Student projects ¶

(Master thesis - 6 months)

Title: Testing the Janzen–Connell hypothesis using sweet chestnut seeds and Phytophthora
Supervisors: Dr. Iva Franić (iva.franic(at)wsl.ch), Dr. Simone Prospero (simone.prospero(at)wsl.ch)
Start: Autumn 2026
Language: English
Description of the project: The Janzen–Connell hypothesis predicts that host-specific natural enemies cause distance- and density-dependent seedling mortality, thereby promoting plant diversity. In sweet chestnut (Castanea sativa), soil-borne Phytophthora pathogens (e.g., P. cinnamomi, P. x cambivora, P. plurivora) infect roots and can cause damping-off and root rot (i.e., ink disease). As these pathogens may accumulate around conspecific trees and at high seedling densities, they could reduce seedling recruitment and contribute to Janzen–Connell effects. However, evidence directly linking Phytophthora abundance to sweet chestnut seedling mortality is limited.

To test this, a factorial experiment will manipulate soil origin (conspecific vs. heterospecific), seed density (low, medium, high), and pathogen presence. Over 8–12 weeks, seedling germination, survival, growth, and root health will be monitored, while Phytophthora abundance in soil and roots will be quantified using molecular and culture-based methods.

We expect that (i) conspecific soils will contain higher Phytophthora inoculum, (ii) pathogen inoculum will increase with seed density, and (iii) seedling survival and performance will decline with increasing pathogen pressure. This study will provide a robust test of the role of Phytophthora in driving Janzen–Connell effects in sweet chestnut and will improve our understanding of pathogen-mediated regeneration dynamics and disease management.

Title: Interactions between the chestnut blight fungus Cryphonectria parasitica and bark-inhabiting bacteria
Supervisors: Dr. Simone Prospero (simone.prospero(at)wsl.ch), Dr. Iva Franić (iva.franic(at)wsl.ch), Ana Diaz Zuñiga (PhD student DiveInBiome; ana.diaz(at)wsl.ch)
Season: no preference (project to be conducted in the laboratory)
Start: Autumn 2026
Language: English
Description of the project: Chestnut blight caused by the invasive ascomycete Cryphonectria parasitica is a lethal disease of sweet chestnut (Castanea sativa). The pathogen kills the bark and the cambium of the host tree leading to the formation of perennial bark lesions called cankers. When these cankers girdle an infected stem or branch, the part distal to the infection point wilts and dies. However, in some parts of Europe, including southern Switzerland, the disease is successfully controlled by the parasitic virus CHV1, which reduces virulence and sporulation of the infected fungal strains. These debilitated strains of C. parasitica still induce the formation of bark cankers, but these remain superficial and are not lethal to the host.

When isolating C. parasitica from passive cankers, it is common to also recover other fungal species and bacteria. Indeed, in an ongoing PhD study (DiveInBiome), we detected a higher bacterial diversity in passive cankers than in healthy bark. However, it remains unclear whether such organisms contribute, alongside CHV1, to the healing process of bark cankers. In this project, you will test the potential of bacteria isolated from passive cankers to inhibit the growth of C. parasitica. The study involves the following steps:

1. Selection of bacterial strains from our collection, which, based on literature information, may have a potential biocontrol effect against fungi.

2. Testing the in vitro effect of 3-4 bacterial strains on the growth of virulent strains of C. parasitica using the “caging” method.

3. Molecular characterization of the selected bacterial strains (Sanger sequencing 16S, phylogenetic analyses).

Title: Improving chestnut bark microbiome characterization through optimized DNA extraction and PNA-clamp design
Supervisors: Dr. Iva Franić (iva.franic(at)wsl.ch), Ana Diaz Zuñiga (PhD student DiveInBiome; ana.diaz(at)wsl.ch)
Start: Autumn 2026
Language: English
Description of the project: Cryphonectria parasitica the causal agent of chestnut blight, infects the bark and cambium of European and American chestnut trees, forming cankers that can eventually kill the host. Infection by Cryphonectria hypovirus 1 (CHV1) reduces the virulence of the fungus, resulting in a benign canker phenotype. As part of the PhD project DiveInBiome, we are investigating the fungal and bacterial communities associated with these cankers and their potential roles in disease development. To improve microbial community characterization, we aim to optimize two key methodological steps: (A) DNA extraction from bark tissue, and (B) PCR amplification of bacterial DNA while minimizing co-amplification of host plant DNA.

