We don't know yet - we still have to figure that out.
There was an experiment several years ago called Biosphere II, in which the object was to create a miniature self-contained ecosystem such as would be capable of traveling interplanetary or interstellar distances. The project failed from this prospective; the enclosed greenhouse in which the ecosystem was placed ran out of oxygen, and more had to be brought in from outside in order to save the people within the environment. There was also an accidentally introduced ant species that took over and generally caused problems.
In order to build an ecosystem capable of traveling interplanetary distances, and then colonizing other planets, we are going to need to understand practical ecology well enough to make a Biosphere II that works. Obviously, we aren't there yet.
Since I don't work for NASA I don't know how scientists will do it. There was an attempt to make a self-sustaining, isolated ecosystem with 20 or so humans living inside in preparation for colonizing other planets. This experiment was called Biosphere 2. It is now located in Arizona, I think, and is open to the public for tours. You should look up which plants and animals (and insects, bacteria, and algae) they included in their ecosystems. Everything was carefully balanced to create enough food and oxygen for the humans living inside, and to recycle the human waste and garbage. bio2
Another thing you can think about is the early Polynesian settlers. The Polynesians settled about 6 million square miles of the Pacific with double-hulled wooden sailing canoes called voyaging canoes. They navigated for weeks across open ocean without the use of a compass, and with mostly cloudy skies, so it was an amazing feat. After a first exploratory trip, where a new island was discovered and probably surveyed, there were additional trips to settle the new island or island group. The settlers brought plants and animals with them to allow them to survive on their new island. These were carefully chosen to provide food, medicine, shelter, clothing (kappa), tools, fishing materials, bowls (to store water), rope, glue, musical instruments, sacred objects, etc. There wasn't much space on these canoes, and pretty much everything got exposed to salt water, so keeping the plants and animals alive was pretty difficult. Species were partly chosen for their ability to survive the voyage and take up limited space and fresh water. Then they had to grow the plants or raise the animals in the new location, and pretty quickly in order to get enough food and housing materials right away. They also had to bring plants with them to eventually build new canoes so they could return home or trade with other islands. Most canoes, or at least the sails and rigging, did not last for more than one or two long voyages. The animals included chickens (moa), pigs (pua'a), dogs and rats. Most people think the rats were accidental stow-aways, but they're pretty sure the Polynesians ate them anyways. To find out the plants they brought with them, check out: canoeplants
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