PhD fellow in Plant-microbiome assembly

The Department of Biology, Faculty of Science at University of Copenhagen (UCPH) is seeking to hire an enthusiastic and talented PhD fellow to study social interactions in the plant root microbiome, commencing December 1st 2022, or as soon as possible thereafter. 

Description of the scientific environment
The PhD student will be part of Section of Microbiology, headed by Prof. Søren J. Sørensen. His research group focuses on social interactions in microbial populations in in-vivo systems such as soils, plants, animals and humans. The section houses state of the art culture-independent experimental infrastructure that enables us to examine how microbes interact at a scale that is relevant for such small organisms and study the roles of the individual species in these interactions. To do so we use techniques such as high throughput sequencing, flow cytometry, ultra-high resolution bioimaging, confocal microscopy and microbial reporter systems.

The group is a part of Department of Biology, Faculty of SCIENCE, University of Copenhagen. We are located in Copenhagen.

Project description
Novel strategies for eco-friendly and sustainable food production seek to explore and exploit the potential of the plant-microbiome to promote growth, acquire nutrients and induce resistance against pests and pathogens.  Yet, we lack a fundamental understanding of the ecological factors controlling the establishment of a beneficial plant-microbiome. Hence, we seek to test the ecological and evolutionary role of microbe-microbe interaction in the assembly and maturation of complex plant root microbiomes. The project is part of the research project “Underground Networking – Social interactions in the Plant Root Microbiome (UNICOM)”, which is financed by the Independent Research Fund, Denmark.

This project investigates the role of microbial interactions as key drivers for microbiome composition and activity, specifically focussing on interspecies cooperation/competition and the resulting priority effects. We work with the overarching hypothesis that microbial communities are composed of collaboromes, rather than independent species, that are characterized by being microscale focal points of interdependent bacteria showing essential microbe-microbe interactions. The emergent properties of these collaboromes present many beneficial consequences for plant growth and health.

The experimental design of this project goes beyond simple co-occurrence in bulk microbiome samples. Instead, it focusses on co-occurrence network analysis on microscale samples, which is complemented with detailed co-localization analyses to identify putative interactions. Finally, selected identified putative interactions are experimentally validated in simple microcosm experiments. 

Principal supervisor isProfessorSøren J. Sørensen ([email protected] ), Section of Microbiology, Department of Biology.The student will be co-supervised by Dr. Tanvi Taparia ([email protected] ). As part of the project, the PhD student will also have the opportunity to collaborate with the group of Prof. Tadashi Fukami at Stanford University and Prof. Laurent Philippot, INRA Center in Dijon. 

The PhD programme
A three year full-time study within the framework of the regular PhD programme (5+3 scheme), if you already have an education equivalent to a relevant Danish master’s degree.

Qualifications needed for the regular programme
To be eligible for the regular PhD programme, you must have completed a degree programme, equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project, e.g. (cell) biology, molecular biomedicine, biochemistry, nanoscience, or human biology. For information of eligibility of completed programmes, see General assessments for specific countries and Assessment database .

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 for approximately 35 ECTS.
• Write scientific articles and your PhD thesis
• Teach and disseminate your research
• To stay at an external research institution for a few months, preferably abroad
• Work for the Department

Formal requirements
We are seeking a highly motivated and ambitious individual with good interpersonal and communication skills. Highly desired candidates will have a solid theoretical background of plant-microbiome interactions. As well as practical experience with techniques in microbiology and molecular biology. A strong interest in bioinformatics and/or bioimaging is also considered advantageous. 

Applicants should hold an MSc degree in Plant-Biology, Microbiology, Bioinformatics, Biochemistry, Biotechnology or similar with good results and good English skills. As criteria for the assessment of your qualification’s emphasis will also be laid on previous publications (if any) and relevant work experience. The MSc degree has to be awarded prior to the employment date.

Nice-to-have qualifications

• Experience with plants experimental work, including cultivation, maintenance and site specific sampling of microbial communities in the rhizosphere; rhizoplan and endosphere.
• Experience with any or all of the following methodology: FISH detection in combination with CLSM microscope imaging and FACS analyses, molecular cloning, preparation of sequencing libraries (Illumina, PacBio, ONT), analysis of sequencing data.

Terms of employment
Employment as PhD fellow is full time and for maximum 3 years.

Employment is conditional upon your successful enrolment as a PhD student at the PhD School at the Faculty of SCIENCE, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

Terms of appointment and payment accord to the agreement between the Danish Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. The position is covered by the Protocol on Job Structure.

Application Procedure
Your application including all attachments must be in English and submitted electronically by clicking APPLY NOW below

Please include 

• Cover Letter, detailing your motivation and background for this project.
• Curriculum vitae
• Original diplomas for Bachelor of Science or Master of Science and transcript of records in the original language, including an authorized English translation if issued in another language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted.
• Other information for consideration, e.g. scientific 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 applicationsis 21 August 2022, 23:59 GMT+2. 

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After deadline, a number of applicants will be selected for academic assessment by an unbiased expert assessor. You are notified, whether you will be passed for assessment.

The assessor will assess the qualifications and experience of the shortlisted applicants with respect to the above mentioned research area, techniques, skills and other requirements. The assessor will conclude whether each applicant is qualified and, if so, for which of the two models. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/ .

Questions
For specific information about the PhD fellowship, please contact the principal supervisor.

General information about PhD study at the Faculty of SCIENCE is available at the PhD School’s website: https://www.science.ku.dk/phd/ .

The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position. 

Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.