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Deciphering microalgae - virus interactions

University of Exeter - College of Life and Environmental Sciences.

Qualification Type: PhD
Location: Exeter
Funding for: UK Students, EU Students
Funding amount: £15,609 per annum
Hours: Full Time
Placed On: 25th October 2021
Closes: 10th January 2022
Reference: 4295

Microalgae are an incredibly diverse and ubiquitous group of photosynthetic organisms which provide more than  half of the oxygen on Earth and are responsible for most of the primary production in oceanic and freshwater  ecosystems. Many model species are intensively studied in laboratories to shed light on fundamental scientific questions, and many more are used in biotechnology processes to produce a myriad of high valued compounds. 

The academic and applied interest in microalgae has driven the development of molecular tools and techniques for their genetic transformation. However, whilst synthetic biology-related tools have developed fast, the availability of suitable genetic elements is limited compared to well-established models such as E. coli, yeast, and mammalian cells. In the oceans, microalgae frequently interact  with viruses, viral infections impact species turnover, nutrient recycling, the fate of algalblooms, and the transfer of genetic information. The co-evolutionary arms race between viruses and bacteria has been intensively  investigated for a  long time and has, for example,  lead to the discovery of the CRISPR/Cas9 bacterial immune system. 

Despite their ecological and economic relevance, very little is known about  how  microalgae counteract viral infections. Although a wide range of microalgal laboratory cultures are available, we are yet to discover viruses for many of them. In this project, the PhD student will identify novel algal viruses and characterise host-virus interactions, with an emphasis on (1) the interaction between the virus and the cell membrane, (2) the microalgae physiological response at the cellular and  population  level, and (3) the identification of genetic elements from the virus (such as promoters, leading sequence, terminator) that may be used in synthetic biology applications. 

We aim to characterise newly isolated viruses (from our own isolations in project, and those available from collaborator’s collections) of key algal species to understand the microalgae-microalgae, microalgae-virus, virus-virus interactions during the infection process: Do microalgae have an immune - antiviral - system and if so, how does it impact viral infection? Furthermore, we expect that outputs from the above research questions - the discovery of new viruses, or the molecular compounds from an immune response - can have tremendous benefit and value for research and industry. 

The  environmental  sampling  of natural  seawater will be performed at PML’s Western Channel Observatory. Seawater samples will be filtered, fractionated and/or concentrated and used to infect selected microalgal strains under laboratory conditions. Infection experiments will be performed in controlled temperature  rooms in both solid and liquid media. When culture lysisis observed, potential viral particles will be characterised using techniques such as flow cytometry and genomics. In  parallel, we will characterise newly discovered and isolated viruses from key algal species, including diatoms. Infection experiments will then be reproduced for physiological studies: virus capsid structure and host-virus membrane interaction will be investigated by high-speed Atomic Force Microscopy; viral modulation of hosts’ gene expressions and metabolic pathways will be studied by metabolomics and transcriptomics.

For eligible successful applicants, the studentships comprise: 

  • A stipend for 3.5 years (currently £15,609 p.a. for 2022/23) in line with UK Research and Innovation rates
  • Payment of university tuition fees;
  • A research budget of £11,000 for an international conference, lab, field and research expenses;
  • A training budget of £3,250 for specialist training courses and expenses

Candidate requirements: 

We seek a highly motivated candidate with interests in molecular biology, bioinformatics, virology and marine sciences. 

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