Development of DNA-based metagenomic methodologies for seabed monitoring and aquaculture management
The project aims to develop a reliable, near real-time method of classifying seabed quality against environmental standards to ensure compliance with regulations.
Salmon farms are required to demonstrate that they meet environmental standards underneath and around their fish-cages as part of their SEPA consent conditions. The major part of compliance monitoring is achieved by taking samples from the seabed, identifying the animals and drawing conclusions on the status of the seabed based on the faunal assemblage structure. This approach is expensive, time consuming and requires considerable taxonomic expertise. We aim to revolutionise this approach by extracting DNA from the sediment and using a DNA sequencer (a ‘next generation sequencer’, NGS) to identify those organisms present. The NGS approach will be cheaper and faster.
Here we propose to (i) develop a protocol for sample collection which results in highly reproducible NGS outputs and then (ii) identify a range of NGS-identified species or groups which are able to classify sediments in the same way as the traditional macrobenthic approach. We will do this by (i) assessing and minimising variance in NGS-output occurring at the scale of the grab and as a consequence of the NGS process itself and (ii) visualise similarities and differences between NGS- and traditional macrobenthic-assemblages, as a function of environmental drivers, and then use statistical models to best align the results from the two approaches.
The potential for the NGS approach has been identified by both the salmon-farming industry and the regulator (SEPA) and has been explicitly supported by the SAIC board. Our long-term vision is to develop protocols for sampling, sample preparation, NGS and data analysis to deliver an intellectual product that ensures that salmon farm continue to meet consenting conditions and that Scotland meets its requirements under the Water Framework Directive. This collaboration, which maintains and expands existing partnerships, links industry (Marine Harvest (Scotland)) and the regulator (SEPA) with academics that specialise in aquaculture management (SAMS) and genomics (The Rivers and Loch Institute). This multi-sector, cross-disciplinary team is uniquely placed to develop and apply this NGS technology. Preliminary results are very encouraging (see Figure 1).
Figure 1: MDS plot confirming that samples taken from the same grab are very similar and that samples are very clearly discriminated on the basis of their bacterial community as determined using sequencing data. This plot is based on raw-sequence reads collated across bacterial family. The distances from the cage-edge are shown on the plot.
Role of SAMS
SAMS is leading and managing the project, collecting samples for analysis and working with UHI River and Lochs Institute to sequence the DNA. SAMS is leading on the bioinformatic and statistical analysis of the resultant sequence data.