Special Interest Group Meeting

In situ detection of fungi in the environment by FISH probes

Dr. Christiane Baschien, Berlin University of Technology / Federal Environment Agency, Germany

For the detection of fungi in the environment a range of molecular methods is available. PCR-based methods, including real time PCR and fingerprinting techniques, are tools for determining genetic variation and specific detection without information about metabolic activity. The spatial distribution of growing mycelia on or within colonized substrata is still poorly understood. Combining both specific in situ detection and information about the physiological status of the targeted cells, fluorescence in situ hybridization (FISH) is an established method in bacterial ecology. The fluorescence signal intensities of the rRNAtargeting FISH probes are correlated with the ribosome content of the target cell, which indicates the viability of the target organism before fixation. A first attempt to use the FISH method for fungi was the detection of Aureobasidium pullulans on leaves (Li 1997). Later, FISH was applied to freshwater fungi in pure cultures and on leaves (Baschien 2001, McArthur 2001). Baker (2004) showed Eurotiomycetes to be more abundant than Dothideomycetes in an mine drainage system by using 18S rRNA-targeting FISH probes. Candida albicans was detected by peptide nucleic acid FISH probes in blood cells (Wilson 2005). More recently, actively growing freshwater fungi and germinating conidia were detected with taxon-specific FISH probes in an alpine stream (Baschien 2008). Pifalls and limitations of FISH, such as autofluorescence, limited permeability of the fungal cell wall, and probe specificity issues are discussed.