6.1 Oberflächen- und Dünnschichtanalyse
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Data for the publication "The role of extracellular polymeric substances of fungal biofilms in mineral attachment and weathering" (https://doi.org/10.1038/s41529-022-00253-1). It includes:
- The Summary of the EPS concentration, EPS sugar components and EPS linkages.
- The Summary of the XPS analysis of freeze-dried biofilm samples of all strains.
- The Summary of the pH, Mg, SI and Fe concentration, biomass and olivine dissolution rate for each time point of all dissolution experiments.
The roles extracellular polymeric substances (EPS) play in mineral attachment and weathering were studied using genetically modified biofilms of the rock-inhabiting fungus Knufia petricola strain A95. Mutants deficient in melanin and/or carotenoid synthesis were grown as air-exposed biofilms. Extracted EPS were quantified and characterised using a combination of analytical techniques. The absence of melanin affected the quantity and composition of the produced EPS: mutants no longer able to form melanin synthesised more EPS containing fewer pullulan-related glycosidic linkages. Moreover, the melanin-producing strains attached more strongly to the mineral olivine and dissolved it at a higher rate. We hypothesise that the pullulan-related linkages, with their known adhesion functionality, enable fungal attachment and weathering. The released phenolic intermediates of melanin synthesis in the Δsdh1 mutant might play a role similar to Fe-chelating siderophores, driving olivine dissolution even further. These data demonstrate the need for careful compositional and quantitative analyses of biofilm-created microenvironments.
Biofilm formation and microbially influenced corrosion of the iron-reducing microorganism Shewanella putrefaciens were investigated on stainless steel surfaces preconditioned in the absence and presence of flavin molecules by means of XANES (X-ray absorption near-edge structure) analysis and electrochemical methods. The results indicate that biofilm formation was promoted on samples preconditioned in electrolytes containing minute amounts of flavins. On the basis of the XANES results, the corrosion processes are controlled by the iron-rich outer layer of the passive film. Biofilm formation resulted in a cathodic shift of the open circuit potential and a protective effect in terms of pitting corrosion. The samples preconditioned in the absence of flavins have shown delayed pitting and the samples preconditioned in the presence of flavins did not show any pitting in a window of −0.3- to +0.0-V overpotential in the bacterial medium. The results indicate that changes in the passive film chemistry induced by the presence of minute amounts of flavins during a mild anodic polarization can change the susceptibility of stainless steel surfaces to microbially influenced corrosion.
Bacterial samples are typically freeze dried or cryo-prepared prior to XPS analysis to allow for measurements in ultra-high vacuum (UHV). The sample environment in the near-ambient pressure (NAP) XPS instrument EnviroESCA allows for measurements in up to 15 mbar water vapor, thus, sample preparation is no longer restricted to UHV-compatible techniques. For instance, biofilms grown in medium can be transferred directly from the medium to the measurements chamber, maintaining a humid environment throughout the measurements. Considering the complexity of bacterial samples, sample preparation must be carefully considered in order to obtain meaningful and reproducible results.
In this talk, various strategies for sample preparation of bacteria and biofilms for NAP-XPS measurements will be discussed. Model systems of planktonic bacteria, artificial biofilms resembling the exopolysaccharide matrix and biofilms have been characterised in various conditions. The stability and homogeneity of the samples was assessed by monitoring the C1s core level peak at different sample locations. The quality of the XPS-spectra is also influenced by the gas environment, which will be exemplified by core level spectra of P. Fluorescens acquired in air, water vapor and ultra-high vacuum.
Near-ambient pressure XPS makes it possible to characterise samples not compatible to ultra-high vacuum, and enables the study of liquid-solid, gas-liquid and gas-solid interfaces. NAP-XPS meas-urements of biofilms, suspended nanoparticles and metal-organic frameworks were performed with EnviroESCA developed by SPECS.
An interesting application is surface characterisation of biofilms, which are bacterial communities embedded in a self-produced polysaccharide matrix. Various model systems ranging from pure polysaccharides of alginate to biofilms harvested directly from the growth medium have been char-acterised in humid conditions[1].
NAP-XPS also makes it possible to characterise nanoparticles in solution. Silver nanoparticles in aqueous solution were characterised and the Ag 3d-spectrum compared to spectra obtained of dried nanoparticles in UHV-conditions[2]. The binding energy of the Ag 3d-core level peak was shifted by 0,6 eV towards higher binding energy for suspended nanoparticles compared to the dried sample measured in UHV. This can be assigned to a change in surface potential at the water-nanoparticle interface.
Metal-organic frameworks (MOFs) are suitable materials for gas storage of small molecules due to their nanoporous, crystalline structure. However, instability in humidity remains an issue for many types of MOFs. XPS-measurements of the MOF-structure HKUST-1 were performed in various NAP-conditions to assess the stability of the sample and its interaction with the gas molecules as water, methanol and pyridine.
Synchrotron XPS in the soft-X-ray regime is suitable for the detection of light elements commonly found in biological samples. Various model systems of biofilms have been developed and characterised at synchrotron- and lab-based facilities. By obtaining the chemical composition at various information depths, the vertical distribution of iodine in an artificial biofilm have been determined.
The proposed ISO Technical Report provides a description of a variety of physical methods of analytical chemistry by which bacteria and biofilms can be analysed. The state of the art, sample requirements and strengths associated with each method are identified. Presented at the DIN-meeting for NA 062-08-16 AA „Chemische Oberflächenanalyse und Rastersondenmikroskopie“
X-ray photoelectron spectroscopy (XPS) provides elemental and chemical information from the outermost ~10 nm of the sample surface. This is in the same order of magnitude as the thickness of the outer bacterial membrane of gram-negative bacteria, as well as outer membrane molecules as exopolysaccharides and lipopolysaccharides, commonly attached to the cell surface. With the development of near-ambient pressure (NAP)-XPS, bacteria can be analysed with minimal sample preparation.
EnviroESCA is a laboratory based NAP-XPS instrument, equipped with a monochromated Al Kα radiation source and a differentially pumped energy analyser connected to an exchangeable sample environment. It allows for measurements in various gas-atmospheres, including water vapor, which makes it possible to characterise bacteria and other biological samples close to their natural, hydrated state. Artificial model-biofilms of exopolysaccharides, planktonic Pseudomonas Fluorescens and biofilms of Escherichia Coli have been characterised in hydrated and dried state.
High-resolution XPS-spectra from carbon, oxygen, nitrogen and phosphorous can be assigned to carbohydrates, lipids and proteins in general agreement with literature. Especially the carbon 1s peak is of interest. A series of measurements of an E. coli biofilm from 11 mbar in humid environment to 1 mbar air reveal changes in the C1s peak, which suggests that the bacterial surface undergo substantial Change.
This application note presents how EnviroESCA can be used to analyze E. coli biofilms on silicon under near ambient pressure conditions in various states of hydration. Such investigations of the outer bacterial cell surface in their hydrated state are essential for studying biological interfaces at work.