Uncultured bacterial diversity in a seawater recirculating aquaculture system revealed by 16S rRNA gene amplicon sequencing

J Microbiol. 2016 Apr;54(4):296-304. doi: 10.1007/s12275-016-5571-4. Epub 2016 Apr 1.


Bacterial diversity in a seawater recirculating aquaculture system (RAS) was investigated using 16S rRNA amplicon sequencing to understand the roles of bacterial communities in the system. The RAS was operated at nine different combinations of temperature (15°C, 20°C, and 25°C) and salinity (20‰, 25‰, and 32.5‰). Samples were collected from five or six RAS tanks (biofilters) for each condition. Fifty samples were analyzed. Proteobacteria and Bacteroidetes were most common (sum of both phyla: 67.2% to 99.4%) and were inversely proportional to each other. Bacteria that were present at an average of ≥ 1% included Actinobacteria (2.9%) Planctomycetes (2.0%), Nitrospirae (1.5%), and Acidobacteria (1.0%); they were preferentially present in packed bed biofilters, mesh biofilters, and maturation biofilters. The three biofilters showed higher diversity than other RAS tanks (aerated biofilters, floating bed biofilters, and fish tanks) from phylum to operational taxonomic unit (OTU) level. Samples were clustered into several groups based on the bacterial communities. Major taxonomic groups related to family Rhodobacteraceae and Flavobacteriaceae were distributed widely in the samples. Several taxonomic groups like [Saprospiraceae], Cytophagaceae, Octadecabacter, and Marivita showed a cluster-oriented distribution. Phaeobacter and Sediminicola-related reads were detected frequently and abundantly at low temperature. Nitrifying bacteria were detected frequently and abundantly in the three biofilters. Phylogenetic analysis of the nitrifying bacteria showed several similar OTUs were observed widely through the biofilters. The diverse bacterial communities and the minor taxonomic groups, except for Proteobacteria and Bacteroidetes, seemed to play important roles and seemed necessary for nitrifying activity in the RAS, especially in packed bed biofilters, mesh biofilters, and maturation biofilters.

Keywords: 16S rRNA gene; amplicon sequencing; bacterial diversity; biofilter; recirculating aquaculture system.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aquaculture / instrumentation*
  • Bacteria / classification*
  • Bacteria / genetics
  • Bacteria / isolation & purification*
  • Bacteroidetes / classification
  • Bacteroidetes / genetics
  • Bacteroidetes / isolation & purification
  • Biodiversity
  • DNA Barcoding, Taxonomic
  • DNA, Bacterial / genetics
  • Genes, rRNA
  • Nitrification
  • Phylogeny
  • Proteobacteria / classification
  • Proteobacteria / genetics
  • Proteobacteria / isolation & purification
  • RNA, Ribosomal, 16S / genetics
  • Seawater / microbiology*
  • Sequence Analysis, DNA*


  • DNA, Bacterial
  • RNA, Ribosomal, 16S