8 PhD Funded Positions in Plant Sciences at Charles University Faculty of Science in Prague, Czech Republic; Deadline for application: March 13, 2023:

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.

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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,

. Apply to the project

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.

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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.

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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.

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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.

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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)

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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.

Apply to the project

Deadline for application: March 13, 2023.

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