A PhD student position is open at the Department of Aquatic Microbial Ecology (www.hbu.cas.cz/en/structure/ame/), Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.

Workplace: Institute of Hydrobiology, Biology Cente CAS
Department: Department of Aquatic Microbial Ecology (AME)
Employment relationship: Employment contract
Job type: Researcher
Researcher profile: R1
Duration: Fixed-term
Job status: Part-time
Hours per week: 28


The PhD student will study freshwater phages and their hosts using high-throughput isolation, comparative genomics, metagenomics and experimental approaches.


Phages (viruses infecting bacteria) are present in all ecosystems and structure microbial communities through the regulation of host populations and the release of host-bound nutrients through lysis. Metagenomic approaches have revealed the huge phage diversity in nature but often failed to assign hosts to phages, especially in freshwater environments. In our lab, we have established a large culture collection of abundant freshwater bacteria. One focus of this project will be to use these bacteria to isolate their phages and hence conclusively identify phage-host pairs.

In collaboration with other members of the institute we will use a polyphasic approach combining cultivation, physiology, genomic and metagenomic approaches to study the host range, natural abundances and dynamics of the isolated phages in a freshwater reservoir and identify host defense mechanisms.


Min. education level: Master’s degree
Field of education: Biological Sciences (e.g. Limnology, Microbiology, Ecology)

  • Applicants should hold a M.Sc. in Biological Sciences (e.g., Limnology, Microbiology, Ecology) and must be strongly motivated to work in an eco-genomics laboratory. In the first year, the majority of the work is expected to be laboratory based (sampling, cultivation and molecular work) and moving towards more computational based work (genome and metagenome analyses) in later stages.
  • Prior experience in cultivation of fastidious bacteria (e.g., using flow cytometry) and phages as well as in linux/unix/perl/python programming might be favorably considered but is not a prerequisite for selection.
  • Candidates must be proficient in English.


  • 1 extra week of holiday, i.e. 5 weeks of paid holiday per year in total for 1 FTE
  • Subsidized lunches in our own canteen
  • Standard health insurance and social security
  • Benefits from Social fund and student benefits
  • Working in a stable, prestigious research institution of international importance
  • Welcome service and further support for foreigners (HR Award)
  • Friendly & stimulating international working environment
  • Work-life balance in a middle-sized university city offering options for outdoor, sport & cultural activities
  • Free language classes (Czech for foreigners, English for Czechs)
  • Opportunity to take part in mentoring programmes as a mentor or a mentee
  • Concessionary mobile tariff and banking services at the contractual operator and bank
  • Access to accommodation in dormitories at the campus shared by the Biology Centre and the University of South Bohemia (for PhD students)


Details of the position:

The position is available immediately and will remain open until a suitable candidate is found. Initially appointment of the position is for 3 years, but can be prolonged. The position is 70 % FTE with an additional stipend when accepted from the university.

About the employer:

The Department of Aquatic Microbial Ecology is an internationally recognized high-class institution for studying freshwater microbes. The Institute of Hydrobiology is the principal institution in the Czech Republic devoted to complex freshwater research of man-made reservoirs and natural lakes. The research portfolio includes the assessment of biotic interrelations and their interactions with abiotic factors. Limnological interactions are studied both within the waterbodies and within whole catchment. The institute performs research on different levels of interactions from the ecosystem, community, population, organismal, through cellular to molecular levels. The insititute is one of the institutes associated in the Biology Centre of the Czech Academy of Sciences in České Budějovice.

The Biology Centre CAS holds the HR Award. Our selection process meets European standards for recruitment of researchers (https://www.bc.cas.cz/en/employees/candidates/otm-r/) and we provide our employees from abroad with welcome service (visa application, administration, relocation & settlement support). Gender equality plan (https://www.bc.cas.cz/en/about-us/gender-equality/) has been accepted in 2022.

About the location:

České Budějovice (2 hours south of the capital Prague) is a middle-sized city with ca. 100K inhabitants, relaxed atmosphere, over 750 years of tradition and a breathtaking countryside around. Both the town and the surrounding countryside provide numerous opportunities for research and leisure activities. There is also a growing international expert community at the Biology Centre CAS (BC CAS, https://www.bc.cas.cz/en/) and the University of South Bohemia (USB, https://www.jcu.cz/en/). In addition, the living costs are still low by international standards. Check out our Guide for Expats (https://www.bc.cas.cz/en/employees/) to read about life in the city and the Czech Republic.


If interested, send us your application via the REPLY button at the bottom of the official job site: https://jobs.bc.cas.cz/en/detail/157. Please submit a professional CV (including your grades), a brief statement of your research interests and work performed (max. 1 page), a list of publications (if any) and the names and contact information of two professional references. Preferably combine all this information into a single PDF file.

Please don’t hesitate to contact Dr Markus Haber for further information about the position: markus.haber@hbu.cas.cz