Comparison of bacterial communities in fish farm sediments along an organic enrichment gradient

Aquaculture is of major industrial importance world wide and this has led to concerns over the impact of fish farming on previously pristine marine environments. Fish farm sediments receive a large amount of organic matter due to uneaten food and fecal materials. This organic enrichment of sediment influences the biogeochemical process and benthic microbial communities. This study was performed to investigate the effect of pollution from marine fish farms on the bacterial community structure in the underlying sediments. Sediment samples were collected at four stations along an organic enrichment gradient on the coast of Wakasa Bay in southern Fukui Prefecture, Japan between April 2004 and December 2006. Sagami Bay sediments were also used as a non-fish farming reference site. The bacterial community composition was assessed using PCR amplification, cloning, sequencing, and phylogenetic analysis of 16S rDNA using directly extracted sediment DNA. Most of the clones sequenced fell into six major lineages of the domain Bacteria: γ-, δ-, ε-Proteobacteria, Acidobacteria/Holophaga, Bacteroidetes, and Planctomycetes. Although there were no significant differences in the bacterial community structures among the sediment samples except for Sagami Bay, a minor change in the composition of 16S rDNA operational taxonomy units (OTUs) between sites was recognized. 16S rDNA sequences related to the γ-Proteobacteria were recovered with relatively higher frequencies from unpolluted sediments than from polluted sediments. In contrast, the most abundant clone sequences from polluted sediment samples were grouped with δ-Proteobacteria. Our data suggests organic enrichment of sediment may influence the composition of bacterial communities; and the δ-Proteobacteria were found and selected for within polluted fish farm sediments.