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Microbiology
Doctoral Programme,
Faculty of Food and Biochemical Technology
The purpose of the study programme is to train specialists with a comprehensive understanding of microbial populations, their activity, phylogenetic and metabolic diversity, mechanisms controlling targeted changes of their genetic information or chemical principles affecting the relationship within microbial communities. The study programme is based on the combination of various forms of tuition and laboratory research, with the main emphasis on independence, initiative and critical approach of students. Alumni of this study programme should be able to routinely use any of the acquired knowledge, skills and competences for industrial or other applications. CareersAlumni of this study programme should have a comprehensive microbiological, biochemical and engineering background that will enable them to fully understand the microbial world. They will dispose of deep theoretical insight as well as practical skills in all key areas of microbiology, including biochemistry of microorganisms, molecular biology, genetic engineering and other closely related fields. The alumni of the study programme will find employment in all areas of biotechnology, food, pharmaceutical or chemical industry, in clinical laboratories, in the field of environmental sciences and agriculture. Last but not least, the alumni should be highly competent to work in academia. Programme Details
Ph.D. topics for study year 2024/25Interaction of Bordetella with Respiratory Epithelia
AnnotationThe classical Bordetella species infect the respiratory tract of mammals. B. bronchiseptica induces chronic respiratory infections in various mammals, while the human-adapted species B. pertussis and B. parapertussis HU lead to an acute respiratory disease known as whooping cough or pertussis. These bacteria establish biofilms on both abiotic surfaces and within the respiratory tract, functioning as an immune evasion mechanism and a focal point for the development of novel antimicrobial agents. The objective of this PhD thesis is to unravel the signaling pathways underlying Bordetella colonization of respiratory epithelia and biofilm formation. The PhD candidate will employ an air-liquid interface model of human nasal epithelia and a microengineered biomimetic system, an organ-on-a-chip, combined with metabolomics, dual RNA-Seq and genetic engineering.
Contact supervisor
Study place:
Institute of Microbiology of the CAS
The role of microorganisms in greenhouse gas production in forested peatlands of northern Europe
AnnotationPeatlands of Northern Europe are an important source of greenhouse gases (GHG) with a strong influence on global climate - methane, nitrous oxide and carbon dioxide. One of the approaches to limit GHG production is the drainage of peatlands and their afforestation. Although this land use change can somehow reduce GHG production, it still partly continues to depend on the management of forests. The fluxes of GHG are, however, also regulated by other factors, such as the seasonal activity of vegetation and microorganisms. Since microorganisms are responsible for GHG production in the soils of forested peatlands, they represent the key to the understanding of GHG production rates and factors that affect them. In this work, we will use field experiments in southern Finland, where GHG production is monitored and where the analysis of microbiome composition and function at different depths of peat can be thus linked to the observed ecosystem-level gas fluxes. This project will offer a combination of fieldwork, labwork and analysis of bioinformatic data. When successful, the results of the thesis should help to indicate what management of peatland forests has the highest potential to mitigate GHG emissions and increase the storage of carbon in forest soils.
Contact supervisor
Study place:
Institute of Microbiology of the CAS
Exploring Respiratory Viral Entry: Comparative Insights from the Interactomes of Coronaviruses and Influenza A Viruses during Early Infection
AnnotationThe entry of viruses into host cells is a crucial initial step, particularly for respiratory viruses with significant pandemic potential such as SARS-CoV-2 and influenza A virus. Analyzing the interactomes of coronaviruses and influenza A virus and comprehending the early interactions between viral and cellular proteins can provide valuable insights for developing targeted or broad-spectrum antiviral therapies. The main goal of this project is to understand the viral and cellular factors influencing the entry of respiratory viruses. We will employ several strains of coronaviruses and influenza A virus, known to exploit different entry routes into the host cell, and will compare their cellular interactome at the time of entry and during early post-entry events. From the identified cellular interacting partners, interesting candidates will be selected and their role in the virus life cycle analyzed. The student will learn how to work with cell cultures in biosafety level 3, perform proteomic and bioinformatic analyses, and conduct siRNA experiments for gene-knockdown in mammalian cells infected with various viruses. The proposed project will broaden our current knowledge about the early phase of infections of mammalian cells with respiratory viruses.
Contact supervisor
Study place:
Institute of Organic Chemistry and Biochemistry of the CAS
Response of microbial soil community and microbe-mediated ecosystem processes to forest harvesting
AnnotationForest harvesting is economically important but due to the ecological importance of forests, it also represents a dramatic event in the ecosystem development. While clearcutting is a common practice in the temperate and boreal forests, variable retention harvesting is an alternative silvicultural practice in which some portion of the pre-harvest stand is retained after harvest. The broad objective is to maintain structural and functional elements from the pre-harvest condition to promote rapid recovery of biodiversity and ecological functions in the regenerating stands compared to clearcut stands. Harvesting of trees has profound effects on ecosystem processes that are associated with changes in the quality and decreases in the quantity of plant C inputs into the surrounding soil, as well as effects on soil nutrient availability and microclimatic conditions. Harvested stands also offer the opportunity to study the effect of reduced primary production on soil processes. Forest harvesting is known to have major effects on the main symbiotic fungi living on the roots of temperate trees, ectomycorrhizae, however, little is known about harvesting effects on symbiotic arbuscular mycorhizal fungi and bacteria. This project proposes to analyse the short-term effects of forest harvesting on the activity and composition of soil microbial communities in forests with dominant ectomycorrhizal and arbuscular mycorrhizal symbiosis and those with mixed ECM/AM. Changes in ecosystem properties and functioning, such as decomposition and N cycling will be linked to the community composition of soil microbes and their transcriptional activity. The project should give a view of the temporary changes of forest stand manipulations as well as answer the response of individual groups of microbes. This is important both for the consideration of future forest management strategies and the predictions of forest management effects on the C balance of forest soils.
Contact supervisor
Study place:
Institute of Microbiology of the CAS
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Updated: 25.3.2022 16:21, Author: Jan Kříž