Yes, species=*, species:wikidata=* and species:wikipedia=* are the proper tags.

>> Is there a proper way to link a commons image to each individual element to depict what it looks like without taking an individual photo of each element that are nearly identical?

If an image of that species exist on commons, is already linked to the wikidata entry somehow, so linking the wikidata entry with species:wikidata is enough if someone wants to see what a species looks like. As a matter of fact, even species:wikipedia=*/wikipedia=* are redundact if species:wikidata=*/wikidata=* are tagged, since they are also connected to the relative wikipedia pages in every language.