Dr. Salome Schneider
Microorganisms such as pathogens, biological control agents, symbionts, or decomposers considerably contribute to ecosystem functions and therefore may influence health and functioning of our planet. The focus of my research is put on the development, evaluation, and optimization of molecular tools to investigate microorganism in their natural environment and evaluate their potential influence on ecosystem functions. Innovation, creativity as well as patience are needed for bringing up such tools and use them in the field. I appreciate the possibility to develop such tools based on basic research and modify them for applied research or the industry.
I'm a member of the Phytopathology group and project leader of the Molecular Diagnostics. The main aim of this project is to monitor quarantine microorganisms in the forest. To do so we also establish, optimize and develop molecular diagnostic tools for relevant pests and pathogens. This includes exploring the potential of new technologies such as Oxford Nanopore.
Before joining the Phytopaths in April 2016 I was working as a postdoc in the DOM group at the Swedish Agricultural University in Uppsala. We developed molecular detection and quantification tools and investigated if the multi-year application of Bacillus thuringiensis subsp. israelensis for mosquito control affected naturally occurring B. cereus group populations in the soil. During my PhD in the Molecular Ecology group at Agroscope Reckenholz, I developed monitoring tools for investigating the interaction between soil, its fungal microbiota and entomopathogens in particular under different agricultural management systems.
As project leader, my responsibilities include the coordination of the work flow for the molecular diagnostics as well connect to other diagnostic laboratories dealing with forest pathogens in Switzerland as well as in Europe. I'm also involved in the monitoring of forest relevant pathogens such as the diseases Dothistroma and Lecanosticta needle blight, Phytophthora spp. and the pine wood nematode Bursaphelenchus xylophilus in Switzerland. It includes the development, evaluation and optimization of high through-put molecular detection tools such as quantitative PCR for fast, reliable and cost-effective diagnostic of forest relevant pathogens. Further information on forest pathogens under quarantine status you can find on the EPPO (European and Mediterranean Plant Protection Organization) as well as on our project homepage.
The seed trade is considered relatively safe from the phytosanitary point of view, compared with the trade in other live plants, and is thus less regulated. The pests potentially carried by seeds are, however, not well known. In order to fulfill phytosanitary regulations, it is important to have technologies allowing for fast and reliable analyses of traded seeds for potential risk at the custom. This is difficult since often it is not known for which pests and pathogens to look for. With Oxford Nanopore technologies (ONT) a promising tool is available that might fulfill the criteria of an easy, quick and cheap screening tool. The aim of this project is to evaluated the potential of ONT for diagnostics by setting up an efficient work flow for fast and robust analysis of fungal communities present in traded seeds. For evaluation, ONT sequencing data are compared with Illumina sequencing data form the same seed lot. Based on this, the potential of ONT as an easy, quick and cheap screening tool can be evaluated. In addition, the quality of generated data can be assessed by comparing to an established metagenomic sequencing methodology. Further steps can be defined that are necessary for using ONT as a diagnostic tools to reduce the risk of pests and pathogens dispersion through traded seeds.
In collaboration with Waldschutz Schweiz we conducted a large monitoring of Dothistroma and Lecanosticta needle blight pathogens in urban areas as well as in the forest in Switzerland in 2016. In a further step the distribution of different mating types were analyzed directly using needle DNA extracts. For both Dothistroma species, existing primers are used for mating type identification whereas for L. acicola, specific primers are developed. This project was part of a semester thesis done by Barryette Oberholzer under my supervision.
As part of his semester thesis under my supervision, Christopher Schefer investigated the abundance of dead bacteria on wood samples by quantitative PCR. Long-term detectability of dead bacteria may have a strong influence on the diagnostics in terms of biology as well as ecology of the pathogen.