PostDoc in Phage Host Hunt

Institute of Hydrobiology

Department of Aquatic Microbial Ecology (AME)

Employment contract

The Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, invites applications for a postdoctoral scientist.

A postdoc position is open in the Department of Aquatic Microbial Ecology (https://www.hbu.cas.cz/en/structure/ame/), Institute of Hydrobiology, České Budějovice, Czech Republic to study freshwater bacteria and their phages using cultivation, comparative genomics, metagenomics and experimental approaches. The position is part of a recently granted project to find phages of abundant freshwater bacteria (see below), but it can be tailored to the applicant’s interest.

Project background: Phages are present in all ecosystems and structure microbial communities through the regulation of host populations and the release of host-bound nutrients through lysis. Metagenomics revealed a huge phage diversity in nature but often failed to assign hosts to phages. Especially in freshwater environments, this is partly due to the lack of cultured reference phages and their hosts. Recent advances in bacterial cultivation enabled the isolation of abundant freshwater bacteria (e.g., Fonsibacter, Planktophila, Methylopumilus). We have established a large freshwater bacteria collection (>7000 isolates) that includes these abundant species. Here we aim to use these bacteria in a high throughput phage isolation approach to isolate new phages and to bona-fide identify phage-host pairs. We will study the host range, natural abundances and dynamics of newly isolated phages. We will completement these approaches with culture independent approaches to quantify isolated phages, identify prophages in the genomes of isolates and in metagenome assembled genomes from long-read metagenomic data of environmental bacteria. The project hence plans to close an important gap in viral ecology by assigning hosts to phages and investigate their natural dynamics in a freshwater reservoir.

• Applicants should have a PhD in Biological Sciences (e.g., Limnology, Microbiology, Ecology, Molecular Biology, Biochemistry, Bioinformatics).
• Applicants must be strongly motivated to work in an eco-genomics setting. The work is expected to be 70% computational and 30% laboratory based.
• Prior experience in linux/unix/perl/python programming is favorably considered but is not a prerequisite for selection.
• Candidates must be proficient in English.

• 5 weeks of paid holiday per year
• Subsidized lunches in our own canteen
• Standard health insurance and social security
• Benefits from Social fund
• 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 Czech language classes
• 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

About the position

Target starting date is January 2024, but an earlier start date is possible.
The position is initially funded for 2 years, with further employment depending on funding and performance.

About the employer & location

The Department of Aquatic Microbial Ecology (www.hbu.cas.cz/en/structure/ame/) is an internationally recognized high-class institution for studying freshwater microbes. The Institute of Hydrobiology (https://www.hbu.cas.cz/en/) 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 catchments. The institute performs research on different levels of interactions from the ecosystem, community, population, organismal, through cellular to molecular levels. The institute is one of the institutes associated in the Biology Centre of the Czech Academy of Sciences in České Budějovice.

The Biology Centre is located in České Budějovice (2 hours south of the capital Prague), 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.

The Biology Centre of the Czech Academy of Sciences 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.

To apply, please submit (preferably all information combined in a single PDF file) via the REPLY button below:
(1) a detailed CV,
(2) a brief statement of your research interests and work performed and
(3) the name and contact information for at least two referees.

Applications will be evaluated monthly starting November 1st, 2023. The position will remain open until a suitable candidate is found.

For further information contact Dr. Markus Haber at markus.haber@hbu.cas.cz.