Freshwater fish are amongst the most highly threatened animals with fish stocks in global decline. Around 95% of the rivers in Wales are now categorised at risk for salmonids, with most salmon stocks in England and Wales in a highly depleted state. In parallel aquaculture, a diverse industry, is the fastest growing food sector. Both natural and farmed environments face multiple challenges from global warming that include increased infection rates and multi-resistant drug pathogens. Recently, the Environment Agency reported that only 14% of rivers and lakes in England and Wales have good ecological status. Both treated effluent discharges and sewage overflows into the environment have contributed to chemical (including antibiotics) and faecal contamination of the environment. Antibiotics used widely to fight infection in terrestrial and aquatic farms are also often used indiscriminately and in unsustainable quantities. Unsurprisingly, aquafarms now face a dramatic increase in fish antibiotic resistance that is exacerbated by climate warming that promotes increased susceptibility to infection. In the UK, increasingly river conditions exceed the optimal temperatures for salmonids (10-15°C) for more than 30% of the year, which contributes to significant fish disease outbreaks. Surprisingly though the impact of bacterial fish pathogens and the physiopathology of such infections are still poorly understood, and few preventative or curative treatments are available.
Out of all disease-causing pathogens found in fish, the most common are bacterial (Bricknell 2017). Genera commonly associated with disease in fish are Vibrio, Aeromonas and Edwardsiella (Colwell and Grimes 1984; Hirai et al. 2015; Chen et al. 2019). Edwardsiella spp. are well-recognised fish pathogens, particularly E. tarda, E. piscicida, E. anguillarum and E. ictalurid, infecting a wild range of freshwater species from salmonids to catfish, but their impact is largely unknown. In fish, Edwardsiellosis - the disease caused by Edwardsiella species - is usually linked with poor water quality, high organic content and high water temperature (Woo and Bruno 2010).
This studentship will investigate the burden of bacterial pathogens in freshwater fish stocks and identify conditions optimal for infection in order to identify risk factors for future emergence of fish pathogens and understand what is required to prevent the disease. Pilot work (2021) has already identified Edwardsiella spp. present at multiple sites on the River Usk, Newport. The project is divided into three aims based on the expertise of the supervisors; the student can select to work on all of these or specialise according to their own interests.
Project Aims and Methods
The aim of this studentship is to quantify the scale and diversity of the bacterial challenge facing freshwater fish stocks. It will assess the impact of infection on wild fish populations (AIM-1) at sites above and below sewage outlets (along the Ogmore and Usk rivers). Using bacteria from the genus Edwardsiella as model organisms, we will assess how abiotic and biotic stressors impact infection (AIM-2) and examine the physiological mechanism underlying increased susceptibility or resistance of fish to infection (AIM-3).
1) IDENTIFICATION OF FISH BACTERIAL PATHOGENS ON FISHERIES AND THE SURROUNDING ENVIRONMENT. Faecal microbiota and necropsy of freshly dead fish will be performed. Biopsies from different tissues will be taken to identify bacterial pathogens using general microbiology techniques and deep sequencing (Dr Berger). Virulence factors and antimicrobial resistance will be assessed using the bioinformatic pipelines established across the partner laboratories. In addition, water samples will be collected to assess the environmental microbiome to identify the range of bacterial pathogens present over time (taking into consideration season and water temperature). Abiotic data will be obtained from Natural Resources Wales and the Environment Agency.
2) IMPACT OF ABIOTIC AND BIOTIC STRESSORS. The student will establish an infection system using rainbow trout in our aquarium as a model organism for studying Edwardsiella spp. (Prof. Cable). We will assess the impact of temperature (to mimic predicted climate warming) alone and in combination with other physicochemical factors, for example phosphorus or dissolved organic carbon, on fish susceptibility to Edwardsiella infection. Using genetically modified bacteria expressing the Green Fluorescence Protein, the student will track the progression of bacterial infections in fish using microscopy techniques.
3) HOST STRESS RESPONSE MECHANISM. Edwardsiella spp. infection requires displacement of both the gut and gills microbiota and expression of virulence factors for the pathogen to invade the host. The student will assess the impact of abiotic and biotic stressors (samples from AIM 2) on the pathogen using transcriptome analysis and on the bacterial microbiota by 16S sequencing. Finally, the student may want to undertake transcriptome profiling of rainbow trout exposed to one of the most important stressors previously observed (AIM 2) to identify the molecular mechanisms underlying the regulation of stress responses.
Candidate requirements
The student will have a biologically-related BSc, and ideally a relevant Masters degree with some practical experience. They will have a strong interest in microbiology, infectious diseases, fish biology and/or quantitative biology. A current UK driver’s licence would be useful for fieldwork.
Candidates must meet Cardiff University's PhD entry requirements (see 'Institution Website' for details).
Project partners
All three supervisors are part of Antimicrobial Resistance Research Cymru and the GW4 AMR network (led by Cardiff University), and the Microbiome Network (led by Imperial College London) who aim to integrate resource and analysis pipeline for AMR and microbiome. The student will have availability to informatic approaches from supervisor-led research projects with Cefas and WorldFish that investigate relationships between fish microbiomes, health and AMR. Advice and samples will also be provided through collaboration with the Environment Agency, Natural Resources Wales, Cefas and local Angling Associations.
Training
The student will interact with stakeholders to understand the challenges associated with disease management in both wild and farmed fish stocks. They will be trained in fish physiology, host-pathogen interaction and bioinformatics, and have the opportunity to gain expertise in a number of techniques (including fieldwork, microscopy, cell culture, transcriptome and next-generation sequencing, microbiome, molecular and cellular biology, and R-statistics). Working with vertebrates, the student will be required to undergo Home Office training; all other licences are in place for this project to begin immediately.
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