"They [the bacteria] have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions."
So these E. coli do something that E. coli can't do. But they're still E. coli. But they're not. Have I divided by zero or something?
All your argument is really saying is that the decidability of wether a particular organism is or isn't a member of a certain species gets less and less well defined the closer you get towards it's genotype, which I won't argue with. I know plenty of people who can't circle their tongue: it doesn't make them any less human.