8 PhD Funded Positions in Plant Sciences at Charles University Faculty of Science in Prague, Czech Republic; Deadline for application: March 13, 2023:
Faculty of Science, Charles University belongs to the leading research institutions in the Czech Republic. We are proud of our rich history and the number of famous scientists who have worked here (including the Nobel prize laureates Einstein and Heyrovsky). The members of our research groups are authors or co-authors of hundreds of publications in the most prestigious journals including Nature and Science. Do you want to contribute to new discoveries in science? Join us in the STARS program!
What do we offer within the STARS program?
All PhD students receive a state-guaranteed scholarship of 10.500,- Czech crowns per month in their first year of study; the scholarship increases slightly (10.500,- + additional 2.000,- once the doctor examination is successfully passed) over the course of 4 years for which it is granted. In addition to the state scholarship, the STARS program students will also be granted the STARS-scholarship of at least 10.000 CZK per month. The STARS-scholarship is guaranteed for 4-year study period for those students, who will obtain grade “A” (excellent) in regular each-year evaluation.
Their net income will therefore be at least 20.500 CZK per month (~800 EUR). The remuneration may be further augmented by the project supervisor. The PhD students accepted for the STARS program will work on the selected scientific project under the guidance of the supervisor.
As STARS PhD students you have access to:
- Supervision
- Advanced methodological courses
- High-tech laboratories and core facilities
- Soft skills training
- Czech language courses for foreign students
Information about Prague: Prague is one of the oldest political, economic and cultural centres of Central Europe. It is the capital as well as the largest city in the Czech Republic with more than 1,230,000 inhabitants. Importance of Prague is reflected in the level of its architecture and living art, quality of life, degree of development of learning, and its cultural significance and reach.
It is one of the world’s most beautiful and monumental cities. It is known as the city of a hundred spires because of its profusion of grand, beautifully-preserved historical monuments from practically every period in history. Those spires are best admired from the Prague Castle, the dominant of Prague and the most significant Czech monument, as well as from the bridges that cross the Vltava River meandering through the city…
Prague is a display of all artistic styles and movements. In 1992 the historical core of the city covering 866 hectares was listed in the UNESCO World Cultural and Natural Heritage Register.
Accommodation: All Charles University students (including STARS students) are eligible for subsidized accommodation in university halls of residence. Shall you have any questions about accommodation, please contact Central Accommodation Office.Private accommodation is not difficult to find in our university city. You can either rent a room in a shared flat or a whole flat.
ESN CU Prague: International Erasmus Student Network Charles University Prague (ESN CU Prague) is a student club which organizes various social, cultural and sports events for both international and Czech students from many faculties, and generally helps international students to handle their stay in Prague.
Prague Public Transport: Prague offers an excellent public transport system with its underground and numerous bus and tram lines. The metro is the quickest way to travel long distances across the city. It has three lines: A (green), B (yellow) and C (red). It closes down for the night shortly after midnight and reopens after 4 a. m. Trams and buses connect the metro system to outlying areas, and are also a handy way to make short journeys in the city centre. The most efficient form of night transport is the network of night trams that runs from about midnight until the metro reopens. Night trams run very precisely in 30-minute intervals.
Individual tickets are available at most tobacconists and newsstands. There are also ticket vending machines installed in all metro stations and at selected surface transit stops. Single transfer ticket can be also purchased as an SMS ticket via a mobile phone. Single tickets cost CZK 24 and CZK 32. The CZK 24 tickets are valid for 30 minutes and CZK 32 tickets for 90 minutes of unlimited travel. It is possible to change between trams, buses, the metro and trains (in area of Prague) without having to buy a new ticket until the time period runs out.
When using local transport regularly, it is advisable to purchase season tickets. Passes are valid for unlimited travel on any bus, tram or metro line throughout the city area. Students above 26 years of age are not eligible for student discounts.
Using taxi: Unfortunately, taxi drivers have quite a bad reputation in Prague. There is no standard price for taxi services, but drivers are required to display their prices, usually on the door. A reasonable price is around CZK 28 per km, but it is a good idea to agree on a price before committing to a ride and be sure that the meter is running while in the taxi. Usually reliable companies whose dispatchers speak English are AAA Taxi (Tel. +420 222 333 222; 14014) or ProfiTaxi (Tel. +420 261 314 151, 14015). Or you can use Uber, Taxify or Liftago, of course.
