A flourishing space settlement needs a functional ecosystem. And almost by definition, that means an ecosystem that can maintain itself. However, setting up a functional ecosystem is not quite easy.
A good ecosystem has a certain balance, but often such balance is vulnerable to minor deviations. We all know the ecological disaster the introduction of rabbits in Australia has been. It is our task not the make those same mistake when we are colonizing space.
Ecosystems consist of different parts: plants (flora), animals (fauna), bacteria, fungi and dead material. In order to establish a viable ecosystem one need to carefully selects the different components. Therefore one needs to understand the ecological function of each component.
Plants serve as a source of food for animals, while certain animals also contribute to pollination. Bacteria and fungi will revert dead plant and animal material to nutrients which inserted back into the cycle of life.
There are many species most space settler did want to have in their colonies. Gerard O’Neill suggested that mosquitoes, wasps and bot flies should be illegal in space settlements, together with other parasites. On the other hand he advocated the introduction of useful insects as honey bees and butterflies (to be used as food for birds) in space habitats.
The decision to exclude certain species, should be taken with care. It should be taken into account whether a certain species does has a certain desired function within the ecosystem and whether those function could be substituted by other species.