Sediment microbial community analysis: Establishing impacts of aquaculture on a tropical mangrove ecosystem

The impact of organic loading from a tropical finfish cage farm was investigated by comparing the microbial community in surface sediments (0–8.5 cm) at sites under fish cages and on a gradient away from the farm lease area. Both total bacteria and Vibrio sp., enumerated by epifluorescence microscopy and TCBS plate counts respectively, were more abundant at cage sites than at the control sites away from the cages. Total bacteria ranged from 1.1 × 10 7 cells g WW − 1 at cage sites to 1.9 × 10 6 cells g WW − 1 at sites away from the cages and Vibrio sp. abundance ranged from 1.6 × 10 5 CFU g WW − 1 at cage sites to 5.3 × 10 2 CFU g WW − 1 at sites away from the cages. Bacterial 16S rRNA gene clone libraries demonstrated highly diverse microbial communities with similar patterns at the phyla and sub-class affiliation level for sites under the cages and sites away from the cages. However, small shifts in relative abundance of 16S rRNA gene sequences of key microbial groups were observed for sites under the cages. For example, 16S rRNA sequences related to ε-Proteobacteria and Vibrio sp. were present at cage sites and absent at sites away from the cages. In addition, a higher relative abundance of sequences related to the δ-Proteobacteria were observed at cage sites compared to sites away from the cages. This study is the first to investigate impacts of finfish cage aquaculture on the microbial community of sediments under fish cages in tropical marine ecosystems and demonstrates that changes in microbial abundance and shifts in sedimentary bacterial communities may be potentially useful indicators of organic perturbations in these environments.