Edit 3: I answered before OP explained how it worked exactly.
I'm guessing that using the portal conserve the momentum and that throwing an object in the portal will make it exit with the same speed and direction.
I also assume portals are one-way.
A lot of species use the portal by throwing different objects into the portals.
Herd-hunting coyotes can indicate to fellow hunters that they find something by pushing a tumbleweed into the portal. The rest of the group know the direction and the approximative distance of the prey with the direction and the horizontal speed the scout pushed the plant or the signaling object into the portal.
Flying squirrels are squirrels that can glide and control their fall speed. They can fall from literally any high. They often enter the portal to glide far away from it. This is useful to escape predators or cross a massive obstacle such as a large river, a small mountain, or just a dry piece of land where they are visible hence vulnerable.
An even better situation is when two portals are close enough that a squirrel can reach one by gliding from the other's exit point. In that case, they can gather food from the richest area (forest, etc), and stash it on the safest area (cliff, mountain, etc)
It's cool. Literally.
Portals are pitch black. I'm guessing it's because the (re)emit no light. In that case, they don't radiate heat either. On hot sunny days, some dominant mammals love to chill in its shadow for this reason: not only you don't have the sun directly in your face, but it also feels like it's pumping heat from you (you naturally radiate heat to it, but contrary to any other room-temperature object, it doesn't radiate back its own heat).
Some small mammals like to bury food in its shadow: the soil is always very cold, and it works as a "fridge" for buried fruits. But careful not to be seen! They are very vulnerable when doing so, and predators know it's a good place for their preys to be. If you're a good hunter, you can leverage the fact that the portal hides your light AND most of the sound. Also, most stashing mammals spy on their peers to steal their buried food! Flying squirrels stash a lot because they can escape predators instantly by jumping into the portal.
Another reason the food lasts long when buried directly under the portal? It's super dry. All the rain falling on the portal never reach the ground after all...
Get free energy for dissemination
If you suspend a paper sheet vertically, air molecules bounce from right to left and left to right all the time, canceling each other pressure. On the surface of the portal, the molecule going into the portal (from left-to-right) never come back. And there's no molecule going in the other direction (from inside the portal's black entry sphere to outside) to cancel it out. This means permanent low pressure at the surface of the portal (and high pressure around the exit point).
To sum up, there is a permanent breeze coming into the portal. It's a vacuum cleaner to the sky!
For plants, it means that if you are near the portal, your spores have a chance to enter the portal and be widely disseminated! A rule of thumb is that you can see the effects up to 50m around the portal. A fun fact to observe is that in that zone, the further away from the plant from the portal, the lighter and smaller its spore, to better leverage this effect.
Plants can't count much on the flying insects near the portal to disseminate the spores, as they are most of the time sucked into the portal.
Magic food dispenser
Remember how a lot of flying insects are sucked into the portal?
Birds know that. Some hang around the exit point and wait for insects to come out.
From the ground, it's easy to spot a portal: follow the insect-eating birds: they cluster up in a specific zone in the sky, and below is a portal.
On the ground, spiders know that too. Building a web close to a portal is always a great idea for a spider. Most of them have super dark webs (no pun intended) to match the color of the portal and catch even more insects. Yum!
A fancy place to raise your kids as a bird
A lot of bird species raise their kids in a nest. When fully grown up, they jump out of the nest and have to learn how to fly... on-the-fly. A lot of them fail even if their parents invested a lot of time and energy. If you manage to build your nest above a portal, you kids have all the time they need to stabilize and make a kickass landing a few kilometers below.
Electromagnetic field, heat, light, and sound are all emitted on the exit point of the portal. This makes it easy to spot for migrating birds. They can use them to orient themselves in long migrations.
BONUS: How animals spot a portal?
- See insectivorous birds clusters above it
- Follow the wind
- Feel the cold on your skin **
- Echolocation ***
- Lack of electromagnetic field (it's absorbed too and emitted on exit)
- Sometime ground-level fog pours out of the exit point
** When you are in front of a fire by a cold night, you feel hot on the fire-facing side of your body and cold on the back. It's because the fire almost doesn't warm the air, you just have direct radiation from the fire. If you hold a piece of paper in front of your face, you will feel cold on your face again! Animals can develop a specialized organ to detect this sharp contrast in heat radiation in their field of view.
*** Bats use their voices and ears as a sonar. The portal will have no echo, which makes it easy to spot even for these almost-blind creatures.
EDIT: BONUS 2: Clouds and fire
Portals will pump ground-level air in a particular point of the sky. Not a specialist, but I think this relatively hot air meeting the cold air in altitude can produce clouds and often even thunderstorms. When this happen, the thunder can spark a fire. And if the fire reach the portal, a lot of incandescent embers can start fire far from the original portal. Luckily, most of it will be washed by the heavy rain of the thundercloud before it reaches the ground again. But in some rare occasions, maybe a big burning branch can fall into the portal and get carried by violent thunder cloud winds to start a fire elsewhere, if it serves your story.
If you think portal-induced fire are common, then the whole flora and fauna will have adapted to it, like the eucalyptus. If you think clouds are enough, it will be easier to spot portals from afar, and the often raining clouds can bootstrap and sustain a very diverse ecosystem. Another alternative is that since portals are not only pumping hot air in the sky but also dust, insects and small particles, the continuous cloud seeding could continuously empty the cloud as it's forming, so no problem. I have the intuition that would still electrically charge the area (the reason behind thunder in the first place) and that travelers would be zapped upon arrival, but I'm not sure of that and maybe the charge can be evacuated with the continuous very light rain.
(I would love to have confirmation by a meteorologist.)