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 
Project description: 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.
Requirements: 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
Deadline for application: 28th November 2018
For any doubt or further information, please contact:
Rosa Trobajo ( IRTA-Aquatic Ecosystems Ctra Poble Nou Km 
5.5 43540 Sant Carles de la Ràpita, Catalonia, Spain
Or Javier Sigró ( Centre for Climate Change (C3), Dept of 
Geography, University Rovira i Virgili (Tarragona) Avda Catalunya 35 43071 
Tarragona, Catalonia, Spain

Xavier Benito
Postdoctoral fellow
National Socio-Environmental Synthesis Center (SESYNC)
University of Maryland
Webpage <> | ResearchGate 
<> | ORCID 

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