Karlovsky lab: BSc and MSc topics

MSc project: Effect of fungal metabolites on predatory and fungivorous mites

Predatory mites are important biological control agents used to control pests. The disadvantage of mites as biocontrol agents is that they don't survive starvation. Therefore, alternative food has to be provided in the absence of prey; commercially available plant pollen (e.g. Nutrimite from Biocare) is commonly used. Some predatory mites also consume filamentous fungi, other mite species preferentially feed on fungi. Mite fungivory is interesting for biocontrol development because it may save costs for alternative food and suppress fungal pathogens of plants. In this project, feeding of selected mite species on plant pathogenic fungi and the effect of mycotoxins and fungal defense metabolites on the food preference of mites will be studied. Cultures of several mite species are established in the lab and two new species, including one known to feed on Fusarium spp., recently arrived.

Relevant publications:
Discovery of major fungal chemical defense against predators

Contact: Ana Flores, Prof. Petr Karlovsky (see homesite for emails and phone numbers)

BSc- or MSc-topic: Effect of mycoviruses of Fusarium graminearum on food preference and fitness of fungivorous animals

For BSc- and MSc-thesis the topic is the same, just the extent of work differs. The task is to find out whether infection of plant pathogenic fungus F. graminearum with mycoviruses affects the attractiveness of the fungus for animals and whether fungal strains infected with mycoviruses become less toxic to animals. In the last year, the first mycovirus was reported to infect the insect that consumed fungal mycelia containing the mycovirus. Therefore, persistence of mycoviruses in the body of animals will be investigated by reverse-transcription real-time PCR. Invertebrates representing a wide phylogenetic range from springtails (primitive hexapods) and woodlice (crustaceans) to storage and crop pests (insects) will be studied. In the MSc thesis, fungivorous nematodes can also be tested.

Relevant publications:
Discovery of major fungal chemical defense against predators
Dissemination of Fusarium proliferatum by meal beetle

Contact: Simon Schiwek, Prof. Petr Karlovsky (see homesite for emails and phone numbers)

MSc-topic: Fungal diet of land isopods - molecular ecological study

The goal of the study is to shed light on the food preference of land isopods (woodlice, German Asseln) for fungi. A unique aspect of the project is that feeding experiments will be carried out in free nature. Territories delimited by plastic cylinders (see hyperlink below) will be established in different habitats and seeded with the same number of individuals of three isopod species. After a week, the animals will be retrieved and brought to the lab. The content of their digestive track will be investigated by extracting the DNA, amplifying taxonomically informative segments of fungal genomes by PCR, and analyzing the amplicons by next-generation sequencing. The experiment is expected to reveal which fungi the isopods consume in their natural environment and show how the species and habitat affect the fungal diet of isopods.

Further information:
Working with experimental arenas in different habitats
Discovery of major fungal defense against predators

Contact:
Lukas Beule, Prof. Petr Karlovsky (see homesite for emails and phone numbers)

Bachelor- oder Masterarbeit: Wirkung von Inhaltsstoffen von Sesam auf Insekten

Sesam (Sesamum indicum L.) akkumuliert in seinen Samen spezifische Sekundärmetaboliten, die als Lignane bezeichnet werden. Diese wirken antioxidativ, tragen zum Geschmack und Aroma von Sesamsamen und Sesamöl bei und sind für die Stabilität von Sesamöl verantwortlich. Außerdem wird ihnen eine gesundheitsfördernde Wirkung zugeschrieben. Naturstoffchemiker und Ernährungswissenschaftler haben die Lignane von Sesam eingehend untersucht, die biologische Funktion dieser Naturstoffe ist jedoch unbekannt. Die Aufgabe ist zu untersuchen, ob Lignane von Sesam den Schutz gegen Insektenfraß verstärken, indem sie auf Insekten toxisch oder repellent wirken. Zusätzlich werden langfristige Effekte untersucht werden und ausgewählte Sesamsorten aus Asien, Afrika und Leteinamerika mit unterschiedlichem Lignangehalt hinsichtlich ihrer Wirkung auf Insekten verglichen.

Contact:
Dr. Mohammad Alhussein, Prof. Petr Karlovsky (see homesite for emails and phone numbers)

MSc project: Analysis of mycotoxins by HPLC-MS

Mycotoxins are fungal metabolites with harmful effects on animal and human health. Legal limits in food and feed have been established and mycotoxin production by various fungi under different conditions is a subject of many studies. In spite of extensive research, a lot remains to be discovered!

Analytical chemistry plays a crucial role in the investigation of mycotoxins by providing elaborated separation and detection techniques. The goal of the MSc project is to help developing a universal strategy to detect all trichothecenes (a large group of mycotoxins produced by many Fusarium species) via HPLC-MS/MS and improving the quantification of beauvericin.

