Characterization of microbiomes and Planctomycete diversity in large-scale aquaria habitats

In commercial large-scale aquaria, microorganisms capable of transforming toxic nitrogen species into more benign species play important roles in system health. Many microbes convert nitrite and ammonium into nitrate via nitrification. However, nitrate is toxic to macrofauna at high concentrations. Some bacteria within the phylum Planctomycetes transform ammonium and nitrite to nitrogen gas via anaerobic ammonium oxidation (anammox). Here, we characterized microbial communities in four habitats at the Tennessee Aquarium and examined the abundance and anammox potential of Planctomycetes using culture-independent approaches. 16S rRNA gene amplicon sequencing of habitats revealed distinct, yet stable, microbial communities and the presence of Planctomycetes (~1-15% of each community). Metagenomic analyses identified the genetic potential for multiple complete nitrogen metabolism pathways. However, no known genes diagnostic of the anammox reaction were found in this survey. Given the low relative abundance of these bacteria, a nested Planctomycete-specific 16S rRNA gene-based PCR approach was used to (i) enrich amplicons representative of group members and (ii) identify anammox bacteria based on diagnostic genetic signatures. This amplicon enrichment identified highly diverse sequences that share <95% 16S rRNA gene sequence identity to cultured Planctomycetes, revealing an opportunity to study novel strains within this phylum. These data indicate that putative anammox organisms are present within these exhibits, but further study is required to confirm their capability to perform the anammox reaction.