Comparison of sulphate-reducing bacterial communities in Japanese fish farm sediments with different levels of organic enrichment

Abstract

Fish farm sediments receive a large amount of organic matter from uneaten food and fecal material. This nutrient enrichment, or organic pollution, causes the accumulation of sulphide in the sediment from the action of sulphate-reducing bacteria (SRB). We investigated the effect of organic enrichment around coastal fish farms comparing the SRB community structure in these sediments. Sediment samples with different levels of organic pollution classified based upon the contents of acid-volatile sulphide and chemical oxygen demand were collected at three stations on the coast of western Japan. The SRB community composition was assessed using PCR amplification, cloning, sequencing and phylogenetic analysis of the dissimilatory sulphite reductase b-subunit gene (dsrB) fragments using directly extracted sediment DNA. Sequencing of the cloned PCR products of dsrB showed the existence of different SRB groups in the sediments. The majority of dsrB sequences were associated with the families Desulfobacteraceae and Desulfobulbaceae. Clones related to the phylum Firmicutes were also detected from all sediment samples. Statistical comparison of sequences revealed that community compositions of SRB from polluted sediments significantly differed from those of moderately polluted sediments and unpolluted sediments (LIBSHUFF, p<0.05), showing a different distribution of SRB in the fish farm sediments. There is evidence showing that the organic enrichment of sediments influences the composition of SRB communities in sediments at marine fish farms.

Fig. 1

Phylogenetic tree from the translated amino acid sequences of PCR-amplified dsrB genes retrieved from fish farm sediments along the coast of Japan. Environmental sequences determined in this study are shown in bold. Bootstrap values based on 1,000 replicates are shown for branches with more than 50% support. Scale bar corresponds to 5% estimated sequence divergence. Numbers in parentheses are the numbers of clones.

Fig. 2

Spatial distribution of dsrB clones in libraries from sediment samples collected at three fish farms

Fig. 3

Rarefaction curves generated for dsrB in clone libraries from samples collected at Gokasho A2 (circle), Shitaba S-7 (square) and Yatsushiro A (triangle).