1) DNA extraction from chestnut bark, especially from canker tissue, is challenging due to the high content of tannins, polyphenols and secondary metabolites that inhibit downstream PCR. This project will optimize DNA extraction protocols by testing different tissue amounts, alternative lysis buffers, and the addition of polyvinylpyrrolidone (PVP).

2) A second challenge is the co-amplification of plant chloroplast and mitochondrial DNA during bacterial 16S rRNA amplification. This project will assess and optimize peptide nucleic acid (PNA) clamps to selectively block amplification of plant organellar DNA during PCR by: (i) evaluating the specificity of universal clamps through in silico sequence alignments (ii) designing and/or testing chestnut specific PNA clamps, and (iii) validating PNA clamp effectiveness by PCR and qPCR.

Some adaptations of the scope of the project based on the student's preferences are possible.

Title: In silico validation and field testing of molecular assays for eDNA-based surveillance of invasive forest pests and their vectors
Supervisor: Dr. Lenin Riascos-Flores (lenin.riascos(at)wsl.ch)
Start: Autumn 2026
Language: English
Description of the project: The goal of this study is to develop molecular tools for the early detection of invasive forest pests and pathogens threatening forests in Switzerland and across Europe. Early detection is key to containing these organisms before they cause severe ecological and economic damage, and environmental DNA (eDNA, i.e. the genetic traces organisms leave in water, air, and on surfaces) offers a sensitive, non-invasive way to find them. Although several assays have already been developed, newly available sequences mean that some of these assays need to be re-evaluated to confirm their specificity.

The project brings together three complementary parts: (1) the in silico validation of molecular markers used to detect a range of forest pests and pathogens, including both fungi and insects, and their vectors, assessing how specifically each assay distinguishes the target from closely related species; (2) testing and comparison of detection methods, benchmarking novel approaches such as passive traps against established sampling techniques; and (3) validation both in the laboratory and with real field samples, working with material collected in the field, including cases of vector borne transmission, such as the pine wood nematode (Bursaphelenchus xylophilus) carried by its beetle vector Monochamus galloprovincialis.

You would gain hands on experience across computational, laboratory, and field work, with a real chance of contributing to a scientific publication. If you are curious about applying cutting edge eDNA approaches to forest health surveillance.

Title: Temporal dynamics of Armillaria populations in the Swiss Alps
Supervisor: Simone Prospero (simone.prospero(at)wsl.ch)
Start: Spring 2027
Language: German or English
Description of the project: The basidiomycete genus Armillaria has a worldwide distribution and plays a central role in the dynamics of numerous woody ecosystems, including natural forests, tree plantations, orchards, vineyards, and gardens. All Armillaria species can degrade dead woody substrates causing white rot and some species exhibit a parasitic ability and can be considered as facultative necrotrophs. In Switzerland, the preferentially saprotroph A. cepistipes is the most common species in coniferous stands where it frequently co-occurs with the pathogenic species A. ostoyae. 

Twenty years ago, we characterized the structure (number and distribution of genotypes) of three populations of both species in the southern Swiss Alps. This project aims to resample the same three populations (or at least 1-2 of them) and assess eventual temporal changes in their composition. Activities include rhizomorph sampling in the field, Armillaria isolation, DNA extraction and microsatellite genotyping.

(Bachelor thesis - 3 months)

Currently there are no open BA-theses.

(semester project, 3 months)

No semester projects open.