How to search for organisms by criteria such as growth substrate and overflow metabolites?
Some of the criteria, I guess are difficult to find (Also for my lack of understanding of those terms). For the rest you can search these databases:-


Growth substrate: I don't really know what you are asking here — growth rate in minimal media/optimal growth medium ? Nevertheless, see the Media Database
Methanogenesis: Ortholog Table - KEGG MODULE M00567 
Nitrogen fixation: Ortholog Table - KEGG MODULE M00175