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If you add native animals, perhaps you could make it possible to capture and keep them in pens, possibly for food or crafting ingredients (milk or some wool equivalent) to make for instance food with different potency/duration.

Alternatively, animals could be a natural hazard. If they were attracted to the especially healthy plants in your greenhouse module(s), you'd need to erect fencing or craft some sort of force field to keep them from damaging your base. You wouldn't need to run around shooting them with a space gun, but rather take a more passive approach to keep them out of your business.