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Metagenomics for the bioassessment of water bodies using mesocosms experiments

  • Full or part time
  • Application Deadline
    Sunday, March 10, 2019
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

About This PhD Project

Project Description

Co-supervisor: Dr Roger Van-Egmond, Unilever

This is a fantastic opportunity to apply cutting-edge DNA technologies, outdoor experiments and bioinformatics to advance our knowledge of the effects of pollution to freshwater ecosystems.

The project is co-funded by BBSRC and Unilever. It is mainly based at the Silwood Park Campus of Imperial College London, but will involve working visits at the Colworth Science Park of Unilever.

Start date: October 2019 (for 4 years)
More information can be found here:
http://www.imperial.ac.uk/people/v.savolainen
http://www.imperial.ac.uk/ecosystems-and-environment

Water bodies and their resident biodiversity are at risk from contaminants, disease agents, biological invasions and abiotic stressors. In the European Union, the Water Framework Directive is designed to provide the means to assess, monitor and manage water bodies in order to ensure safety, economic and natural resources sustainability. Traditionally, biological quality is assessed by obtaining abundance and diversity measures of existing communities using morphological methods. There is the need for conventional approaches to be supplemented with new technologies as they are time- consuming, sometimes lacking accuracy and needing extensive taxonomic expertise. Here, we propose to explore new approaches for the assessment of water bodies, which benefit from the latest development in (eco)metagenomics, bioinformatic and chemical biology. Recent molecular advances, including the use of environmental DNA (eDNA) extracted from the water column, is revolutionizing this field, by generating novel high through- put data that could enable us to track and describe focal species as well as the wider food web within which they are embedded, and how they respond to external changes.

The student will advance eDNA and metagenomic approaches using mesocosms available at Imperial College. Mesocosm-based approaches are increasingly being recognized as spanning the critical gap between field observations and lab experiments, by offering realistic levels of biocomplexity, whilst also affording a degree of control and replication of experimental conditions. The student will assemble artificial communities in the mesocosms and evolve how eDNA metabarcoding can recover presence and abundance of those organisms, employing cutting-edge molecular computational methods to better exploit metagenomic data and derive maximum value. Subsequently the student will test how eDNA can be used to uncover the impact that a range of chemical stressors may have on these artificial communities.

Student Eligibility

The standard BBSRC residency and Imperial College eligibility criteria still apply. Besides a BSc at 2:1 or better, the student should hold, or expect to obtain, a Masters degree (at Merit level or better). However, outstanding candidates without a Masters may be considered.

If you are interested, please send a full CV, letter of motivation and names of 2 referees to no later than 10 March 2019

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