International airport and cheap flights: The international Vaclav Havel Airport Prague is one of the main destinations in Europe which services around 15 million passangers per year. Currently 70 airlines connect Prague with more than 160 destinations worldwide by direct scheduled flights. Besides the traditional carriers there is also a growing number of low-cost companies providing discount plane tickets to most of the main European cities and other interesting destinations.
Culture: Prague is also one of the cultural centres of Europe boasting more than ten major museums, along with countless theatres, galleries, cinemas, and music venues. The city regularly host a number of prestigious exhibitions, events and international festivals. Prague is a city to create, exhibit and perform in.
Check our STARS projects in plant sciences below:
1- PhD Project (1): Cytoskeletal control of plant peroxisomal structure and function:
Research group: Plant Cell Biology and Biotechnology, group Cytoskeleton
Peroxisomes are spherical organelles of 0.2–1.5 μm diameter that are found in all eukaryotic cells. Peroxisomes are surrounded by a single membrane and represent versatile organelles essential for various metabolic pathways. These organelles are a metabolic hub as they host numerous metabolic pathways such as β-oxidation of fatty acids and metabolism of reactive oxygen species. Plant peroxisomes function cooperatively with other organelles such as mitochondria, chloroplasts and oil bodies through contacts sites that enable exchange of metabolic products between these organelles. Peroxisomes are highly plastic and motile and move rapidly on the actin cytoskeleton. We suggested that actin is also involved in peroxisomal membrane remodelling, because we found out that peroxisomes are associated with an actin nucleating ARP2/3 complex.
The goal is to uncover the mechanism of ARP2/3 association with peroxisome by means of methods of co-immunoprecipitation/protein mass spectrometry analysis and correlative light electron microscopy methods (CLEM). Identification of protein interactors and their localization co-by CLEM will allow to determine the function of actin in peroxisome membrane remodeling. In close cooperation with the Laboratory of Electron Microscopy of the Faculty of Science of Charles University, the CLEM method for plant cells study will be introduced.
Five relevant publications of the research group:
Martinek J, Cifrová P, Vosolsobě S, Krtková J, Sikorová L, Malínská K, Mauerová Z, Leaves I, Sparkes I, Schwarzerová S: ARP2/3 complex associates with peroxisomes to participate in pexophagy in plants. bioRxiv,
Bellinvia E, García-González J, Cifrová P, Martinek J, Sikorová L, Havelková L, Schwarzerová K. CRISPR-Cas9 Arabidopsis mutants of genes for ARPC1 and ARPC3 subunits of ARP2/3 complex reveal differential roles of complex subunits. Sci Rep 2022 12(1):18205
Stelate A, Tihlaříková E, Schwarzerová K, Neděla V, Petrášek J. Correlative light-environmental scanning electron microscopy of plasma membrane efflux carriers of plant hormone auxin. Biomolecules 2021;11(10).
García-González J, Kebrlová Š, Semerák M, Lacek J, Kotannal Baby I, Petrášek J, Schwarzerová K. Arp2/3 complex is required for auxin-driven cell expansion through regulation of auxin transporter homeostasis. Front Plant Sci 2020;11.
Cifrová P, Oulehlová D, Kollárová E, Martinek J, Rosero A, Žárský V, Schwarzerová K, Cvrčková F. Division of labor between two actin Nucleators—the formin FH1 and the ARP2/3 Complex—in arabidopsis epidermal cell morphogenesis. Front Plant Sci 2020;11.
2- PhD Project (2): The master regulators of endosperm development in Arabidopsis:
Research group: Plant Repro Evo lab
Despite decades of dedicated research, the role of genomic imprinting in plants remains elusive. The aim of this PhD project is to address this question with a different angle compared to what has been done so far. By deciphering the action of imprinted genes in gene regulatory networks controlling endosperm development, the project will unravel the biological role and relevance of imprinted genes. In parallel, the project will study the implication of transposable elements during sexual reproduction, as these elements are tightly connected to genomic imprinting.
