Assessing benthic recovery following cessation of salmon farming using eDNA metabarcoding (ABReDNA)

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Salmon farming enriches local sediments with organic matter (OM) to an extent that depends on the local hydrodynamic regime, site characteristics and hosted fish biomass. The OM accumulation/bacterial assimilation drives changes in the macrobenthos and these changes are used as indicators in regulatory-compliance assessment for active farm sites. Most licensed sites are still in production and there is currently little information on the dynamics of sediment recovery following cessation of farming. The student will join an international team developing the eDNA approach to ecosystem monitoring, specifically focussed on aquaculture. This PhD student, with CASE collaborators SEPA, will make a substantial contribution to our current knowledge focussing on two main areas: 1. Sources of variability in metabarcoding data, including 'laboratory' and PCR effects. The student will conduct a variance analysis to put lab-effects (e.g. PCR) into context by comparing PCR results, from the same samples, as prepared in different laboratories. 2. Similarities between eDNA- and macrobenthic recovery. Using macrobenthic-validated metabarcoding approaches to track benthic recovery at a fish-farm site, the student will assess how bacterial assemblages change, over time, and will map these changes onto macrobenthic changes to assess differences between the two approaches.