MSCA COFUND Doctoral Fellowships “Microbiome in Plant Virus Infections”

This PhD topic is part of the INNOCHEMBIO Doctoral Programme, which is funded through the Marie Skłodowska-Curie Actions (MSCA) COFUND action. The main objective of INNOCHEMBIO is to train future experts of sustainable chemistry and biotechnology, helping Europe to take the next steps in the green transition. This project aims to investigate viral disease development combined with plant transcriptome and metabolome profiling in response to native and/or artificial microbial communities. This PhD position will be hosted at TalTech with main supervisor Dr. Merike Sõmera and will contain a secondment to co-supervisor Prof. Sébastien Massart at University of Liège (BE).

Research field:	Chemistry and biotechnology
Supervisor:	Merike Sõmera
Availability:	This position is available.
Offered by:	School of Science Department of Chemistry and Biotechnology
Application deadline:	Applications are accepted between July 01, 2025 00:00 and August 31, 2025 23:59 (Europe/Zurich)

1. General description of programme and host

The PhD fellowship is part of the Marie Skłodowska-Curie Actions (MSCA) COFUND doctoral programme INNOCHEMBIO (https://taltech.ee/en/innochembio), which is co-funded by the European Union (Grant agreement 101217295). The main objective of INNOCHEMBIO is to train future experts to help Europe take the next steps in the green transition. The solutions and trained experts can reduce the environmental impact of the chemical and agricultural industries, offer eco-friendly analytical techniques, and assess the safety of new materials. INNOCHEMBIO funding will co-finance 15 PhD positions, for which the application process in the first call will start on the 1st of July in 2025.
For 12 PhD positions the hosting institution will be Department of Chemistry and Biotechnology (DCB) at Tallinn University of Technology (TalTech) which combines three divisions – Chemistry, Gene Technology and Biomedicine, and Food and Biotechnology. DCB is developing solutions to the great challenges of the 21st century – climate change, environmental protection, carbon neutrality, renewable energy, and biodiversity conservation. DCB hosts the second biggest PhD programme in TalTech with nearly a hundred enrolled students.

For 3 PhD positions the hosting institution will be the implementing partner – National Institute of Chemical Physics and Biophysics (NICPB). NICPB is a public research institution that conducts both fundamental and applied research, developing novel directions in fields ranging from material sciences to informatics. NICPB houses the Laboratory of Environmental Toxicology and several laboratories focused on fundamental research in NMR technologies with expertise dating back decades. The PhD training activities conducted by NICPB are funded through TalTech.

Importantly, each PhD project has one co-supervisor from another European country, which is detailed under the specific offer (see under supervisors' section). In total, INNOCHEMBIO has 19 associate partners from 11 European countries.

2. Description of specific PhD project

Plant viruses are a significant threat to global food security, causing substantial yield losses and economic impacts. Many plant viruses are disseminated by insect vectors, mainly by aphids and planthoppers. The changing climate fosters an increase in insect-transmitted disease outbreaks due to their increased population growth and number of vector generations per year during the longer vegetation periods. The climate change effect has been amplified by a recent EU regulation prohibiting and reducing the outdoor chemical pesticide compounds for growing sustainable and healthy food. Therefore, there is a need for new mitigation measures to reduce the range and economic impact of plant virus outbreaks. An increasing number of studies indicates that plant microbiome may provide protection against virus infections or reduce the severity of infection by changing the plant metabolism.

The general goal of the study is to achieve an understanding of the biology of tritrophic interactions between plants, their endophytes and viruses, particularly with respect to pathogenesis and symbiosis in order to predict and mitigate disease impacts. The objectives of the research project are to understand the differences between the microbiomes of infected and healthy plants in the context of studied viral disease; what are the key microorganisms supporting plant health; how these microbes or their consortia change the plant transcriptome and metabolome; and how the to initiate the assembly of supportive microbiome. Our recent studies have been focused on cereal viruses. Thus, the preferred research subject will be virus diseases of cereal crops, e.g. yellow dwarfing of cereals caused by cereal/barley yellow dwarf viruses, or wheat dwarfing caused by wheat dwarf virus.

The techniques used during the research project will include microbial isolation, cultivation and characterization, extraction of nucleic acids, preparation of sequencing libraries, analysis of the bioinformatic data, the statistical analyses, laboratory experiments with microbiome assembly and virus transmission using insect vectors.