Finally, the PhD student will screen genomes of natural populations to better understand the evolutionary role of genomic imprinting. The project will focus on wild outcrossing species of Arabidopsis, namely A. arenosa and A. lyrata. The project will heavily rely on bioinformatic analyses and therefore, the successful candidate is expected to have experience in any of these analyses, and/or to have t he will to strongly develop in these areas.
Five relevant publications of the research group:
Sammarco I, Pieters J, Salony S, Toman I, Zolotarov G, Lafon Placette C (2022). Epigenetic targeting of transposon relics: beating the dead horses of the genome? Epigenetics,
İltaş O, Svitok M, Cornille A, Schmickl R, Lafon Placette C (2021). Early evolution of reproductive isolation: a case of weak inbreeder/strong outbreeder leads to an intraspecific hybridization barrier in Arabidopsis lyrata. Evolution,
Lafon Placette C (2020). Endosperm genome dosage, hybrid seed failure and parental imprinting: sexual selection as an alternative to parental conflict. Am J Bot 107(1): 1–3 (invited article).
Lafon Placette C, Hatorangan MR, Steige K, Cornille A, Lascoux M, Slotte T and Köhler C (2018). Paternally expressed genes likely underpin the endosperm balance number in Capsella genus. Nat Plants 4:352–357.
Lafon Placette C, Johannessen IM, Hornslien KS, Ali MF, Bjerkan KN, Bramsiepe J, Glöckle BM, Rebernig CA, Brysting AK, Grini PE and Köhler C (2017). Endosperm-based hybridization barriers explain the pattern of gene flow between Arabidopsis lyrata and Arabidopsis arenosa in Central Europe. PNAS,
3- PhD Project (3): Soil microbiota and soil resources as drivers of diversity and stability in grasslands:
Research group: Population Ecology Group
The ongoing change in climate and human disturbances are an increasing threat to the functioning of ecosystems globally. Ecosystems are increasingly losing their natural stability, resulting in a drastic loss of biodiversity, functioning and the ecosystem services they provide. Interactions between plants and soil microbiota are pivotal in creating stable and diverse plant communities and therefore key interactions to address in our efforts of protecting and restoring natural ecosystems.
In this project, we will develop an integrated framework on the plant-soil-microbiota interactions that underlie stability and diversity in grassland communities. The PhD candidate will work in a team that is testing the main hypothesis that plant community instability results from a loss of negative interactions between plants and soil microbiota. This loss is expected to, in time, result in dominance of plant species and eventually in instability of the plant community as a whole. The PhD candidate will be involved in setting-up, maintaining and sampling of plant species in 13 year old permanent plots at a successional grassland field site (see figure).
The PhD candidates’ focus will be on defining plant species trait shifts that associate with a loss of negative interactions between plants and soil microbiota. Plant traits included are plant shoot traits (SLA, LDMC, seed weight and number), plant root traits (root diameter, SRL, phenol content), plant spatial growth (local density) and plant dispersal distance. The PhD will associate shifts in plant traits to long-term plant developmental patterns, microbial rhizosphere communities and rhizosphere biogeochemistry.
Five relevant publications of the research group:
Aldorfová (Florianová), A., Knobová, P., & Münzbergová, Z. (2020). Plant–soil feedback contributes to predicting plant invasiveness of 68 alien plant species differing in invasive status. Oikos, 129(8), 1257–1270.
Florianová, A., & Münzbergová, Z. (2018). Drivers of natural spread of invasive Impatiens parviflora differ between life-cycle stages. Biological Invasions, 20(8), 2121–2140.
in ’t Zandt, D., Herben, T., van den Brink, A., Visser, E. J. W., & de Kroon, H. (2021). Species abundance fluctuations over 31 years are associated with plant–soil feedback in a species‐rich mountain meadow. Journal of Ecology, 109(3), 1511–1523.
in ’t Zandt, D., Kolaříková, Z., Cajthaml, T., & Münzbergová, Z. (2022). Plant community stability is associated with a decoupling of prokaryote and fungal soil networks. BioRxiv.
Kuťáková, E., Mészárošová, L., Baldrian, P., & Münzbergová, Z. (2020). Evaluating the role of biotic and chemical components of plant-soil feedback of primary successional plants. Biology and Fertility of Soils, 56(3), 345–358.
