Specifically how do the ones for getting animals and getting seeds work? Do I have to plop down the appropriate building on them or near them? Do I only get 1 seed/animal for doing that or more over time? Read the answers in this guide.
Guide to Green Bonus Icons
The gathering and animal bonuses are just sure-fire ways of getting that resource once.
The fish, pasture, and fertile land is more of a permanent bonus.
However, since droughts can kill off the fish bonus (and have no way of adding it back), that makes pastures and fertile land the only thing that matters in the long run.
Finally, a tip: start a game (or restart using the same conditions until you roll a good set of bonuses in the right spots), and send pawns to gather the plants at the gathering bonus spots immediately (no need for gathering huts). Build a bridge to get to the other side soon if possible too.
Animals (and their bonuses) can wander off map, and as plants die and get replaced, gathering bonuses can also disappear. Get them fast.