Link to the project: https://taltech.ee/en/innochembio/somera

3. Supervisory team

• Tallinn University of Technology (main supervisor): Dr. Merike Sõmera
• University of Liège (Belgium): Prof. Sébastien Massart (The PhD student will stay 6-16 months at the co-supervisor's lab as mutually agreed upon).
• Tallinn University of Technology: Dr. Inga Sarand

4. Requirements

• Excellent command of written and spoken English.
• Compliance with the rules of INNOCHEMBIO (e.g. eligibility, adhering to MSCA mobility rules, etc.).
• The primary workplace will be in Estonia. Therefore, candidates from outside the EU must be eligible to obtain a visa. The position is expected to start in the first half of 2026.
• University degree (M.Sc.) in microbiology, plant pathology, or a related field, and a keen interest in bioinformatics.
• Experience with sterile methods and basic molecular methods are necessary.
• Prior experience in rhizospheric or plant microbiome isolation and characterization by metabarcoding/metagenomics is an advantage.
• We value accountability and reliability and seek a candidate who is motivated to acquire new skills.
• The applicant should be curious, self-driven and able to work effectively independently and in a team environment.

5. Duties and Responsibilities

• Undertake postgraduate research for specific doctoral research project at TalTech or NICPB, respectively.
• Present and publish research in both academic and non-academic audiences. Attend and participate in academic and non-academic conferences, events and seminars.
• Attend and participate in all training events and supervisory meetings.
• Be seconded to the associated partner as necessary to fulfil the grant obligations.
• Prepare progress reports and similar documents on research for funding bodies, as required.
• Actively contribute to the public engagement and outreach activities of the project.
• The above job descriptions are not exhaustive, the PhD candidate may be required to undertake other tasks, which are broadly in line with the above duties and responsibilities.
• Full-time employment (40 hours per week), temporary contract for 4 years.

6. Eligibility requirements

• The applicant must be a doctoral candidate (i.e. not already in possession of a doctoral degree at the date of the recruitment).
• At the time of recruitment, the researcher must not have resided or carried out their main activity (work, studies, etc.) in Estonia for more than 12 months in the three years immediately prior to the recruitment date. Compulsory national service and/or short stays such as holidays are not taken into account.

7. Benefits

• Competitive funding scheme, with a minimum gross monthly salary of EUR 2500. Topped by additional mobility allowances as well as optional family allowances (if applicable).
• Covered tuition costs, research costs and funding for short term mobility (i.e. conference attendance).
• Interdisciplinary and international research projects.
• Early-stage researcher position, with corresponding social and medical benefits in Estonia.
• Becoming a Marie Skłodowska-Curie PhD fellow.

8. How to Apply

All applications must be sent through TalTech’s official application platform Glowbase and only applications submitted here will be considered for the programme. We ask the candidates not to contact the supervisors directly, in case of questions please write at innochembio@taltech.ee. Each application must include the following material: CV, 1-page motivation letter, copies of BSc and MSc study records and diplomas, scanned copy of valid photo ID, 2 reference letters, eligibility statement. NB! Details on the exact nature of these documents and how to insert them in Glowbase can be found at our official INNOCHEMBIO website: https://taltech.ee/en/innochembio/application-process

9. Selection Process

The selection and recruitment process will be in accordance with the European Charter and Code of Conduct for the Recruitment of Researchers. The recruitment process will be open, transparent, impartial, equitable, and merit-based. There will be no overt/covert discrimination based on race, gender, sexual orientation, religion or belief, disability or age. To this end, the following selection criteria will be considered.

The application deadline is 31 August 2025. The application process will be carried out in 3 steps. In short, first an eligibility check is performed. All eligible candidates will proceed to stage 1, where they will be evaluated by independent evaluators based on the application documents. Lastly, shortlisted candidates from stage 1 will proceed to stage 2, where they will be interviewed via teleconference, which will be used to determine a candidate to whom an offer will be made. All candidates will be informed about the progress in due course after each step of the process. The selection process is described on the guide for applicants available here: https://taltech.ee/en/innochembio/application-process.

10. Disclaimer

By applying for this position, the applicants

1. give their consent to circulate their application and personal data within the INNOCHEMBIO consortium and with the evaluators;
2. confirm that the data provided is valid and accurate;
3. confirm compliance with the eligibility requirements;
4. commit to undertaking the planned secondment at the co-supervisor’s institution.