Basically I work on solid state fermentation of fungus and find it really difficult to confirm if my seed cultures are pure.
I guess the first difference which is the most conspicuous one when you are using a microscope is the size of a cell. Bacterial cells are much smaller and it is possible to observe them with a ocular with high magnification (e.g. x100), whereas fungi cells are possible to observe with a lower magnification ocular (e.g. x40). Moreover, if you are working with fungi I assume you know the shape of the cells you would expect to see. As far as I'm concerned the shape of the cells you observe can be a pretty good determinant as well.
You could contact Dr.Michael Hoppert ([email protected]), Göttingen University, Institute of Microbiology and Genetics.; He uses immunological techniques for similar questions (bacteria in biofilms). Tell him that you got his address from me.
You can stining. By methylene blue or gram dyes .and show the stininig cell
You can do centrifugation of fermenter sample around 1000 g for 5 to 10 min , which will first remove the fungal growth and followed by supernatant smear gram staining to check bacterial contamination.
Also the fermenter sample may strike plated on SCDM agar ( Soyabean Casein Digest Medium) and need to incubate at 35-37 deg. for 24 hr. If any bacterial contamination is present ,it will grow faster and will be helpful prove present or absent of bacterial contamination .
You could stain with lactophenol cotton blue stain which helps detect septa special mycelia and spore structures. On the other hand, the gram stain reaction will help detect bacteria which could be either gram positive or gram negative. This is in addition to colony and cellular morphology
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