Optimisation of Raman spectroscopy for the analysis of Basidiomycota : spores, latex and mycelium

For several decades, Raman spectroscopy has been used in different research fields. As a result of progression in the instrumentation during the last years, Raman spectroscopy became available for the analysis of complex biomaterials. In this work, the opportunities of the technique for the analysis of Basidiomycota are explored. The chemical composition of spores of Lactarius species is studied. These spores are mostly comprised of lipids and saccharides: they contain large amounts of triolein and smaller amounts of amylopectin (amyloid ornamention) and chitin. Furthermore, the Raman spectra are compared with those of spores of the genera Collybia, Laccaria, Mycena and Russula. By using a chemometric identification protocol (interference elimination, autoscaling, PCA and LDA) the genus was correctly assigned to a spore print in 90% of the cases, whereas the species could not be deduced from the Raman spectra. It is shown that Raman spectroscopy is a good additional method for the analysis of Lactarius latex. 2D correlation analysis of the latex spectra gives an overview of the major compositional changes and may discriminate between the different reaction steps. The reaction sequence of Lactarius lacunarum latex is studied. Different types of reaction sequences are observed in different species, which might be of taxonomic importance. The last section of this work discusses an explorative study of mycelium cultures of common wood rots. The Raman spectra are discussed and compared with the Raman spectra of infected and unifected Fagus and Pinus wood. In this way, it was shown that hyphae of a wood rot fungus can be detected in infected wood, although the spectral differences in cellulose and lignin bands can be much larger relative to the bands of the fungus. White rots can be detected through the presence of several Raman bands (e.g. at 916 and between 1000 and 1008 cm-1), whereas carotenoid vibration bands between 1510 and 1540 cm-1 are typical for brown rots

Use of dendrograms of slice spectra as a new graphical tool for the interpretation of two-dimensional correlation spectra

In this paper a procedure is established to identify spectral bands that show similar behavior in two-dimensional correlation spectra. Slice spectra of bands that are affected in a single spectral event are highly similar. It is shown that this can be used to simplify the interpretation of two-dimensional (2D) correlation diagrams. One functional group frequently gives rise to multiple spectral bands in a Raman spectrum. In such occasions, the sequential order rules assign a sequential order, which is invalid, to the changes in these bands. We therefore apply cluster analysis to the slice spectra of bands with intensity changes during the experiment. Results indicate that cluster analysis of selected slice spectra can help in the interpretation of 2D correlation spectra in an intuitive and graphical way.. The procedure should he used together with the widely used sequential order rules to determine the order of spectral events. The procedure enabled us to reveal the reaction steps in two simulated datasets and a dataset that comprises Raman spectra of oxidating latex of Lactarius fluens (Basidiomycota, Fungi)

The Biodata toolbox for MATLAB

This paper describes "The Biodata toolbox for MATLAB". a free software toolbox for MATLAB. Biodata is the result of a PhD project in Raman spectroscopy and is available under the GNU Public License 3. It is a system that consequently stores spectra and related data in a single data structure. Biodata provides a framework for straightforward utilisation of preprocessing algorithms that apply existing chemometric models on unknown data. This paper is not an attempt to summarize or review work on the supported techniques, such as 2D correlation analysis, spectral processing or sample identification, but it is rather intended to inform the reader on the existence, functionality and applicability of the Biodata 1.0 toolbox for MATLAB

Chemotaxonomical identification of spores of macrofungi: possibilities of Raman spectroscopy

Confocal Raman spectroscopy is a non-destructive analytical method which is useful to obtain detailed information about the molecular composition of biological samples. Its high spatial resolution was used to collect spectra of single basidiospores of macrofungi of the genera Collybia, Gymnopus, Laccaria, Lactarius, Mycena and Russula. These spectra can be divided into three major taxon-related groups, with general compositional differences, such as the relative amount of lipids compared to proteins. In this study, collapsing of thin-walled spores during storage was often observed, a phenomenon which has been given little attention in the literature. The Raman spectra are treated with different chemometric preprocessing techniques, including Savitsky-Golay, standard normal variate (SNV) preprocessing and extended multiplicative scatter correction (EMSC). By using linear discriminant analysis, approximately 90% of the spectra can be assigned to the correct genus, but identification on the species level was not possible