The candidate will work with modern instrumentation (check check here) and gain insight into the world of chromatography and mass spectrometry under close supervision.

Contact: Prof. P. Karlovsky, Dr. Anna Rathgeb

MSc project: Characterization of fungal isolates from maize harvested in the Philippines

This project will be supervised by Prof. Christian Cumagun. A set of fungal isolates (Aspergillus spp., Fusarium spp.) from maize grown in the Philippines will be characterized regarding their taxonomic affiliation, genetic diversity and potential to produce mycotoxins.

Contact: Prof. Ch. Cumagun, Prof. P. Karlovsky

MSc project: Metabolic diversity of endophytic fungi acting as antagonists of plant pathogens

This project will be supervised by Prof. Christian Cumagun. A set of fungal endophytes from the Philippines selected due to their ability to suppress fungal pathogens will be characterized their production of volatile compounds (collaboration with Prof. C. Müller, Bielefeld) and soluble metabolites (Dr. Anna Rathgeb).

Contact: Prof. Ch. Cumagun, Prof. P. Karlovsky

MSc project: Function of MAR pathway in fungi

Fungi produce a range of species-specific secondary metabolites. It is assumed that the biological function of these metabolites relies in modulating ecological interactions of fungi with other organisms. A new biosynthetis pathway hypothesized to be involved in ecological relationships has recently been discovered in our laboratory. We named the pathway MAR. Gene disruption mutants were generated for the key gene of the pathway. The task of the MSc proeject is to test the effect of the gene disruption on a range of organisms (nematodes, arthropodes, mycoparasites) in order to discover the natural target of the metabolites.

Contact: Mohammad Alhussein, Maria Vinas, Prof. P. Karlovsky

MSc project: Alternative biological functions of fungal NLP proteins

NLPs are small proteins produced by many bacteria and fungi. NLPs of phytopathogenic fungi are cytotoxic, cause strong necrosis in the leaves of dicotyledoneous plants. The role of NLPs in plant infection is unknown.
The task is to test fungal mutants with disrupted production of NLPs in different systems in order to reveal the biological function of the proteins. Nonhost plants and unconventional targets will be tested to solve the puzzle that most mutants of pathogenic fungi that do not produce NLPs are not impaired in their pathogenicity.

Contact: Mohammad Alhussein, Ling Su, Prof. P. Karlovsky

MSc project: infecton of Brassica napus with Verticillium longisporum and the role of NLP proteins

V. longisporum is a fungal pathogen infecting oilseed rape and other crucifers. The pathogen invades plant roots and colonizes hypocotyl. At late stages of infection the fungus invades the entire stem and produces microsclerotia. The disease caused by "V. longisporum" is different from "Verticillium wilt" caused by other Verticillium species in vegetables, cotton and other plants because V. longisporum does not cause wilting.
NLPs are small proteins secreted by V. longisporum and other phytopathogenic fungi. NLPs are cytotoxic, causing necrosis after infiltration into plant leaves. The role of NLPs in plant infection is unknown.
The task is to culture a special variety of B. napus called Rapid Cycling Brassica, which completes its entire growth cycle within two months, inoculate plants with V. longisporum strains (wild-type and strains impaired in the production of NLPs) by dipping their roots to spore suspension, monitor disease progress, take samples and analyze the expression of NLP genes by RT qPCR and the presence of NLP proteins in the plant by Western Blotting.

Contact: Ling Su, Prof. P. Karlovsky

MSc project: Analysis of fungal colonization of maize

Maize grains collected at several sampling locations in Germany in 1998 and 2005-2007 and kept deep frozen since then will be used. It was not possible at the time when the samples were collected to quantify the biomass of fungal pathogens infecting maize in a species-specic way. The task is to extract total DNA and determine the content of DNA of fungal pathogens using species-specific real-time PCR assays in 384-well microplates. The assays comprise all important mycotoxin-producing fungi colonizing maize grains, including seven Fusarium species and aflatoxin-forming Aspergillus species. The results on historical material will be compared with the current situation. The study should reveal whether species spectrum of fungi infecting maize ears changed during the last 18 years.

Prerequisites: Understanding maize production and plant pathology.
Hands-on experience with classical PCR and/or qPCR would be useful but is not obligatory.

