Minimising the Impacts of Intensive Aquaculture in the face of Climate Change

Cluster Leader: Dr Sonia Consuegra, Swansea University

Aquaculture has become increasingly important for sustainably meeting global food demands. As extensive aquaculture is constrained by space and costs, the intensification of aquaculture will be required to meet this demand. Intensification of aquaculture means that farmed fish will have to thrive on less food, less space and less water – and in a setting of increasing temperatures due to climate change. Research is needed, therefore, to find solutions for the industry to: 1) reduce its ecological footprint, 2) improve fish domestication, 3) reduce the risks posed by parasites and diseases. In addition, aquatic routes, including aquaculture, are one of the most prominent ways for invasive species to spread. Research is urgently required to identify the most effective ways to detect and monitor aquatic invasives in order to prevent further spread and support effective eradication.

AquaWales aimed to bridge – for the first time – the genetic and environmental (epigenetic) components of fish domestication, as well as to develop new genetic-based methods to survey for invasive species.

Research activities:

  • Controlled experiments to compare gene expression patterns to investigate ways to improve fish resilience to crowding and infections (diseases and parasites).  Three contrasting fish species used in aquaculture were used (Nile tilapia (Oreochromis niloticus), Atlantic salmon (Salmo salar) and sea bass (Dicentrarchus labrax) and reared at different stocking densities, exposed to pathogens and temperature variations.
  • Developing novel environmental DNA (eDNA) based detection protocols to detect and map three major aquatic invasive species (AIS) in the UK: the American signal crayfish (Pacifastacus leniusculus) and its pathogen, the topmouth gudgeon (Pseudorasbora parva), and Chinese mitten crab (Eriocheir sinensis).

Key findings:

  • Discovery of a number of epigenetic markers for tilapia and Atlantic salmon that correspond to different rearing conditions and disease resistance in aquaculture.
  • The finding that environmental cues have a unique influence on the use of immune-related genes during a common fungal infection of captive fish.
  • The finding that there is a marked difference between the diversity and function of the microorganisms (microbiome) found in and on wild and captive Atlantic salmon; influenced by diet as well as artificial rearing conditions. Microbiomes could be manipulated to enhance targeted traits in captive fish and therefore improve their health.
  • Development of novel eDNA methods to successfully identify the invasive signal crayfish, the native white-clawed crayfish and their shared pathogen (causing crayfish plague). eDNA revealed the presence of invasive species in areas where previous eradication attempts had been undertaken and where the invasive was thought absent. Results also showed that areas of invasive and native crayfish co-existence are characterised by the absence of the pathogen, confirming results from other regions. This novel approach can now be used more widely to support conservation measures.
  • British populations of signal crayfish carrying crayfish plague are more genetically diverse than those free of the plague.
  • Signal crayfish genetic diversity in the UK is low; suggesting that populations are either still carrying ‘founder effects’ (where small-scale introductions limit genetic diversity), or have been heavily influenced by eradication measures, or both.

Publication highlights:

  • Uren Webster, T.M., Rodriguez-Barreto,D., Martin,  S.A., van Oosterhout, C., Orozco-ter Wengel, P.,   Hamilton, A.,   Cable, J.,  Garcia de Leaniz, C., S. Consuegra, S. (2018). Contrasting effects of acute and chronic stress on the transcriptome, epigenome, and immune response of Atlantic salmon. Epigenetics 13: 1191.
  • Robinson, C., Uren-Webster, T., Cable, J., James, J., Consuegra, S. (2018) Simultaneous detection of invasive signal crayfish, endangered white-clawed crayfish and the crayfish plague pathogen using environmental DNA. Biological Conservation 222: 241-252.
  • Pawluk, R.J., Uren Webster, T.M., Cable, J., Garcia de Leaniz, C., Consuegra, S. (2018). Immune-related transcriptional responses to parasitic infection in a naturally inbred fish: roles of genotype and individual variation. Genome Biology and Evolution 10: 319-327.

The AquaWales researchers included:                                                               

Swansea University

  • Sonia Consuegra                       
  • Carlos Garcia de Leaniz          
  • Tamsyn Uren-Webster            

Cardiff University

  • Jo Cable                                       
  • Pablo Orozco-ter Wengel        
  • Amy Ellison                                  

Aberystwyth University

  • Peter Brophy                  
  • Rebekah Weatherhead            

Natural Resources Wales

  • Peter Gough                                
  • Tristan Hatton-Ellis                    

Research Centre in Biodiversity and Genetic Resources (CIBIO), Portugal

  • Raquel Xavier

Industry and third party partners:

  • Jack James, PontusAqua                   
  • Brendan Gara, SkillFish
  • Dave Kilbey, Natural Apptitude
  • Eric Roderick, FishGen
  • Stephen Marsh-Smith, Wye & Usk Foundation
  • David Hall, Cardiff Harbour Authority

Please see the ‘NRN-LCEE Final Overview 2013-2019’  for further details of the Cluster’s research.