Website University of Warsaw, Faculty of Biology, Institute of Evolutionary Biology

PhD position in the project:
Freshwater microbial communities in the eutrophication gradient: diversity and interactions of protists and bacteria (MicroDivEr)

Application deadline: June 15th, 2021

Project description: The project focuses on freshwater ecosystems, which, although extremely important for the functioning of the biosphere, are less studied than marine ecosystems. The planned research will cover the natural experimental system of the lakes of the Masurian Lake District. Despite their common origin and close location, these lakes differ in many aspects, including different trophic status. In the proposed project, we will identify eukaryotic microorganisms and bacteria occurring in the lakes of the Masurian Lake District. To do so, we will use sequencing methods for short DNA fragments. A reference database is, however, needed to identify organisms based on DNA sequences correctly. Therefore, we will expand the existing database using single-cell sequencing and nanopore sequencing. Analysis of the co-occurrence of protists and bacteria will help to identify their interactions. Sequencing of protist genomes and total genomes of their microbiomes will provide insight into the nature of these interactions. We are particularly interested in the relations of protists and endosymbiotic bacteria and protists’ interactions with pathogenic bacteria. Finally, we will determine how environmental factors affect the diversity of microorganism communities and their interactions. The completion of the project will help to uncover the diversity and interactions of microorganisms in freshwaters. Identifying the interactions of protists and pathogenic bacteria will help pinpoint the natural, environmental reservoir of these bacteria. This will facilitate the prediction of their future outbreaks, which might threaten human and animals’ health. Research in lakes with different trophic status will allow assessment of the impact of the lake productivity on the composition of their microorganism communities. This will help predict changes in freshwater ecosystems resulting from human-induced eutrophication and contribute to their more effective protection.

Specific Tasks
• Collection of water samples (Masurian Lakeland, Poland), isolation and culturing of microbial eukaryotes
• DNA & RNA isolation from environmental samples, PCR, preparation of libraries for total genome, transcriptome & amplicon sequencing, Nanopore sequencing
• Analysis of high-throughput sequencing data: assembly of genomes and transcriptomes, amplicon data analysis
• Publication of the obtained results in conference talks & papers, active participation in publishing original research articles

• Master’s degree in biology, biotechnology or related field (obtained before September 23rd, 2021)
• Enrollment into the University of Warsaw’s Doctoral School of Exact and Natural Sciences, following the recruitment schedule for the year 2021/2022
• Being self-motivated, organized, and highly team-oriented
• Proficiency in English (oral and written)
• Familiarity with microscopy & molecular biology techniques, eagerness to learn bioinformatic techniques and willingness to work in the field will be additional assets.

What do we offer?
We offer a PhD position funded as part of the National Science Centre OPUS project “Freshwater microbial communities in the eutrophication gradient: diversity and interactions of protists and bacteria (MicroDivEr)”.
• Starting date: October 1st, 2021
• Scholarship up to 48 months.
• Minimum salary: 4 000 PLN per month.
• Location: Institute of Evolutionary Biology, Faculty of Biology, University of Warsaw

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