Biofilm

vignette|Lorsque le biofilm est indécelable, il forme un voile microbien. Lorsqu'il est suffisamment épais pour être visible à l'œil nu, il forme un tapis microbien (ici un biofilm autotrophe constitué de cyanobactéries). vignette|Cloître de l'abbaye du Thoronet. Les pierres exposées au ruissellement des eaux de pluie montrent des croûtes constituées de biofilms de lichens épilithiques, de cyanobactéries responsables de la biopatine noire, de parasites (virus ou microchampignons) qui attaquent ces bactéries photosynthétiques et d'autres micro-organismes qui s'en nourrissent. Ce biofilm ne doit pas être confondu avec un encroûtement de salissure (sulfin, couche friable d'aspect spongieux et sans cohérence superficielle). vignette|Dans le ravin des Arcs, le niveau maximum des eaux est marqué par la bande beige de calcaire, révélée par abrasion mécanique, et la ceinture verte d'algues. Au-dessus, l'altération microbienne du calcaire forme sur la roche taraudée des croûtes biologiques ble

Probing the growth and mechanical properties of Bacillus subtilis biofilms through genetic mutation strategies

Lei Wang, Chen Zhang

Bacterial communities form biofilms on various surfaces by synthesizing a cohesive and protective extracellular matrix, and these biofilms protect microorganisms against harsh environmental conditions. Bacillus subtilis is a widely used experimental species, and its biofilms are used as representative models of beneficial biofilms. Specifically, B. subtilis biofilms are known to be rich in extracellular polymeric substances (EPS) and other biopolymers such as DNA and proteins like the amyloid protein TasA and the hydrophobic protein BslA. These materials, which form an interconnected, cohesive, three-dimensional polymer network, provide the mechanical stability of biofilms and mediate their adherence to surfaces among other functional contributions. Here, we explored how genetically-encoded components specifically contribute to regulate the growth status, mechanical properties, and antibiotic resistance of B. subtilis biofilms, thereby establishing a solid empirical basis for understanding how various genetic engineering efforts are likely to affect the structure and function of biofilms. We noted discrete contributions to biofilm morphology, mechanical properties, and survival from major biofilm components such as EPS, TasA and BslA. For example, EPS plays an important role in maintaining the stability of the mechanical properties and the antibiotic resistance of biofilms, whereas BslA has a significant impact on the resolution that can be obtained for printing applications. This work provides a deeper understanding of the internal interactions of biofilm components through systematic genetic manipulations. It thus not only broadens the application prospects of beneficial biofilms, but also serves as the basis of future strategies for targeting and effectively removing harmful biofilms.

KEAI PUBLISHING LTD2022

Electrochemical imaging of metabolic activity in tissue and biofilms

Sorour Darvishi

Non-invasive and semi-invasive bioimaging is of great interest for the rapid diagnosis and efficient as well as specific treatments of biological systems affecting human health, such as cancer tissue and biofilms. Electrochemical bioimaging is one of the diverse methods that can reach high sensitivities in small liquid volumes. When using (sub)micrometric electrodes, it can reach a high spatial-temporal resolution. The electrochemical processes can be based but are not limited to electron transfer reactions and the detection of metabolic activity indicators. An electrochemical scanning probe platform can be used, such as Scanning Electrochemical Microscopy (SECM), in which a micrometric electrochemical probe is translated in close proximity to a sample immersed in an electrolyte solution. In most SECM modes, the SECM tip detects locally electro-active species that are generated or consumed by active surface sites allowing to create surface reactivity maps of biological entities. It has in particular found applications for studying normal and cancer cells, yeast, and bacteria. In this thesis it was looked at utilizing Soft SECM probes as an analytical tool for sensing and analyzing complex biological samples, such as skin and three-dimensional biofilms in an as less as possible invasive manner, potentially forming the basis for the development of point of care devices for early detection and treatment. Electrochemical analysis was completed by fluorescence imaging as a state-of-the-art methodology. The study of melanoma and bacterial biofilms as the two major targets in this thesis was divided into five main chapters. The electrochemical detection of melanoma was based on the specific detection of tyrosinase, a melanoma protein marker. In Chapter 3, a non-invasive electrochemical melanoma detection approach is based on using adhesive tapes to collect and fix cells from a suspicious skin area and transfer the cells into an SECM for their analysis with soft probes. The enzyme was tagged with antibodies that contained a peroxidase label for the production of an electrochemical probe. In Chapter 4, tyrosinase was addressed with a microneedle type electrochemical biosensor containing a TYR-sensitive redox molecule for TYR sensing. Thereafter, Soft-Probe-SECM was used to investigate the electrochemical surface reactivity of Escherichia coli (E. coli) biofilms (Chapter 5) and to follow the effects of various antibiofilm treatments, such as gentamicin, sodium azide, silver nanoparticles, and flashlight (Chapter 6). Finally, in Chapter 7, an antibiofilm nanocarrier based on a DNA origami nanostructure for E. Coli biofilm treatment was studied. The DNA origami was loaded with doxorubicin (DOX) to enable the transport of DOX into the three-dimensional structure of the biofilm. In this way, the biofilm protection barrier against DOX, as generated by the extracellular polymeric matrix, was overcome. The biofilms were studied by confocal laser scanning microscopy and microelectrode arrays.

EPFL2022

Electrochemical imaging of metabolic activity in tissue and biofilms

Sorour Darvishi

EPFL2022

Biodiesel production: bioprocess development of an artificial biofilm using bio-encapsulation of an E. coli strain genetically engineered for lipase cell-surface display

Probing the growth and mechanical properties of Bacillus subtilis biofilms through genetic mutation strategies

Electrochemical imaging of metabolic activity in tissue and biofilms

Biodiesel production: bioprocess development of an artificial biofilm using bio-encapsulation of an E. coli strain genetically engineered for lipase cell-surface display

Probing the growth and mechanical properties of Bacillus subtilis biofilms through genetic mutation strategies

Electrochemical imaging of metabolic activity in tissue and biofilms