Molecular methods and population genetics. High throughput sequencing of “legacy” DNA markers to explore the biodiversity of soil organisms.
Supervisor: Clément Schneider
Type: Internship+Thesis
The aim of this project is to improve molecular laboratory methods for the sequencing of so called legacy DNA markers (nu-rDNA, mtDNA) useful for streamlined phylogenetic placement and identification of soil organisms. We propose an internship that focus on methodology. The offer could be further expended as a master thesis, in which you would analyses the diversity and connectivity of Springtails species populations in three monitoring sites of Germany, through population genetics. The project offers training in molecular method, laboratory work and bio-informatics, including first hand insight into third generation high-throughput DNA sequencing (Oxford Nanopore). Your main qualities are motivation, thoroughness and ability to show autonomous thinking, in particular in bibliography search and reading to find new ideas. Determination is also required to break through the lab work (lots of trial and error and troubleshooting is anticipated). Familiarity with a coding language and/or Linux environment is a major plus to harness the bio-informatics steps.MSc Thesis: Establishment of a fine grain monitoring scheme for soil mesofauna communities combining meta-genomics and image analysis (Deep-Learning).
Supervisor: Clément Schneider
Type: Thesis
Soil mesofauna communities are an essential part of soil ecosystems and their richness and composition can provide bio-indicators of soil wellness. However their analysis through traditional means is time-consuming The aim of this project is to establish a fine grain monitoring scheme of soil mesofauna communities combining image analysis (deep-learning) and meta-genomics. During the master thesis, the student goal is to establish a protocol and strategy to leverage innovative approaches (image analysis and meta-genomics) to allow monitoring of soil animals at high spatial and temporal resolution. In practice, the imaging and laboratory methods are pre-established and will require only transfer knowledge to the student. In turn the student is expected to help fine-tuning the methods and apply them to a real world study case. The project is for students interested the development and application of innovative tools for biodiversity monitoring. Programming skills are required (R or Python).”
Laboratory experiment: How environmental structure supports biodiversity?
Supervisor: Anton Potapov
Type: Internship+Thesis
What drives biodiversity in ecosystems? This is one of the most fundamental questions in ecology. However, there is still a lot to learn. In this innovative project, we would like to run experiment(s) to understand how ecosystem structure (distribution of resources and habitats in space and time) affects biodiversity of organisms at different scales (micro/macro). During the project, the student will construct different mini-ecosystems in the laboratory and populate them with organisms to see responses in soil biodiversity. The project is suitable for students who are interested to develop and test new bold ideas in the field of general ecology.
Field experiment: How soil detritivores support litter carbon sequestration in soil organic matter
Supervisor: Anton Potapov
Type: Internship+Thesis (not earlier than autumn 2024)
Did you know that soil invertebrates can consume >90% of fallen leaves in the forest? In fact, top layers of the soil are often consisting mainly of invertebrate faeces. This facilitates microbial growth in soil, but can it also facilitate productions and stabilisation of soil organic matter? To address this question, we participate in a cross-European pilot experiment with isotopically labelled invertebrate faeces. The student would prepare and implement a subset of the experiment near of Görlitz as a part of international team. The project is suitable for students who are interested in experimentation with soil functions and carbon cycling.