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Online monitoring of microbial and algal communities with nexus to ecotoxicology

Timely developing and testing of real-time molecular diagnostic approaches along with use of flow-cytometry, confocal microscopy and SEM to profile algal and microbial communities in freshwater aquaculture.
It is envisaged that the operational aquaculture parameters will inform composition and stability of these important microbial/algal communities in addition to studies on the contributory role of microbes and algal (and metabolites) on commensurate process.
Next-generation studies will investigate development and assessment of bespoke ecotoxicological assays for aquaculture effluent in terms of putative relationship between discharge to receiving waters and environmental protection.
This thematic area will also inform development of disease mitigation technologies for pond and future RAS system.

Figure 1: Example of use of SEM for visualising microbial communities (x18,000 magnification)


An important objective of the ECOAQUA project is real-time monitoring of seasonal variations within the microbial communities of culture water. Whilst traditional methods involve total plate counts, only 1% of the bacterial species will grow via this method. Therefore more advanced techniques are required to obtain an accurate representation of both bacterial and algal variations in aquaculture waters over time. Denaturing gradient gel electrophoresis (DGGE) is a molecular biology approach which can be applied to monitor profiling of these communities based on the separation of DNA sequences, thereby generating a pattern of the microbial diversity that exists in fish farms. Each microbial and algal species present in the culture water will be represented by a particular band on the acrylamide gel. The bands can be excised from the gel and sequenced in order to identify each species present. Any variation in bands present over time is representative of a varying biological ecosystem over that time. A major advantage of this is the potential to visually observe the impact that treatments or interventions have on microbial diversity when introduced to aquaculture site.

Images above: DGGE gels showing bands of mixed populations
Image above: DGGE equipment