Bachelor and Master Thesis Projects:
Please contact, by email, Eva Stukenbrock or project-related persons for more info to the individual projects.
Plant-pathogen-microbe interactions (with Liz Florez, Victor Flores-Nuñez and Eva Tanneau)
We aim to understand how plant pathogens and the plant microbiome interact with each other in their host. The student projects will focus on the characterization of pathogens and microorganisms from diverse hosts and their mechanisms of interaction. The specific aims are:
Relevant papers:
- Flores-Nunez, V. M., & Stukenbrock, E. H. (2024). The impact of filamentous plant pathogens on the host microbiota. BMC biology, 22(1), 175.
- Hassani, M. A., Özkurt, E., Seybold, H., Dagan, T., & Stukenbrock, E. H. (2019). Interactions and coadaptation in plant metaorganisms. Annual Review of Phytopathology, 57(1), 483-503.
Unraveling patterns of adaptive evolution in fungal plant pathogens (with Thais Dal'Sasso and Lucas Bonometti)
Becoming a pathogen involves major genome adaptations. Effector-like proteins play a direct role in the infection of plants by fungal pathogens, while Nod-Like Receptors (NLR) are suspected to be a main component of fungal immunity. Both effector-like and NLR gene families are very dynamic, and a fast evolution of these gene families could drive pathogen adaptation and host-pathogen interactions. We use computational analyses to study effectors and fungal NLR genes in the plant-pathogenic genus Zymoseptoria. In particular, we aim to understand how these families evolved within Z. tritici and between different Zymoseptoria species, using comparative genomics, population genomics, and structure predictions.
Relevant papers:
- Witold Dyrka, Marina Lamacchia, Pascal Durrens, Bostjan Kobe, Asen Daskalov, Matthieu Paoletti, David J. Sherman, Sven J. Saupe, Diversity and Variability of NOD-Like Receptors in Fungi, Genome Biology and Evolution, Volume 6, Issue 12, December 2014, Pages 3137–3158, https://doi.org/10.1093/gbe/evu251- Sánchez-Vallet, A., Fouché, S., Fudal, I., Hartmann, F. E., Soyer, J. L., Tellier, A. & Croll, D. The genome biology of effector gene evolution in filamentous plant pathogens. Annu. Rev. Phytopathol. 56, 21–40 (2018). https://doi.org/10.1146/annurev-phyto-080516-035303
- Systematic exploration of domain assortments in NOD-like receptors uncovers two types of NACHT domains in Sordariales fungi. L. Bonometti, F. Charriat, N. Hensen, S. Minana Posada, H. Johannesson, P. Gladieux. bioRxiv 2024.11.26.625400; doi: https://doi.org/10.1101/2024.11.26.625400
Fungi as members of animal microbiomes (with Clara Igelmann)
All animals harbour complex microbial communities consisting of bacteria, archaea, algae and fungi. These microorganisms live in a close and interdependent relationship with their host forming a metaorganism, and they have a significant impact on host development, metabolism, behaviour and immunity. The freshwater polyp Hydra is a well-established and versatile animal model for metaorganism research. While the functional relevance and composition of its bacterial microbiome has been described, the fungal microbiome remains largely unexplored.
We aim to gain insight into the diversity and function of fungi that colonise animals by characterising the fungal microbiome of Hydra and investigating its functional relevance in the animal model, both in terms of its influence on Hydra-associated bacteria and on the host itself.
Relevant papers:
- Fraune S., Anton-Erxleben F., Augustin R., Franzenburg S., Knop M., Schröder K., Willoweit-Ohl D., Bosch T. C. G. (2015). Bacteria–bacteria interactions within the microbiota of the ancestral metazoan Hydra contribute to fungal resistance. The ISME Journal, 9(7), 1543–1556.
- Deines P., Lachnit T., BoschT. C. G. (2017). Competing forces maintain the Hydra metaorganism. Immunological Reviews, 279(1), 123-136.
The evolution of new opportunistic human pathogens (with Marco Guerreiro)
Pathogenic fungi are highly diverse, and an increasing threat to crops, animals and humans. Most of the human pathogenic fungi are found in the environment. These opportunistic pathogens are able to transition from a saprotrophic lifestyle and become human pathogens, while other closely related species are exclusively saprotrophic. Currently, little is known about the genomic and biological mechanisms enabling this transition from saprotrophic to pathogenic lifestyles. By using comparative evolutionary genomics, physiology and fungal biology, we aim to understand the adaptive evolution of saprotrophic fungi to a human host.
