PhD Student Position in the Biology of Candidate Phyla Radiation

Hydrobiologický ústav

Oddělení mikrobiální ekologie vody

Pracovní smlouva

A PhD student position is open to study the peculiar biology of Candidate Phyla Radiation (CPR), also known as ‘Ca. Patescibacteria’ using metagenomics, metatranscriptomics, comparative genomics, EpicPCR and reverse genomics.

Background
‘Ca. Patescibacteria’ is a phylum described only in 2015 and represents one of the biggest discoveries in microbiology in the last decade. It is believed to encompass between ~15% and 26% of bacterial diversity, but only a few cultures are available to date. These few representatives were found to be obligate episymbionts on other prokaryotes. Most of what we know about ‘Ca. Patescibacteria’ is derived from genomic data, but in general CPRs have extremely unusual characteristics, such as a very limited number of metabolic pathways, reduced genomes and cell sizes, and peculiar ribosomes that lack proteins which were considered essential for survival. Many genomes were found to have minimal amino acid and cofactor biosynthesis pathways, and till now no CPR has been identified to produce membrane phospholipids, which adds to the enormous intrigue regarding their lifestyle strategies. In the current project, we aim to provide unique information about CPRs temporal variability, functional potential, and ecological role in freshwater lakes. Additionally, we will approach one of the most difficult aspects in need of clarification – the identity and range of CPR hosts. Our final goal is to bring new CPRs into culture using reverse genomics and study their behavior and biology in detail.

• Applicants should hold a M.Sc. in Biological Sciences (e.g., Limnology, Microbiology, Ecology).
• Candidates must be strongly motivated to work in an eco-genomics laboratory.
• Prior experience in cultivation of fastidious bacteria (e.g., using flow cytometry) as well as in shell/perl/python/R programming might be favorably considered but is not a prerequisite for selection.
• Candidates must be proficient in English.

• 5 weeks of paid holiday yearly (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
• PhD students have access to accommodation in dormitories at the campus shared by the BC and the USB

The position is available from the spring of 2024 and will remain open until a suitable candidate is found. The position can be funded for up to 5 years.

The Department of Aquatic Microbial Ecology (https://www.hbu.cas.cz/en/structure/ame/) 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 the whole catchment. 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 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.

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.

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 and send via the "REPLY" button below.

Please don’t hesitate to contact Dr. Cecilia Chiriac for further information about the position: cecilia.chiriac@hbu.cas.cz