PhD scholarship in Engineering and phenotypic profiling of beneficial aquaculture microbiomes

We offer a PhD fellowship at the Department of Biotechnology and Biomedicine (DTU Bioengineering) at the Technical University of Denmark. The PhD project is part of the Horizon2020 EU project Marine Biodiversity as Sustainable Resource of Disease-Suppressive Microbes and Bioprotectants for Aquaculture and Crop Diseases (MARBLES) and will be carried out in the Bacterial Ecophysiology and Biotechnology (BEB) Group headed by Professor Lone Gram at DTU Bioengineering. The PhD student will also work closely with the Center for Microbial Secondary Metabolites, CeMiSt.

MARBLES will use both sequence- and cultivation-based approaches to access and exploit marine microbial biodiversity for sustainable bioprospecting to discover microbial consortia, pure cultures and bioactive molecules for application in aqua- and agriculture and in the clinic. MARBLES will test anti-pathogen effects of microbiomes from marine environments (algae, sponges, fish) to uncover the bioactive agents in disease-suppressive microbiomes. Also, MARBLES will explore host- and microbe-derived chemicals that elicit production of bioactive compounds, as elicitors to revitalise drug screening. The sustainable production of bioprotectants and biologics will increase the effectiveness of fish production - reducing the pressure on harvesting wild fish - and aid the transition of the crop agriculture sector towards bio-based and circular solutions. The MARBLES consortium comprises 14 European institutions and is led by Professor Gilles van Wezel, University of Leiden.

The BEB group at DTU is focused on using beneficial bacteria as biocontrol agents, probiotics or sources of novel compounds with the aim of controlling pathogens without antibiotics and producing compounds that can support industry and society in a green transition. We use a broad range of techniques spanning from classical culturing, over molecular genetics to state-of-the-art omics technologies. The group typically has 5-10 PhD students and postdocs and CeMiSt, a collaboration between three DTU departments, is based on 10 senior faculty and >15 PhD students and postdocs. The purpose of CeMiSt is to unravel the biological role of microbial secondary metabolites in natural microbiological communities.

We are seeking a candidate to explore and engineer advanced, disease suppressive aquaculture microbiomes to contribute to the overall aim of MARBLES. Microalgae are used a live feed in many aquacultures and you will obtain and characterize the diversity of microalgal microbiomes using both sequence-based and cultivation-based techniques. You will select and develop (high throughput) bioassays against relevant fish pathogens and create beneficial microalgal microbiomes that inhibit fish pathogens and enhance algal growth. You will be involved in a forefront PhD project on algal microbiomes, with strong international collaboration, a productive scientific environment, and a good work-life balance.

Responsibilities and qualifications
Your PhD project will contribute to sustainable development of both aquaculture and horticulture by providing microbiomes or pure bacterial cultures that facilitate algal growth and disease resistance with particular emphasis on establishing minimal, beneficial microbial consortia. You will use amplicon and metagenomic sequencing as well as cultivation-based approaches to track the composition of the engineered microbiomes. You will employ molecular techniques and flow cytometry to assess pathogen inhibition. You will isolate bacteria and re-create microbial consortia using both classical microbiology techniques and high throughput technologies and assess their effect in microalgal systems.

Your experience within the following areas of microbiology will be an advantage

• Marine microbiology and ecology (bacteria and algae)
• Molecular biology
• Sequence-based analyses of microbiomes
• Experience with R or Python

The project involves collaboration with other scientists in an inter-disciplinary and international research environment, so it is important that you have good communication skills in English and are interested in many aspects of science. You should be able to work independently and willing to contribute to a positive and inspirational work atmosphere.

Expected starting date: March 2022.

You must have a two-year master's degree (120 ECTS points) in molecular biology, biology, engineering or a similar degree with an academic level equivalent to a two-year master's degree.

Approval and Enrolment
The scholarship for the PhD degree is subject to academic approval, and the candidate will be enrolled in one of the general degree programmes at DTU. For information about our enrolment requirements and the general planning of the PhD study programme, please see the DTU PhD Guide .

Assessment
The assessment of the applicants will be made by Senior Scientist Eva Sonnenschein and Professor Lone Gram.

We offer
DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and an academic freedom tempered by responsibility.

Salary and appointment terms The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union. The period of employment is 3 years.

You can read more about career paths at DTU here .

Further information
Further information may be obtained from Professor Lone Gram or Senior Scientist Eva Sonnenschein at [email protected] or [email protected]  

Please do not send applications to this e-mail address; follow the electronic application and submission procedure as explained below.

You can read more about DTU Bioengineering on http://www.bioengineering.dtu.dk .

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark .

Application
Please submit your online application no later than 26 November 2021(Danish time).

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply online", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

• A letter motivating the application (cover letter)
  Please provide contact details for two referees in your motivation letter
• Curriculum vitae
• Grade transcripts and BSc/MSc diploma
• Excel sheet with translation of grades to the Danish grading system (see guidelines and Excel spreadsheet here )

Candidates may apply prior to ob­tai­ning their master's degree, but cannot begin before having received it.

All interested candidates irrespective of age, gender, race, disability, religion or ethnic background are encouraged to apply.

The Department of Biotechnology and Biomedicine (DTU Bioengineering) addresses challenges of societal and scientific importance within biotechnology, biomedicine, food technology and human health. The department is based on both basic and applied research and employs tools from biochemistry, biophysics, chemistry, cellular biology, immunology, microbial ecology and physiology, bioinformatics and bioengineering. Research is conducted within three main areas: Microbial ecology and physiology, Industrial biotechnology and cell factories, and Biomedicine and health. The department has extensive collaboration with national and international research units and industries. DTU Bioengineering has approx. 300 employees, of which 2/3 is scientific staff. The department is located at DTU Lyngby Campus.

Technology for people
DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN’s 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear vision to develop and create value using science and engineering to benefit society. That vision lives on today. DTU has 12,900 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. DTU has campuses in all parts of Denmark and in Greenland, and we collaborate with the best universities around the world.