4- PhD Project (4): Seasonal dynamics and interaction turnover of plant-pollinator networks in the alpine tropics:
Research group: Plant Ecology Group (Department of Botany) / Department of Zoology
PhD position open for a motivated student in the field of Pollination biology. The position is part of a project on Plant-pollinator networks in mountain ecosystems. Namely, the project will compare the dynamics of the plant-pollinator networks between aseasonal tropical high mountains (equatorial Andes; data will be collected by the Czech-Ecuadorian research team) with plant-pollinator networks in seasonal temperate mountains (Rocky Mts. Colorado, USA; data will be collected by US colleagues).
The PhD position and related research project are based in Prague. But the student is expected to collect field data on plant-pollinator interactions in high-elevation environment during an extended period of time (about 6-12 months) in Ecuador.
Candidates are expected to:
- have obtained Master degree (or equivalent) in botany, zoology/entomology, or ecology,
- have solid statistical and data analytical skills,
- be independent regarding (field) work organization,
- communicate in English and Spanish.
Salary of approx. 1000 EUR/month offered for 3.5 years of the project duration, starting between July–October 2023.
5- PhD Project (5): Molecular basis of convergent adaptation in wild Arabidopsis:
Research group: Cell growth laboratory + Plant Ecological Genomics
When does evolution repeat itself? Evolution is driven by a combination of deterministic forces and stochasticity, whose relative importance remains a matter of debate. Leveraging the natural variation of wild relatives of the plant model Arabidopsis, this project focuses on functional characterization of key candidate genes that were repeatedly recruited in adaptation to a strong selective pressure, toxic serpentine soils. By studying genes harboring independent mutations, the project aims at uncovering general mechanisms determining which portion of genome evolves in a predictable manner.
The candidate will address the function of novel gene alleles on molecular and cellular level by using methods of molecular biology (molecular cloning, CRISPR/Cas9, protein biochemistry), cell biology (protein localization) and advanced microscopy (live cell imaging, image analysis), as well as the bioinformatic approaches of ecological genomics (selection scans, environmental association analyses), resulting in a unique experimental profile of the candidate.
Strong motivation for plant molecular and/or evolutionary biology and independence is a requirement, previous experience with molecular biology methods is beneficial. The PhD will be carried out under the co-supervision of Matyáš Fendrych and Filip Kolář. The student will join established international team of M. Fendrych at Department of Experimental Plant Biology.
Five relevant publications of the research group:
Konečná V, Bray S, Vlček J, Bohutínská M, Požárová D, Roy Choudhury R, Bollmann-Giolai A, Flis P, Salt DE, Parisod C, Yant L, Kolář F (2021): Parallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles. Nature Communications 12: 4979
Bohutínská M, Vlček J, Yair S, Laenen B, Konečná V, Fracassetti M, Slotte T, Kolář F (2021): Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives. Proceedings of the National Academy of Sciences 118: e2022713118
Serre NBC, Kralik D, Yun P, Slouka Z, Shabala S, Fendrych M. 2021. AFB1 controls rapid auxin signalling through membrane depolarization in Arabidopsis thaliana root. Nature Plants 7: 1229-1238.
Serre NBC, Wernerova D, Vittal P, Dubey SM, Medvecka E, Jelinkova A, Petrasek J, Grossmann G, Fendrych M. 2022. The AUX1-AFB1-CNGC14 module establishes longitudinal root surface pH profile. bioRxiv 2022.11.23.517700
Wu S, Wen Y, Serre NBC, Laursen CCH, Dietz AG, Taylor BR, Drobizhev M, Molina RS, Aggarwal A, Rancic V, Becker M, Ballanyi K, Podgorski K, Hirase H, Nedergaard M, Fendrych M, Lemieux MJ, Eberl DF, Kay AR, Campbell RE, Shen Y. 2022. A sensitive and specific genetically-encoded potassium ion biosensor for in vivo applications across the tree of life. PLoS Biology 20: e3001772.
