Why does it never seem to occur to them that coffee is not actually a product that is spontaneously produced, but is actually a plant that grows?
That any sensible colonist or expedition supply officer would take seeds with them?
Coffee is a bit fiddly to germinate, but I'm a certified black thumb and I managed it myself in a London climate by doing it indoors on a windowsill under a plastic Coke bottle. It even got to 2 foot high before I went away on holiday and forgot to get it watered and it died. Any half-decent biologist could grow it. Parrish or Katie could do it in their sleep.
Sure, you don't want to introduce new plants into an ecosystem, but the city would of necessity have greenhouses, and that is an enclosed ecosystem. Not a problem.
So - please, please, please - if you are about to write Atlantis fanfic that's set after the first year and reconnection with Earth - use your logic!
Definitely one of the most important seeds (along with Camellia sinensis) to add to your expedition's survival packs.