Relevant papers:
Guerreiro MA, Yurkov A, Nowrousian M, Broders K, Stukenbrock E. (preprint 2024). Genomic and physiological signatures of adaptation in pathogenic fungi. Preprint available at Research Square https://doi.org/10.21203/rs.3.rs-5041869/v1
Fisher MC, Gurr SJ, Cuomo CA, Blehert DS, Jin H, Stukenbrock EHStajich JE, Kahmann R, Boone CDenning DW, Gow NAR, Klein BS, Kronstad JW, Sheppard DC, Taylor JW, Wright GD, Heitman J, Casadevall A, Cowen LE.2020.Threats Posed by the Fungal Kingdom to Humans, Wildlife, and Agriculture. mBio11:10.1128/mbio.00449-20. https://doi.org/10.1128/mbio.00449-20
Molecular plant-pathogen interactions in times of climate change (with Anica Schmauch and Maxim Faroux)
Plant pathogens must defeat the plant immune system to colonize their host. The secretion of effectors by the pathogen alters host physiology to suppress immune responses. We aim to identify which plant molecular pathways are targeted by effector molecules produced by fungal pathogens belonging to the genus Zymoseptoria. In the light of climate change we aim to investigate how robust plant immune reponses are under increased temperatures and how high temperatures influence virulence by the pathogen.
Relevant papers:
- Highly flexible infection programs in a fungal plant pathogen. Haueisen J, Moeller M, Eschenbrenner CJ, Grandaubert J, Seybold H, Adamiak H, Stukenbrock EH. 2018. Evolution and Ecology. 1–20. doi:10.1002/ece3.4724.
Identifying host range of Zymoseptoria spp. in domesticated and wild grasses (with Rune Hansen)
Host infection is a crucial step for the completion of life cycle for many fungal plant pathogens and therefore identifying the host range of such organisms is extremely relevant. The genus Zymoseptoria comprises fungal plant pathogens of different grass species, in which Z. tritici represents an important pathogen of wheat. We have identified a population of Zymoseptoria spp. infecting wild, uncultivated grass hosts from the genus Aegilops spp. in Iran. Similarly, another population of Zymoseptoria spp. has been isolated from domesticated wheat, also sampled in Iran. We aim to identify the host range of these populations through comparative grass infection assays using cultivated wheat (Triticum aestivum), several Aegilops species as A. tauschii and A. geniculata and other wild grasses under greenhouse or phytochamber conditions.
Relevant papers:
- Kumar, A., Kapoor, P., Chunduri, V., Sharma, S., & Garg, M. (2019). Potential of Aegilops sp. for improvement of grain processing and nutritional quality in wheat (Triticum aestivum). Frontiers in plant science, 10, 308.
- Stukenbrock, E. H., Quaedvlieg, W., Javan-Nikhah, M., Zala, M., Crous, P. W., & McDonald, B. A. (2012). Zymoseptoria ardabiliae and Z. pseudotritici, two progenitor species of the septoria tritici leaf blotch fungus Z. tritici (synonym: Mycosphaerella graminicola). Mycologia, 104(6), 1397-1407.
Unraveling the biology of the sugar beet infecting pathogen Cercospora beticola (Bsc or Msc thesis project in collaboration with the EnvGen group and the company Strube Research)
This project will focus on the infection biology and fungicide resistance of the fungus Cercospora beticola that causes spot disease on sugar beet. The student project will use microscopy analyses, plant experiments, infection assays and in-vitro experiments to study virulence and fungicide tolerance of this important pathogen. Please contact Eva for more information: estukenbrock [a] bot.uni-kiel.de
Relevant papers:
- Rangel, L. I., Spanner, R. E., Ebert, M. K., Pethybridge, S. J., Stukenbrock, E. H., de Jonge, R., ... & Bolton, M. D. (2020). Cercospora beticola: The intoxicating lifestyle of the leaf spot pathogen of sugar beet. Molecular Plant Pathology, 21(8), 1020-1041.
Please contact, by email, Eva Stukenbrock or project-related persons for more info to the individual projects.