6- PhD Project (6): Evolutionary drivers of convergent serpentine adaptation in European Brassicaceae:
Research group: Plant Ecological Genomics
When and under which circumstances does evolution repeat itself? Evolution is driven by a combination of deterministic forces and stochasticity, whose relative importance, however, remains a matter of debate. Knowing how predictable is evolution can provide insights into predictive evolution of crops, pathogens or species under climate change.
This project will address mechanisms driving convergent genome evolution in natural environments. By leveraging fascinating natural diversity of European Brassicaceae which repeatedly adapted to exceptionally strong selective pressure, toxic soils called serpentines, the project aims at uncovering general mechanisms determining which portion of genome evolves in a predictable manner. The successful candidate will conduct extensive sampling of 13 Brassicaceae species in the Balkans, perform controlled common garden experiments and will be involved in population genetic analyses of genome-wide data. We will build on our previous research in wild Arabidopsis but the project will extend beyond this system in order to discern generality.
Strong motivation for evolutionary biology and independence is a requirement, previous experience with intense fieldwork, experiments and/or population genomic analysis is beneficial. The student will join an established international team of Ecological Genomics at the Department of Botany and the position will be funded by a highly selective Junior Star project.
Five relevant publications of the research group:
Wos G, Arc E, Hülber K, Konečná V, Knotek A, Požárová D, Bertel C, Kaplenig D, Mandáková T, Neuner G, Schönswetter P, Kranner I, Kolář F (2022): Parallel local adaptation to an alpine environment in Arabidopsis arenosa. – Journal of Ecology 110: 2448–2461 .
Konečná V, Bray S, Vlček J, Bohutínská M, Požárová D, Roy Choudhury R, Bollmann-Giolai A, Flis P, Salt DE, Parisod C, YantL, Kolář F (2021): Parallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles. – Nature Communications 12: 4979 .
Bohutínská M, Vlček J, Yair S, Laenen B, Konečná V, Fracassetti M, Slotte T, Kolář F(2021): Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives. – Proceedings of the National Academy of Sciences 118: e2022713118.
Wos G, Bohutínská M, Nosková M, Mandáková T, Kolář F (2021): Parallelism in gene expression between foothill and alpine ecotypes in Arabidopsis arenosa. – The Plant Journal 105: 1211-1224.
Čertner M, Sudová R, Weiser M, Suda J, Kolář F (2019): Ploidy-altered phenotype interacts with local environment and may enhance polyploid establishment in Knautia serpentinicola (Caprifoliaceae). – New Phytologist 221:1117–1127.
7- PhD Project (7): Title of the PhD project: What are the long-term drivers of tropical peat accumulation in South America?:
Research group: Carbon and Wetlands Group (CAWG)
Tropical peatlands are among the most carbon dense ecosystems globally (Honorio-Coronado et al., 2021) but we lack an understanding of the long-term drivers of tropical peat (and carbon) accumulation. The expected results will transform our understanding of the drivers of tropical peat & carbon accumulation and provide crucial insights into their vulnerability to climate and land-use change, across wide spatial gradients. They will also inform the parallel development of a dynamic tropical peat model, which the PhD will contribute to.
The successful applicant will collect new peat cores in Guyana (in collaboration with Guyanese researchers), which previous research hints could be substantially older than those of Amazonia (van der Hammen., 1963). They will establish timing of peat initiation by obtaining basal dates for each core (if possible, taken from a variety of peat-forming ecosystems, e.g. Aguajal palm swamp, Honorio-Coronado., 2021) using radiocarbon dating. The cores will be further sampled (5-10 dates) to establish outline age/ depth models. Following this, periods of interest (based on some combination of the paleoenvironmental proxies- charcoal, δ2H, δ13C, br-GDGT and pollen analysis) will be dated more intensively at higher resolution to understand the primary drivers of peat & carbon accumulation.
The cores from Guyana will be compared against peat initiation and age/ depth models from cores previously collected in Peru (collaboration with Dr Ian Lawson-University of St Andrews) and the same paleoenvironmental proxies will be applied to the Peruvian cores The student will become a member of an exciting new team led by an early-career group leader and collaborate closely with colleagues at the Universities of St Andrews and Guyana. The successful applicant will have an MSc level degree in one of the following fields (or equivalent/ similar field): Ecology, Environmental Science, Soil Science, Botany, Earth Science, Palynology.
