PhD student position in the application of high-throughput sequencing DNA tools (metabarcoding) in aquatic ecology, announced jointly by the Centre for Climate Change (C3) at the University Rovira i Virgili (URV) and the Marine and Continental Waters Program of the Institute for Food and Agricultural Research Technology (IRTA) in Sant Carles de la Ràpita (Spain).
Ref of the PhD position: 2018PMF-PIPF-22
Topic: Diatom metabarcoding: developing new tools for bioassessment of aquatic ecosystems
Deadline for application: 28th November 2018
Aquatic ecosystems are essential to planetary function and to humans and hence their protection and restoration are of vital importance. The Water Framework Directive and Marine Strategy Framework Directive were adopted by the EU more than 10 years ago to ensure good functioning of water bodies in terms of biological communities and hydrological and chemical characteristics. Diatoms and plankton are among the principal biological indicators used to monitor waters for these directives and, until now, they have been assessed through microscope-based assessments of communities. This thesis project aims to develop innovative alternatives to microscope-based assessments, using high-throughput sequencing (HTS) and DNA metabarcoding. This will include (1) understanding how methodological and biological parameters affect the relationship between DNA reads (from HTS) and cell numbers, (2) developing DNA reference databases, (3) developing appropriate bioinformatics pipelines for converting HTS reads into ecological assessments, and (4) refining knowledge about the relationship between species occurrences and ecological factors in particular critical cases (to test current assumptions about species’ ecology). To do this, the candidate will assemble and use matched sets of HTS data, microscope-based diatom counts, and physico-chemical data. As well as providing the basis for new biomonitoring systems, the project may provide novel data on the biogeography of microalgae and protists, touching on general questions of dispersal and differentiation in populations of microscopic organisms. Initially, the focus will be on diatom biomonitoring of Catalan rivers, but the project may extend into coastal habitats and include the opportunity to develop new methods of detecting pathogenic or toxic species and to analyse the ‘hidden’ diversity of previously unrecognized or unidentifiable organisms.
The candidate must have a degree in biology or related disciplines. Preference will be given to candidates familiar with bioinformatics tools for the analysis of DNA sequence data or practical experience in molecular techniques such as DNA extraction, PCR and DNA sequencing. Good analytical skills will be an advantage, and some knowledge of algae, including diatoms, would be helpful though not essential. Knowledge of R would also be an asset. Good communication skills in written and spoken English are necessary. Applicants should note that the research activities will take place at the IRTA centre in Sant Carles de la Ràpita (under the supervision of Dr. Rosa Trobajo and Dr. David G. Mann) but that the PhD student will work in close collaboration with other labs working on similar projects, both in Spain and internationally.
We offer: 3-year contract within URV
Foreseen starting date: End January 2019
Details of the call:
In “Conditions of the competition” the regulatory bases of the program are given. In “List of grants offered” all the scholarships offered in this call are listed and, the reference of the PhD on diatom metabarcoding is 2018PMF-PIPF-22. In “Application form” is where you can apply.
Details of the qualifications and documentation required can be found at:
Note that In addition to the documentation listed there, candidates should also include a letter of intent/motivation
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