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Development and implementation of a new method to assess fungal diversity – a case study in species rich calcareous grasslands

(field work only possible between July and October)

Due to irregular fructification times the assessment of fungal diversity in a particular habitat is usually time-consuming and costly. Next generation sequencing techniques allow for new strategies to assess the diversity of fungi via the collection of airborne spores and subsequent meta-barcoding. Within this master project, these new methods will be applied and tested to assess the fungal diversity of calcareous grasslands which typically host a rich mycoflora. Therefore, simple passive spore traps will be placed on selected study plots and diversity of trapped fungal spores investigated using common next generation sequencing meta-barcoding techniques. In parallel, fungal diversity will be assessed using traditional surveying methods around spore traps. Does the method produce relevant and usable results? Do we find the same species as detected with traditional methods? What are the advantages and disadvantages of this new method? These and other questions should be addressed during the project.

Ectomycorrhizal diversity of the none-native tree species Douglas fir

(possible year round)

Non-native tree species are frequently planted in our forests due to their advantageous traits (faster growth, less susceptible to diseases etc.) compared to native species. In addition, due to climate change species are often selected based on their ability to deal with a warmer and drier climate. However, what’s the effect of these alien species on our native fungal diversity? How many of our native species can colonize these non-native trees and are there species that were introduced along with the non-native tree species? To find an answer to these questions will be the goal of this master thesis. You will study the ectomycorrhizal diversity of Douglas fir Pseudotsuga menziesii (other possible species: Japanese larch Larix kaempferi, black pine Pinus nigra, northern red oak Quercus rubra etc.) in different planted stands by morphotyping ectomycorrhized root tips and subsequent genotyping (using next-generation sequencing). Results will be compared to the known myco-flora of Douglas fir in its native range.

Unknown introduction of a Larix endophyte from Asia?

(possible year round, optimally in spring)

Alien invasive fungi nowadays are a major problem in our forests potentially causing massive dieback on particular native tree species such as e.g. Ulmus sp. Fraxinus excelsior or Castanea sativa. One group of fungi that pose a particularly high risk are the so called endophytes – that are fungi that colonize plant tissues without necessarily causing symptoms. These fungi are typically not detected or overlooked when shipping plant material from one continent to another. Moellerodiscus advenula (syn=Lambertella advenula) is a needle endophyte of Larix decidua. The species is probably very frequent on needles of L. decidua but very rarely reported possibly due to its minute size. Thus, its distribution in Switzerland is vastly unknown. Recently, the same species has been reported on Japanese larch Larix kaempferi in Japan. Preliminary genetic analyses have identified fixed differences in the ITS region between M. advenula from Japan and Europe, possibly indicating cryptic speciation within M. advenula. L. kaempferi is frequently planted for timber production in Europe. The aim of this master thesis is to (i) better characterize the frequency of occurrence and the distribution of M. advenula in Switzerland; (ii) to verify whether M. advenula is also found on L. kaempferi planted in Europe and (iii) to genetically screen samples of M. advenula to check which ITS genotypes are present in Europe.

Do meadows along railways provide a good surrogate habitat for fungi typically found in nutrient-poor meadows?

(possible start date in July-August)

Meadows along railways are often extensively managed, i.e. not fertilized and cut infrequently. Besides, we can find different types of meadows ranging from dry and nutrient-poor (often steep slopes next to railways) to wet and nutrient-poor meadows. Even though they are particularly species rich, these types of meadows disappear and get fragmented more and more especially in the Swiss plateau (Mittelland). There are also a range of specialized agaric fungi to be found on these types of meadows (e.g. genus Hygrocybe) and a lot of them are endangered due to habitat loss. Therefore, meadows along railways could provide an excellent surrogate habitat and stepping stone to connect the remaining habitats, for fungi typically growing in such pastures. During this master thesis, the fungal species richness will be monitored in pastures along selected railways using traditional methods. Thereby we would like to find an answer to the following questions: (i) Do we find the typical set of species expected in meadows along railways? (ii) Could these habitats serve as surrogate habitat for these species? (thesis includes field work, microscopic identification of species, statistical analyses)

Developing a metabarcoding method for the characterization of fungal communities in deadwood

(possible year round)

Metabarcoding is more and more often used to characterize the fungal communities in deadwood. Thereby, communities are characterized by drilling holes into the deadwood to be analyzed and collecting the drilling dust. Subsequently, DNA is extracted from the collected material, sequenced, and bioinformatically analyzed. Virtually all studies carried out so far identified a surprisingly high fungal species richness within the deadwood which contrasts with estimates from classical observation-based approaches. In addition, considering the one species – one niche hypothesis, a deadwood should provide a limited number of niches in a certain point in time. This leads us to the question which of both estimate is more realistic/correct? Within this master thesis we will therefore try to identify common sources of errors in the commonly applied metabarcoding approach. We will make tests with different drilling depths and different stages of wood decomposition while trying to exclude typical sources of contaminations. (thesis will include field work, lab work and bioinformatic analysis)