NOB targets Nitrobacter species. Nitrospira-group NOB were targeted with a group wide probe (S-G-Ntspa-0685-a-A-22) and the probe S-*-Ntspa-0454-a-A-19 which is more specific.; The probes were used to investigate the nitrifying bacterial consortia of freshwater and saltwater aquaria under a variety of conditions. The data showed that Nitrosomonas europaea, and close relatives, the AOB traditionally considered to be the active nitrifier in aquaria, were below detection limits in freshwater aquaria. However, Nitrosomonas species accounted for nearly 20% of the rRNA hybridization signal in saltwater aquaria nitrifying bacterial assemblages. Nitrobacter winogradskyi and closely related alpha subdivision NOB were not detected in any freshwater or saltwater aquaria examined in these investigations.; Denaturing gradient gel electrophoresis (DGGE) and bacterial rDNA clone libraries were used to discover a Nitrospira-like clone (710-9). The importance of Nitrospira-like NOB rather the alpha subdivision NOB was demonstrated by time series analysis of DNA extracted from aquaria and amplified with the PCR and run on DGGE. Results showed that the appearance of the Nitrospira-like bacteria correlated with the oxidation of nitrite to nitrate. Molecular probing showed that rRNA from Nitrospira-group bacteria make-up nearly 5% of the rRNA hybridization signal of the total nucleic acids extracted in freshwater aquaria. In total, the data indicate that Nitrospira species are active NOB in both freshwater and saltwater aquaria.; The efficacy of several bacterial mixtures containing the traditional nitrifying bacteria, Nitrosomonas europaea and Nitrobacter winogradskyi, for the acceleration of nitrification in freshwater and saltwater aquaria was investigated using molecular probes and DGGE. Results demonstrated that no mixture accelerated the establishment of nitrification in aquaria environments compared to non-inoculated control aquaria. No evidence for the presence of Nitrosomonas europaea in freshwater was found, and Nitrobacter winogradskyi was not detected in either case. The evidence showed that the mixtures do not have an effect on the colonization and species composition of the bacterial consortium of developing aquarium biofilters.; The presence of AOB, NOB, and methane-oxidizing (MOB) in Mono Lake was investigated with molecular methods. AOB were not detected in Mono Lake. NOB related to the Nitrospira-group were detected by PCR primers but not molecular probes, while the presence of MOB was not clear from the results obtained.; During the course of this study bacteria previously considered to be important, active members of the microbial community were shown to be, in fact, absent from the consortium. Instead novel bacterial types were detected and their role in the cycle of nitrogen in aquaria was implicated.