Contact: Prof. Petr Karlovsky

MSc project: biological function of fumonisins

Fumonisins are mycotoxins produced mainly by Fusarium verticillioides and Fusarium proliferatum in maize and other host plants. Fumonisins are tocix to farm animals, causing pulmonary edema in pigs and encephalomalacia in horses. They have been proven to act as carcinogents in rodents and suspected to contribute to cancer of the esophagus and spina bifida in humans. The biological function of fumonisins remains unknown. Infection experiments with Fusarium verticillioides strains with disrupted fumonisin synthesis lead to controversial results; in some experiment fumonisins appeared to be involved in disease development, in other experimehts the disrupted mutants were as virulent as fumonisin-producing strains (e.g., Dastjerdi and Karlovsky 2015). The goal of the MSc project is to clarify whether fumonisins are involved in interactons between Fusarium verticillioides and fungivorous arthropods. Small arthropods (springtails and woodlice) will be fed with wild-type Fusarium verticillioides strains and with genetically engineered strains with disrupted fumonisin synthesis pathway. Food preference and the fitness of fungivores feeding on strains producting and not producing fumonisins will be recorded and compared. The fate of fumonisins ingested by the animals will be monitored by HPLC-MS/MS.

Contact: Dr. Katharina Pfohl

Masterarbeit: Inhibition des Pilzwachstums durch Metaboliten von Landasseln

Ziel der Arbeit besteht in der Untersuchung von antifungalen Substanzen, die (i) auf der Kutikula von Landasseln und (ii) als Rückstände der Asselaktivität im besiedelten Substrat vorkommen, und die Überprüfung ihrer Wirksamkeit an Pilzkulturen. Solche Substanzen sind für die Entwicklung von antifungalen Wirkstoffen für den Pflanzenschutz und die Humanmedizin interessant. Darüber hinaus wird die Untersuchung unser Verständnis der chemischen Ökologie von Landasseln erweitern.

Methoden:
- Pflege von Asselkulturen, Anzucht von Pilzkulturen
- Extraktion antifungaler Substanzen aus Bestandsmaterial
- experimentelle Überprüfung extrahierter Substanzen an Pilzkulturen
- Datenanalyse und -auswertung

Bachelor- bzw. Masterarbeit: Futterwahl von Landasseln im natürlichen Habitat

Ziel der Arbeit besteht in der Untersuchung von Pilzen, die im Verdauungstrakt diverser Landassel-arten aufzufinden sind, mithilfe von DNA-analytischen Methoden.

Methoden: Sammeln von Asseln im Freiland, Mikroskopische Präparation der Verdauungstrakte, DNA-Extraktion, DGGE und artspezifische qPCR.

Fungal diet of soil mesofauna

Many small soil invertebrates (soil mesofauna, defined by size between 0.1 and 2.0 mm) feed on fungi. Colembola, mites and fungivorous nematodes have been studied extensively in this respect. The goal of this project is to look at other, less known invertebrates that feed on fungi and study their diet and food preference.
Techniques: Barlese funnel, microscopy, PCR, DGGE.

Volatile compounds in soil ecology

Plant roots and microbes in the rhizosphere secrete diverse metabolites to modulate symbiotic and/or pathogenic interactions. Richard Splivallo's group addresses the role of bacteria-truffle interactions in truffle aroma and studies plant root volatiles. Interesting topics are available in both fields. A new portable GC-FAIMS system will be available for the project.
Techniques: Analysis of volatiles (SPME, GC), microscopy.

Enzymatic detoxification of mycotoxins

Genes encoding enzymes that detoxify mycotoxins will be overexpressed and their enzymatic activities will be studied. The project will be supported by Ruth Pilot. (Screening for new active microbial strains is not intended in this project.)
Techniques: Heterologous gene expression, purification of recombinant proteins, enzymatic assays with TLC or HPLC.

Mycotoxins and Fusarium species in Amaranthus

Raana Dastjerdi in our lab found out that certain weeds are heavily colonized with Fusarium spp. Amaranthus, which is grown for organic markets, is one of these weeds. The goal is to study how Fusarium spp. infect the plant and which role mycotoxin play in this process.
Techniques: Plant inoculation, qPCR, mycotoxin analysis.

Ecological role of mycotoxins in nematode/fungus interactions

Free-living nematode Aphelenchoides saprophilus feeds on fungi. Certain mycotoxins may protect fungi from predation. The task is to study ecological role of mycotoxins in the protection of fungi against nematodes or (by interest) other soil invertebrates. This project was initiated by Marie Reuther.
Techniques: Nematological methods, qPCR, mycotoxin analysis.

Secondary metabolites of Botrytis cinerea

Interesting secondary metabolites of B. cinerea have been identified in collaboration with TU Kaiserslautern by metabolic profiling. The task is to purify these metabolites and study their biological activities. The work may involve genetically engineered Botrytis strains, the project is supported by Kuang Yi.
Techniques: Purification of natural products by flash chromatography, preparative HPLC and TLC; bioassays.

Mycotoxins in fungal interactions

Secondary metabolites play key roles in interactions among fungi such as competition and mycoparasitism. The goal is to study fungal fitness in mixed cultures involving genetically engineered strains with modified abilities to synthesize and/or inactivate mycotoxins.
Techniques: Microbial techniques, DNA-based techniques for biomass analysis.