Welcome to the Opitz Group: Ecology of Bacterial Communities
If you are interested in doing your Masterthesis or Bachelorthesis directly in the group of Dr. Opitz please contact Opitz@physik.uni-muenchen.de
Winterterm 2016/17: 3 Masterthesis available
We, the bacterial biophysics group, together with our theoretical collaboration partners, are investigating bacterial behavior in response to changing environmental conditions. Besides nutrient availability, the presence of toxins or antibiotics affects bacterial growth and with it, possible interactions between competing bacteria. A detailed analysis of the underlying regulating mechanisms is a prerequisite to fully understand bacterial reactions to external inputs. Once key factors affecting bacterial behavior are known and well understood, we can not only follow bacterial colony development, but also manipulate bacterial interactions, thereby altering the composition of bacterial colonies over time. On a single cell level, bacterial reactions to external inputs, are often heterogeneous due to differences in protein concentrations. Receptor proteins sensing the external condition are located in the bacterial cell membrane and often represent transporter systems. The specificity of a receptor or transporter protein can be used to detect and discriminate different bacterial species and allows the development of sensing tools for medical applications.
Research of the Opitz Group (former Leisner):
Bacterial communities represent complex and dynamic ecological systems. They appear in the form of free-floating bacteria as well as biofilms in nearly all parts of our environment, and are highly relevant for human health and disease. Spatial patterns arise from heterogeneities of the underlying 'landscape' or self-organized by the bacterial interactions, and play an important role in maintaining species diversity. Interactions comprise, amongst others, competition for resources and cooperation by sharing of extracellular polymeric substances. Another aspect of interactions is chemical warfare. Some bacterial strains produce toxins such as colicin, which acts as a poison to sensitive strains, while other strains are resistant. Stable coexistence of these strains arises when they can spatially segregate, resulting in self-organizing patterns.
In this research project, we want to employ the Escherichia coli Col E2 system, comprising a poison producing, a sensitive, and a resistant strain, to quantitatively study the emerging pattern formation. By a combination of experimental and theoretical methods (in collaboration with LS Frey, LMU), we aim at a characterization and quantification of the single cell interactions, as well as the influence of external heterogeneities and stochastic effects on the resulting patterns.
Markus F. Weber, Gabriele Poxleitner, Elke Hebisch, Erwin Frey and Madeleine Opitz
Chemical warfare and survival strategies in bacterial range expansions
J.R.Soc. Interface 6 July 2014 vol. 11 no. 96 2014172
E. Hebisch, J. Knebel, J. Landsberg, E. Frey and M. Leisner
High variation of fluorescence protein maturation times in closely related Escherichia coli strains
PLOS ONE, 8(10): e75991 (2013)
Heterogeneity in Colicin expression
In a combined theoretical (LS Frey, LMU) and experimental approach we plan to study the heterogeneous gene expression of the Escherichia coli Colicin E2 operon in individual cells. Colicin E2 represents one class of toxins produced by bacterial cells to kill closely related bacteria, when environmental conditions become unfavorable. Using fluorescence time-lapse microscopy we aim to quantitatively analyze the kinetics of Colicin expression from the Colicin operon and investigate further factors such as small RNAs regulating Colicin release and its impact on the establishment of heterogeneity. In particular, we are interested in changes of expression dynamics in dependence of SOS response and how this affects the amount and time-point of Colicin release.
Mader A., von Bronk B., Ewald B., Kesel S., Schnetz K., Frey E., Opitz M.
