Hi Paul,

with exudates you mean everything bacillus (e.g.) secretes while growing, right? If so, i guess it is difficult to separate the TSB components from everything else. What you could do is make a negative control, where you use only TSB and treat it exactly the same way as your samples (incubation time, rotation, extraction...) and check if there is an effect on mycorrhizal development.

 If there are chances your compounds of interest are in the cell, everything would be easier ;)

You could check, if there is a protocol for "resting cells". Then you could wash your cells properly and hope they still are in a state where they secrete compounds into their environment, at least for a small amount of time. I only know of biocatalyses done in that way to have active cofactor recycling. From what i heard, the cells are still alive and working for another 24 h.

Here goes one article that might help. Yours sincerely. mariangela

Paul

1. Replace TSB with simpler chemically defined medium, B. subtilis is prototroph and does not require complex media. Interpretation of results and chemical identification of extracellular products is much easier with simple medium having one single C-source (glucose or citrate or pyruvate etc).

2. Blank medium as control is anyway necessary (as advised by Florian Nadler). 

3. Bilayer agar has some advantages but such experimental system is too artificial. The potential stimulatory effect of extracellualr proteins could be overlooked because of their low diffusion rate through agar. Liquid and sand/liquid systems could be more natural and simpler. 

4. Do not miss possible role of volatile metabolites produced by Bacillus. I would set up separate experiment with growth chambers for fungi and bacilli are connected only via gas phase