Microbial – deposit feeder aquaculture bioremediation systems

Research output: ThesisDoctoral Thesis (not awarded by UHI)


Land-based intensive aquaculture produces large volumes of particulate organic waste that can be upcycled into high value secondary biomass. In this research, the application of two key principles underpinning low-cost bioremediation technologies, namely the addition of rate limiting (i) electron acceptors (oxygen), and (ii) donors (carbon) is investigated in a sediment-based aquaculture effluent treatment system integrating the sea cucumber, Holothuria scabra. Growth trials of H. scabra, combined with next generation sequencing (NGS) technologies, were used to examine the response of sea cucumbers and sediment bacterial communities under contrasting redox regimes, describing fully oxic and redox-stratified sediments. The oxic system resulted in high taxonomic and functional diversity of bacteria with a range of dissimilatory metabolisms required for successful bioremediation of aquaculture wastes; however, the final biomass of H. scabra was significantly lower than the redox-stratified sediments (449.22 ± 14.24 g m-2 versus 626.89 ± 35.44 g m-2). Improving the resource quality of aquaculture waste through carbon supplementation was investigated. Increasing the carbon/nitrogen ratio from 5:1 to 20:1 with soluble starch significantly increased the biomass production of H. scabra compared to controls (1011.46 ± 75.58 g m-2 versus 702.12 ± 35.93 g m-2). A benthic flux incubation study, combined with NGS, demonstrated that carbon supplementation did not change the pathway of nitrogen cycling by mediating a shift from net release of ammonium to net assimilation, as hypothesised. A final study elucidated the critical role of the sea cucumber microbiome during aquaculture waste bioremediation, demonstrating that endogenous bacteria are primed, at ecological and genomic levels, to respond to nitrogen - a key nutrient limiting deposit feeder growth. Deposit feeder–microbial aquaculture bioremediation systems have the potential to rectify current inefficiencies of nitrogen use in the aquaculture production chain by offering a more economically and environmentally sustainable alternative to closing the nitrogen cycle loop.
Original languageEnglish
Awarding Institution
  • Newcastle University, United Kingdom
Award date21 Mar 2017
Place of PublicationNewcastle
Publication statusPublished - 2017


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