Exploring chemotaxis in magnetotactic bacteria

Magnetotactic bacteria (MTB) are a diverse group of bacteria characterized by their capacity to biomineralize magnetite nanoparticles called magnetosomes. The latter allow MTB to passively align along magnetic field lines. This feature makes MTB of great interest to develop magnetic-guided microrobots used for medical applications such as targeted drug delivery. To make the latter efficient, it is not only essential to understand MTB magnetic behavior but also how MTB react to diverse chemical stimuli.
The aim of this internship is to broaden our understanding of chemotaxis in MTB. Several MTB species can be grown in the lab and will be investigated during the thesis. Typically, tethered cells and motility assays involving the use of microfluidics, microscopy and image analysis approaches will be developed to investigate, on a single-cell and population level, the chemotaxis responses of the strains to different chemical stimuli. These responses will be studied with bacteria grown in different growth conditions and in the absence or presence of a magnetic field using a custom-made magnetic microscope. Altogether, the data generated will give first insight into how MTB give an integrated response to chemical and magnetic stimuli and will therefore open new routes for the further development of targeted drug delivery.

The role of the signaling nucleotide ppGpp in plant resilience to climate change.

Amidst the growing challenges of climate change, crops face threats from rising temperatures and prolonged droughts, leading to reduced photosynthetic efficiency and the need for rapid stress acclimation. In this PhD project we will investigate the role of the nucleotide guanosine tetraphosphate (ppGpp) signalling pathway, a known regulator of plastid function and photosynthesis. Recent preliminary work from our and other labs indicate that ppGpp plays a pivotal role in plant stress acclimation, and we have indications that perturbation of ppGpp signalling affects plant responses to heat stress. This research aims to explore how ppGpp is involved in plant acclimation to heat and drought stress. Using a combination of physiological evaluations, biochemical techniques, transcriptomics, and biosensors this study will investigate the modulation of ppGpp levels under stress conditions, its impact on plastid genome expression, and its intersection with other signalling pathways. The ultimate goal is to enhance our understanding of ppGpp's role in plant acclimation, offering insights for improving crop resilience in a climate-challenged world.

Metal partitioning in coccolith-based calcite and biotechnological applications of metal-doped coccolith materials

Despite established cultures of coccolithophore microalgae and attainable large-scale production of coccolith biominerals (gram quantities of calcite mineral from litres of culture), the coccolith as an advanced functional material has made little progress in bionanotechnologies. This project will quantitatively describe metal doping into and on the surface of coccolith-based calcite for several transition metals, main group elements and lanthanides. Elucidating the potential of coccolithophore to incorporate metal ions into/onto biogenic calcite production will not only reveal the biotechnological possibilities for coccolith materials but will offer insights on the role of metals in the biomineralization process and the biological screening effect. Metal-doped coccolith materials will be subjected to physical and chemical characterization (focus placed on strategic metals that have enchanced incorporation into biogenic calcite or can be replaced/deposited on coccoltih surface). Select metal-doped coccolith candidates will be pursued for biotechnological application accordingly based on their physical and optical properties (e.g., catalytic activity for transition metals and photoluminescence for lanthanides).

RootExu-C : Plant genetic control of root exudation and microbiome assembly

Ongoing breeding programs selected for crop varieties with high yield under favorable conditions: sufficient water supply (irrigation) and high levels of chemical fertilizers (N, P). However, increased abiotic stresses (drought, salinity, high temperatures) as well as ecological concerns demand for new traits to transition to more sustainable production systems. One approach may consist in better control and exploitation of root microbiota, which have the potential to protect their host plants from abiotic and biotic stresses, and to improve nutrition and productivity. It is assumed that plant innate immunity and root exudates scale and structure root microbiota, but exact mechanisms remain unknown. In this project, I propose to analyze “root-adhering soil” (RAS), the soil aggregated around roots, as a global proxy for shoot-to-root carbon allocation, root exudation and recruitment of exopolysaccharide-producing microbiota in Solanum lycopersicum (tomato). A respective PhD student shall analyze the RAS trait in a tomato natural variation panel towards the identification of underlying genes. Further, he/she shall directly inactivate candidate genes assumedly involved in root exudation (multiplex CRISPR/Cas). Lines with contrasting RAS phenotypes, from natural and/or induced variation, will be analyzed for microbiota recruitment and exudate composition. This will provide fundamental knowledge on the genetic control of root exudation and microbiome assembly and scaling cues. RAS may represent a valuable trait for the adaptation and performance of plants under lower input conditions, and may also facilitate enhanced storage of carbon in agricultural soils.

Molecular and physiological characterization of sugar biosynthetic pathways in brown macroalgae

The aim of this PhD project is to characterize sugar biosynthetic pathways in brown macroalgae at the molecular and physiological levels. Brown macroalgae produce two main types of storage sugars: mannitol (a simple sugar) and laminarin (a polymer made up mainly of glucose units, with the optional addition of a few mannitol units). As these biosynthetic pathways have been poorly described so far, the main aim of this PhD project is to identify and characterize the enzymes responsible for the catalytic activities of these two interconnected biosynthetic pathways in the brown macroalga Ectocarpus. Original molecular and cellular biology approaches, including genome editing, will be used to generate the biological material needed to characterize these biosynthetic pathways and their role in brown macroalgal physiology.

Nano- and micropatterned biomineral-based materials: Orientation-specific assembly of coccoliths into arrays

Coccoliths of coccolithophorid algae are anisotropically-shaped microparticles consisting of calcite (CaCO3) crystals with unusual morphologies arranged in complex 3D structures. Their unique micro- and nanoscale features make coccoliths attractive for various applications in nanotechnology. It is anticipated that the range of applications of coccoliths can be further extended by (bio)chemical modification and functionalization as well as possibilities for their arrangement into 2D and 3D arrays. However, methods for both aspects are still lacking.
The aim of this project is thus to develop methods for regioselective functionalization of coccoliths and their assembly into arrays. Regioselective functionalization of the margin area and central area of coccoliths will be achieved by exploitation of local differences in the composition of the insoluble organic matrix of coccoliths. The existence of local differences in the composition of biomacromolecules within this matrix has only very recently been demonstrated. In particular, we will regioselectively introduce proteins/(poly-)peptides that can serve as “anchoring points” for in vitro modifications into the insoluble organic matrix of coccoliths by genetic engineering of a coccolithophore. These engineered coccoliths form the basis for the construction of coccolith arrays. Three independent approaches for the assembly of such arrays will be pursued. The structural and physico-chemical properties of the coccolith-based magnetite-calcite hybrid material will be determined by means of a number of analytical methods.
This interdisciplinary project will benefit greatly from the complementary expertise of the binational groups. In the long term, we aim to create an advanced pool of methods to regioselectively endow coccoliths with desired properties and to develop new biomineral-based materials for nanotechnological applications.