Plant-pathogen-microbe interactions (with Liz Florez, Victor Flores-Nuñez and Eva Tanneau)
We aim to understand how plant pathogens and the plant microbiome interact with each other in their host. The student projects will focus on the characterization of pathogens and microorganisms from diverse hosts and their mechanisms of interaction. The specific aims are:
- Understand differences in microbiome composition and function in wild and cultivated plants.
- Identify mechanisms of interaction between plant pathogens and the microbiome, and characterize how these interactions affect disease progression.
- Study the role of pathogen effectors in manipulating the plant microbiome.
Relevant papers:
- Flores-Nunez, V. M., & Stukenbrock, E. H. (2024). The impact of filamentous plant pathogens on the host microbiota. BMC biology, 22(1), 175.
- Hassani, M. A., Özkurt, E., Seybold, H., Dagan, T., & Stukenbrock, E. H. (2019). Interactions and coadaptation in plant metaorganisms. Annual Review of Phytopathology, 57(1), 483-503.
Unraveling patterns of adaptive evolution in fungal plant pathogens (with Thais Dal'Sasso and Lucas Bonometti)
Becoming a pathogen involves major genome adaptations. Effector-like proteins play a direct role in the infection of plants by fungal pathogens, while Nod-Like Receptors (NLR) are suspected to be a main component of fungal immunity. Both effector-like and NLR gene families are very dynamic, and a fast evolution of these gene families could drive pathogen adaptation and host-pathogen interactions. We use computational analyses to study effectors and fungal NLR genes in the plant-pathogenic genus Zymoseptoria. In particular, we aim to understand how these families evolved within Z. tritici and between different Zymoseptoria species, using comparative genomics, population genomics, and structure predictions.
Relevant papers:
- Witold Dyrka, Marina Lamacchia, Pascal Durrens, Bostjan Kobe, Asen Daskalov, Matthieu Paoletti, David J. Sherman, Sven J. Saupe, Diversity and Variability of NOD-Like Receptors in Fungi, Genome Biology and Evolution, Volume 6, Issue 12, December 2014, Pages 3137–3158, https://doi.org/10.1093/gbe/evu251- Sánchez-Vallet, A., Fouché, S., Fudal, I., Hartmann, F. E., Soyer, J. L., Tellier, A. & Croll, D. The genome biology of effector gene evolution in filamentous plant pathogens. Annu. Rev. Phytopathol. 56, 21–40 (2018). https://doi.org/10.1146/annurev-phyto-080516-035303
- Systematic exploration of domain assortments in NOD-like receptors uncovers two types of NACHT domains in Sordariales fungi. L. Bonometti, F. Charriat, N. Hensen, S. Minana Posada, H. Johannesson, P. Gladieux. bioRxiv 2024.11.26.625400; doi: https://doi.org/10.1101/2024.11.26.625400
Fungi as members of animal microbiomes (with Clara Igelmann)
All animals harbour complex microbial communities consisting of bacteria, archaea, algae and fungi. These microorganisms live in a close and interdependent relationship with their host forming a metaorganism, and they have a significant impact on host development, metabolism, behaviour and immunity. The freshwater polyp Hydra is a well-established and versatile animal model for metaorganism research. While the functional relevance and composition of its bacterial microbiome has been described, the fungal microbiome remains largely unexplored.
We aim to gain insight into the diversity and function of fungi that colonise animals by characterising the fungal microbiome of Hydra and investigating its functional relevance in the animal model, both in terms of its influence on Hydra-associated bacteria and on the host itself.
Relevant papers:
- Fraune S., Anton-Erxleben F., Augustin R., Franzenburg S., Knop M., Schröder K., Willoweit-Ohl D., Bosch T. C. G. (2015). Bacteria–bacteria interactions within the microbiota of the ancestral metazoan Hydra contribute to fungal resistance. The ISME Journal, 9(7), 1543–1556.
- Deines P., Lachnit T., BoschT. C. G. (2017). Competing forces maintain the Hydra metaorganism. Immunological Reviews, 279(1), 123-136.
