Upon discovering Vertical Shaft and its resident Larian, I've immediately set to work feeding the Phyta to the Larian for nutritious compost. After a while, however, the Phyta stopped reproducing - the "eggs" they laid upon eating a seed simply disappeared instead of hatching into a new Phyta. This made me wonder: are the resources limited in some way? Is it possible to run out of a type of item/creature? What are the limiting factors? Do they regenerate after a time?
Phyta and Cycots will stop reproducing once Biomass Level 5 has been reached. When this happens, they will continue to eat seeds, but their eggs will just "dissolve" rather than hatch into a creature.
This is to prevent overpopulation, but if the Biomass Level goes down to 4 or less, the creatures will immediately start populating again until level 5 has been reached. Other than that, those species should continue to populate so long as they are kept "well fed" with seeds.
Seeds are only limited so far as there can only be a certain amount (usually 2 or 3) laying around in a level or sitting in your inventory. Once these seeds have been destroyed, eaten by creatures, or planted, the old plant will start producing more seeds again.
This means that seeds are "virtually infinite"; so long as you don't destroy every single plant in the game, you should be able to return to old places and continue to refill your inventory with seeds once you run out.
(I have not tested if it is possible to completely destroy a species of either plant or animal, or if the game prevents you from doing so)
As compost is created from creatures, and both creatures and the seeds to breed them with are infinite, compost is an infinite resource as well.