Metagenomic analysis shows diverse, distinct bacterial communities in biofilters among different marine recirculating aquaculture systems

While biofilters are widely used to metabolize ammonia and other metabolic waste products in recirculating aquaculture systems, their microbial communities are not thoroughly characterized. While inroads have been made characterizing microbial communities within single biofilters, replicated comparisons across biofilters and facilities have been lacking. We hypothesized that microbial communities might differ among filter types and facilities. We characterized and compared the bacterial communities of nine nitrification biofilters in five commercial recirculating marine aquaculture operations by amplifying and sequencing the 16S rRNA gene using the Illumina-MiSeq DNA sequencing platform. Our results demonstrated the usefulness of the approach for elucidating bacterial community structure in aquaculture biofilters; among almost 249,000 usable DNA sequence reads-a mean of 27,663 for each biofilter-we detected a mean of 682 operational taxonomic units. Higher species diversity was observed in the submerged biofilters at farms 3 and 4 (HF_SB1, HF_SB2, HF_SB3, MB_SB1, MB_SB2, and MB_SB3), and a bead filter at farm 2 (XYF-MBBR) than in a bead filter at farm 1 (DF_MBBR) and a fluidized sand filter at farm 5 (TY_FSF). At the phylum level, Proteobacteria were the most frequently observed taxa (representing 36-50 % of reads in the overall data set for a given filter); other frequently observed phyla were Bacteroidetes (13-34 %), Chloroflexi (2-23 %), Nitrospirae (1-7 %), Planctomycetes (1-4 %), and Actinobacteria (2-5 %). However, in fluidized sand filters, after Proteobacteria, the subdominant phyla were Bacteroidetes (19 %), Nitrospirae (17 %), and Planctomycetes (11 %). At the genus level, the nitrite-oxidizing genus Nitrospira was frequently observed in sand filter TY_FSF (16.4 %), bead filter DF_MBBR (7.6 %), submerged biofilter MB_SB1 (7 %), and bead filter XHF_MBBR (7.36), and less frequently in submerged biofilters HF_SB3 (1.94), HF_SB2 (1.77 %), and HF_SB1 (1.63 %), and bead filters MB_SB2 (0.8 %) and MB_SB1 (0.2 %). Observations of the ammonia-oxidizing genus Nitrosomonas varied widely within and among filter types, ranging from 0.06 % in submerged bed filter HF_SB3 to 2.82 % in bead filter DF_MBBR. Principal components and cluster analyses classified the bacterial communities in the nine biofilters into groups corresponding to the respective recirculating marine aquaculture operations and the associated filter types.