The evolution of new opportunistic human pathogens (with Marco Guerreiro)
Pathogenic fungi are highly diverse, and an increasing threat to crops, animals and humans. Most of the human pathogenic fungi are found in the environment. These opportunistic pathogens are able to transition from a saprotrophic lifestyle and become human pathogens, while other closely related species are exclusively saprotrophic. Currently, little is known about the genomic and biological mechanisms enabling this transition from saprotrophic to pathogenic lifestyles. By using comparative evolutionary genomics, physiology and fungal biology, we aim to understand the adaptive evolution of saprotrophic fungi to a human host.
Relevant papers:
Guerreiro MA, Yurkov A, Nowrousian M, Broders K, Stukenbrock E. (preprint 2024). Genomic and physiological signatures of adaptation in pathogenic fungi. Preprint available at Research Square https://doi.org/10.21203/rs.3.rs-5041869/v1
Fisher MC, Gurr SJ, Cuomo CA, Blehert DS, Jin H, Stukenbrock EHStajich JE, Kahmann R, Boone CDenning DW, Gow NAR, Klein BS, Kronstad JW, Sheppard DC, Taylor JW, Wright GD, Heitman J, Casadevall A, Cowen LE.2020.Threats Posed by the Fungal Kingdom to Humans, Wildlife, and Agriculture. mBio11:10.1128/mbio.00449-20. https://doi.org/10.1128/mbio.00449-20
Molecular plant-pathogen interactions in times of climate change (with Anica Schmauch and Maxim Faroux)
Plant pathogens must defeat the plant immune system to colonize their host. The secretion of effectors by the pathogen alters host physiology to suppress immune responses. We aim to identify which plant molecular pathways are targeted by effector molecules produced by fungal pathogens belonging to the genus Zymoseptoria. In the light of climate change we aim to investigate how robust plant immune reponses are under increased temperatures and how high temperatures influence virulence by the pathogen.
Relevant papers:
- Highly flexible infection programs in a fungal plant pathogen. Haueisen J, Moeller M, Eschenbrenner CJ, Grandaubert J, Seybold H, Adamiak H, Stukenbrock EH. 2018. Evolution and Ecology. 1–20. doi:10.1002/ece3.4724.
Identifying host range of Zymoseptoria spp. in domesticated and wild grasses (with Rune Hansen)
Host infection is a crucial step for the completion of life cycle for many fungal plant pathogens and therefore identifying the host range of such organisms is extremely relevant. The genus Zymoseptoria comprises fungal plant pathogens of different grass species, in which Z. tritici represents an important pathogen of wheat. We have identified a population of Zymoseptoria spp. infecting wild, uncultivated grass hosts from the genus Aegilops spp. in Iran. Similarly, another population of Zymoseptoria spp. has been isolated from domesticated wheat, also sampled in Iran. We aim to identify the host range of these populations through comparative grass infection assays using cultivated wheat (Triticum aestivum), several Aegilops species as A. tauschii and A. geniculata and other wild grasses under greenhouse or phytochamber conditions.
Relevant papers:
- Kumar, A., Kapoor, P., Chunduri, V., Sharma, S., & Garg, M. (2019). Potential of Aegilops sp. for improvement of grain processing and nutritional quality in wheat (Triticum aestivum). Frontiers in plant science, 10, 308.
- Stukenbrock, E. H., Quaedvlieg, W., Javan-Nikhah, M., Zala, M., Crous, P. W., & McDonald, B. A. (2012). Zymoseptoria ardabiliae and Z. pseudotritici, two progenitor species of the septoria tritici leaf blotch fungus Z. tritici (synonym: Mycosphaerella graminicola). Mycologia, 104(6), 1397-1407.
Unraveling the biology of the sugar beet infecting pathogen Cercospora beticola (Bsc or Msc thesis project in collaboration with the EnvGen group and the company Strube Research)
This project will focus on the infection biology and fungicide resistance of the fungus Cercospora beticola that causes spot disease on sugar beet. The student project will use microscopy analyses, plant experiments, infection assays and in-vitro experiments to study virulence and fungicide tolerance of this important pathogen. Please contact Eva for more information: estukenbrock [a] bot.uni-kiel.de
Relevant papers:
- Rangel, L. I., Spanner, R. E., Ebert, M. K., Pethybridge, S. J., Stukenbrock, E. H., de Jonge, R., ... & Bolton, M. D. (2020). Cercospora beticola: The intoxicating lifestyle of the leaf spot pathogen of sugar beet. Molecular Plant Pathology, 21(8), 1020-1041.