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PhD fellow in bacteriophage-mediated regulation of the phyllosphere microbiome

Københavns Universitet (KU)

The Environmental Microbial Genomics (EMG) group at the Department of Plant and Environmental Science (PLEN), Section for Microbial Ecology and Biotechnology at the University of Copenhagen is offering a PhD scholarship in bacteriophage biocontrol of the phyllosphere microbiome starting June 1st, 2021 or as soon as possible thereafter.

Description of the scientific environment
The EMG group uses sequence-based analyses to describe genomic traits of keystone species and their prevalence and impact in natural and artificial microbial communities and metagenomes, including information on bacteriophages and how other mobile genetic elements shape microbial evolution and traits. Group activities span microbes in both natural, agricultural and health related systems. Several projects on bacteriophage biology, ecology and host interactions are currently running in the group. More information on the research group can be found on https://plen.ku.dk/english/research/microbial-ecology-and-biotechnology/environmental-microbial-genomics/.

Project description
The position is advertised in connection to a newly established multidisciplinary program, The MATRIX: “Microbiome Assisted Triticum Resilience In X-dimensions”, funded by the Novo Nordisk Foundation. Overall, the program addresses the taxonomic diversity and functional potential of the wheat phyllosphere microbiome. Today, more than one third of crop yields are lost due to abiotic and biotic stress factors, such as drought, salinity, pests and disease. In the MATRIX program several key microorganisms and regulatory mechanisms involved in wheat growth promotion and protection against biotic and abiotic stresses will be identified. By combining new microbiome-assisted approaches with machine learning and predictive modelling the MATRIX aims to quantitate and predict microbiome-mediated changes and their effect on wheat resilience and productivity under various climate change scenarios, which can be used as a novel tool to improve future wheat yield management strategies. More information on the MATRIX project is linked at https://plen.ku.dk/english/research/microbial-ecology-and-biotechnology/environmental-microbial-genomics/microbiome-assisted-triticum-resilience-in-x-dimensions-the-matrix/.

The PhD candidate will conduct independent research related to the role of bacteriophages (phages) in regulating e.g. pathogens associated with the wheat phyllosphere. In particular, the PhD candidate is expected to isolate and characterize phages against key microorganisms (pathogenic as well as beneficial) from the wheat flag leaf. A well characterised biobank of isolated phages targeting various key organisms of the wheat phyllosphere microbiome will be used by the student in planta not only to control the prevalence of pathogens, but also to manipulate the microbial composition to mediate adaptation and stimulation of wheat health. The project will be conducted in close collaboration with a postdoc and a PhD fellow, who both are involved in bacteriophage bioinformatics in the group.


  • Candidates must have a MSc in biology, biotechnology, microbiology or a similar degree from other relevant research fields
  • Experience working in a microbiological laboratory is required
  • Experience with bacteriophage isolation and other standard bacteriophage-related techniques is expected
  • Experience working with plant pathogens is an advantage but not a requirement
  • Knowledge of phage therapy and/or phage biocontrol is preferred
  • Relevant scientific publications in reputable journals is advantageous, but not a requirement

Inquiries about the position can be made to Principal Supervisor: Prof. Lars Hestbjerg Hansen, Department of Plant and Environmental Science. E-mail: lhha@plen.ku.dk. Phone: +45 28752053.

Job description
The position is available for a 3-year period and your key tasks as a PhD student at SCIENCE are:

  • To manage and carry through your research project
  • Attend PhD courses
  • Write scientific articles and your PhD thesis
  • Report the findings to relevant stakeholders
  • Teach and disseminate your research
  • To stay at an external research institution for a few months, preferably abroad
  • Work for the Department

Terms of employment
The position is covered by the Memorandum on Job Structure for Academic Staff.

Terms of appointment and payment accord to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State.

The starting salary is currently at a minimum DKK 330,817 (approx. €44,108) including annual supplement (+ pension at a minimum DKK 53,761). Negotiation for salary supplement is possible.

Application Procedure
The application, in English, must be submitted electronically by clicking APPLY NOW below.

Please include

  • Cover Letter, stating which PhD project you are applying for and detailing your motivation and background for applying for the specific PhD project
  • Curriculum vitae
  • Diplomas and transcripts of records (BSc and MSc)
  • Other items for considerations, e.g. list of publications (if any)
  • 1-3 reference letters (if any)

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

The deadline for applications is March 18th 2021, 23:59 GMT +1.
After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Interview Committee.

You can read about the recruitment process athttps://employment.ku.dk/faculty/recruitment-process/.
General information about PhD programmes at SCIENCE is available at https://www.science.ku.dk/phd.

Interviews will be held in April 2021.

Københavns Universitet giver sine knap 10.000 medarbejdere muligheder for at udnytte deres talent fuldt ud i et ambitiøst, uformelt miljø. Vi sikrer traditionsrige og moderne rammer om uddannelser og fri forskning på højt internationalt niveau. Vi søger svar og løsninger på fælles problemer og gør ny viden tilgængelig og nyttig for andre.

Lars Hestbjerg Hansen
E-mail: lhha@plen.ku.dk

Ansøgningsfrist: 18-03-2021

Ansættelsesdato: 01-06-2021

Arbejdstid: Fuldtid

Afdeling/Sted: Department of Plant and Environmental Sciences

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