Changes in microbial communities associated with the conditioning of filter material in recirculating aquaculture systems of the pufferfish Takifugu rubripes

We investigated changes in microflora associated with the conditioning of filter material in a recirculating aquaculture system for the culture of the pufferfish Takifugu rubripes using a clone library method of partial 16S rRNA gene sequences. Total bacteria on the pebbles used as filter material increased from 8.4 × 109 cells g− 1 at peak ammonia concentrations (8 days) to 1.3 × 1010 cells g− 1 at the end of the study (44 days). As filter material became conditioned, the occurrence of Clostridia, α-Proteobacteria and γ-Proteobacteria on the surface of the pebbles increased, whereas Flavobacteria, Sphingobacteria and Mollicutes decreased. The occurrence of ammonia-oxidizing bacteria related to Nitrosomonas decreased from 3.00% at day 8 to 0.95–1.04% at days 15–44. Phylogenetic analysis of the clones related to the genus Nitrosomonas using a Bayesian method revealed that two clones obtained in this study formed a cluster with N. aestuarii in the N. marina sublineage of the N. oligotropha lineage, whereas another two clones formed a cluster with Nitrosomonas sp. Nm143 of the Nitrosomonas sp. Nm143 lineage with high Bayesian posterior probabilities support. Two clones formed a separate cluster from those of the other Nitrosomonas lineages. Our results demonstrated the importance of effective utilization of nitrifying bacteria in aquaculture, since number of these bacteria did not vary for the duration of the experiment.