Amount of colicin release in Escherichia coli is regulated by lysis gene expression of the Colicin E2 operon
PLoS ONE 10(3): e0119124. doi:10.1371/journal.pone.0119124 (get article)
This project is part of the SPP1617
Mechanics of Bacterial Biofilms
Bacteria embed themselves with secreted biopolymers (EPS) forming a community that is referred to as a biofilm. Due to their high mechanical resilience and their resistance to antibiotic treatment, such biofilms constitute a significant problem both in industry and health care. However, the molecular reason for this outstanding sturdiness of bacterial biofilms is not understood. In this project, we aim at analysing the mechanical resistance of bacterial biofilms towards externally applied forces (e.g. shear forces) both for developing (early stages of biofilm formation) and mature biofilms. As a model system, we will study biofilms formed by the organism Bacillus subtilis, a non-pathogenic bacterium that mainly resides in soil but has also been suggested to be a commensal resident of the human gut. We will investigate different wild-type strains of Bacillus subtilis that differ in the expression profile of exopolymeric substances of their biofilm matrix, as these EPS are thought to directly affect the mechanical properties of the biofilm. Using a combination of different experimental techniques, we aim at bridging the gap between the biomolecular level and the macroscopic behavior such as the biomechanical properties and the formation dynamics of bacterial biofilms.
S. Grumbein,M. Werb, M. Opitz and O. Lieleg
Elongational rheology of bacterial biofilms in situ
Journal of Rheology, accepted (2016)
S. Kesel, S. Grumbein, I. Gümperlein, M. Tallawi, A-K. Marel, O. Lieleg and M. Opitz
Direct comparison of physical properties of Bacillus subtilis NCIB 3610 and B-1 biofilms
Applied and Enviromental Microbiology, 82(8):2424-2432 (2016)
S. Kesel, F. Moormann, I. Gümperlein, A. Mader, M. Morikawa, O. Lieleg and M. Opitz
Genome sequence of the biofilm producing Bacillus subtilis strain B-1 isolated from an oil field.
Genome Announcements, 2(6):e01163-14 (2014)
S. Kesel, A. Mader, P.H. Seeberger, O. Lieleg and M. Opitz
Carbohydrate-coating reduces adhesion of biofilm forming Bacillus subtilis to gold surfaces
Applied and Enviromental Microbiology Published ahead of print 18 July 2014, doi:10.1128/AEM.01600-14 (article)
S. Grumbein, M. Opitz and O. Lieleg
Selected metal ions protect Bacillus subtilis biofilms from erosion
Metallomics, 2014, Advance Article, DOI: 10.1039/C4MT00049H (article)
Cantilever array biosensors
Biosensor research is a highly interdisciplinary field, as biosensor applications are needed in life sciences, health care and medical diagnostics as well as environmental screening. As such, a variety of biosensors have been developed for the detection of different molecules. In the past years, improvements in biosensor research comprised high selectivity, reduced detection volumes and increased parallelization. Cantilever-based biosensors represent one class of biosensors and have been used to study DNA or protein interactions, but also allow the analysis of eukaryotic or prokaryotic growth even able to weigh single bacterial cells. The advantage of this technique is the possibility of analysing of up to 8 samples in parallel in real-time without the need of additional labelling. Cantilever can hereby be coated with different sensing layers depending on the analyte studied, a process named functionalization.
Carbohydrates (glycans) are one class of biosensing molecules. Carbohydrate-protein interactions are thereby important for cell adhesion, signal transduction or virus infection. Glycan cantilever array sensors were shown to detect specific carbohydrate-protein interactions with pico-molar sensitivity. Recently, we were able to detect and discriminate different Escherichia coli strains using this method. In the next steps, we want to analyse the suitability of this method as a reliable sensing tool for medical diagnostics. This project is performed in collaboration with Prof. Seeberger and Dr. Hartmann (MPI Berlin).
A. Mader, K. Gruber, R. Castelli, B. Hermann, P.H.Seeberger, J. Raedler and M. Leisner Discrimination of Escherichia coli strains using Glycan Cantilever Array Sensors NanoLetters, Publication Date (Web): December 5, 2011 (Letter), DOI: 10.1021/nl203736u (get article)
Kathrin Gruber, Tim Horlacher, Riccardo Castelli, Andreas Mader, Peter H. Seeberger, and Bianca A. Hermann
Cantilever Array Sensors Detect Specific Carbohydrate−Protein Interactions with Picomolar Sensitivity
ACS Nano, pp 3670–3678, 5, 2011 (get article)