CharonY

One can either add the substances to the (slightly cooled) agar while before pouring it into the petri dish). Alternatively there are antibiotic discs to test them. Or you can put a sterile filter disk on a plate with bacteria and drop around 10µl on it. For E. colis you might want to ask nearby universities, however you won't (or at least shouldn't) get Streptococci or Salmonella. Both species are usually human pathogenes and may not be cultivated outside specially equipped laboratories! Edit: forgot to add: most chemicals can be acquired by e.g.Sigma, but you may need an authorization to buy there (depends a bit on local laws).

I suppose you mean a change in protein abundancy? That's theoretically possible but for a true quantification you got to use techniques like radioactive labelling or DIGE, or the usage of heavy nitrogen. With 2D PAGES as compared to 1D you get a better resolution and therefore you can visulize more proteins. And in fact there are plenty of papers regarding the proteome of fungi. I don't think that there are 2d gels only woth ribosomal proteins around though, since one of the strength of this technique is the visualisation of a lot of proteins in one gel. If one could separate the ribosmal proteins from all others (at the moment i'd have no clue how short of His-tagging and purifying them) an 1D PAGE should suffice.

None of these qualify as new species. They are just mutant strains.

Ah I think you are confusing stop codon with terminator here. An operon can contain several ORFs, but not the other way round. A gene ends with its stop codon