Diversity of marine and brackish water nitrite-oxidizing consortia developed for activating nitrifying bioreactors in aquaculture

Nitrite is a well-known toxicant in aquaculture, produced as intermediate in nitrification. Two nitrite-oxidizing bacterial consortia, one from marine environment and the other from brackish water, were developed by enrichment technique at National Centre for Aquatic Animal Health, for removal of nitrite from recirculating aquaculture systems. In the present study, bacterial diversity of the consortia was assessed based on 16S ribosomal RNA and the functional gene analysis. Clone libraries of 16S ribosomal RNA gene and nitrite oxidoreductase A gene were constructed, and amplified ribosomal DNA restriction analysis was carried out to cluster the clones. Dendrograms generated through molecular characterization showed 29 and 27 clusters in marine and brackish water consortia, respectively. Phylogenetic analyses of representative clones from each cluster depicted profound diversity in the consortia consisting autotrophic nitrifiers belonging to Proteobacteria, anaerobic ammonia oxidizers, Actinobacteria, Bacteroidetes and heterotrophic denitrifiers. Functional gene analysis corroborated with the presence of specific nitrite oxidizers. Quantitative polymerase chain reaction showed the abundance of nitrite oxidizers in the order of 1.51 +/- 0.38 x 10(9)/g and 4.88 +/- 0.42 x 10(7)/g in marine and brackish water consortia, respectively. Diversity indices and pattern of distribution of organisms within the consortia were analyzed using Geneious, VITCOMIC, Mega 5 and Primer software. The marine nitriteoxidizing consortium showed higher Shannon-Wiener diversity and mean population diversity than brackish water consortium, suggesting that the former was having more diverse flora and higher potential to be used as startup cultures for activating nitrifying bioreactors subsequent to acclimatization to the required salinity.