References:
Honorio-Coronado, E. N., Hastie, A., et al. Intensive field sampling increases the known extent of carbon-rich Amazonian peatland pole forests. Environ. Res. Lett. 16, 74048.
van der Hammen, Thomas. (1963). A palynological study on the Quaternary of British Guiana. Leidse Geologische Mededelingen, 29(1), 125–168.
Hastie, A., Honorio Coronado, E.N., Reyna, J. et al. Risks to carbon storage from land-use change revealed by peat thickness maps of Peru. Nat. Geosci. 15, 369–374 (2022).
Kuneš, P, Abraham, V, Herben, T. Changing disturbance-diversity relationships in temperate ecosystems over the past 12000 years. J Ecol; 107: 1678– 1688 (2019).
Hastie, A., Lauerwald, R., Ciais, P., Regnier, P. Aquatic carbon fluxes dampen the overall variation of net ecosystem productivity in the Amazon basin: An analysis of the interannual variability in the boundless carbon cycle. Glob Change Biol. 25: 2094– 2111, (2019)
Kuneš, P.; Svobodová-Svitavská, H.; Kolář, J.; Hajnalová, M.; Abraham, V.; Macek, M.; Tkáč, P.; and Szabó, P. The origin of grasslands in the temperate forest zone of east-central Europe: long-term legacy of climate and human impact. Quaternary Science Reviews, 116: 15–27, (2015)
8- PhD Project (8): Evolution of reproductive isolation in a diploid – polyploid plant system:
Research group: Certner lab
Polyploidization (whole genome duplication) is widely regarded as an important mechanism of sympatric speciation, particularly in plants where it drives reproductive isolation of many crop species from their wild relatives. While often perceived as a strong and instantaneously forming reproductive barrier, empirical data show its strength may vary considerably across plants.
In the project, the successful applicant will be assessing rates and evolutionary significance of inter-ploidy introgression across a diploid – tetraploid hybrid zone, looking for genomic signatures of selection and complementing it with multigenerational manipulated crosses that will allow studying separately the contribution of different components to overall reproductive isolation. By using an interdisciplinary approach combining field research, ex situ experiments, and population genomics on a carefully selected non-model species from the Asteraceae family, we will aim at providing new insights into the reproductive isolation of polyploids. The project builds on a detailed knowledge of the plant system and preliminary data gathered during previous research.
The student will become a member of a gradually forming team led by an early-career group leader and interact with collaborating teams abroad. Strong interest in evolutionary biology and ability to work independently are required, previous experience with manipulated pollinations and bioinformatics is welcome.
Five relevant publications of the research group:
Čertner, M., Rydlo, J., Dudáš, M. & Hroudová, Z. (2022): A unique diploid – triploid contact zone provides insights into the evolutionary mechanisms of cytotype coexistence in flowering rush (Butomus umbellatus) – Perspectives in Plant Ecology, Evolution and Systematics, 54: 125659.
Morgan, E. J., Čertner, M., Lučanová, M., Deniz, U., Kubíková, K., Venon, A., Kovářík, O., Lafon Placette, C. & Kolář, F. (2021): Disentangling the components of triploid block and its fitness consequences in natural diploid-tetraploid contact zones of Arabidopsis arenosa – New Phytologist, 232: 1449-1462.
Čertner, M., Sudová, R., Weiser, M., Suda, J. & Kolář, F. (2019): Ploidy-altered phenotype interacts with local environment and may enhance polyploid establishment in Knautia serpentinicola (Caprifoliaceae) – New Phytologist, 221(2): 1117-1127.
Kolář, F., Čertner, M., Suda, J., Schönswetter, P. & Husband, B. (2017): Mixed-ploidy species: Progress and opportunities in polyploid research – Trends in Plant Science, 22(12): 1041-1055.
Čertner, M., Fenclová, E., Kúr, P., Kolář, F., Koutecký, P., Krahulcová, A. & Suda, J. (2017): Evolutionary dynamics of mixed-ploidy populations in an annual herb: dispersal, local persistence and recurrent origins of polyploids – Annals of Botany, 120(2): 303-315.
Deadline for application: March 13, 2023.