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I would think the first, and when you went back to civilization you spread the immunity so humans dont get infected yet local lifeforms become the kharaa. I believe in natural selection the outbreak happens on the fringe of the Mongolian States which may be encroaching on the original lost alien worlds to the bacteria.
But it wasn't tell the very end of development that unknown worlds changed carar to actually be connected to the natrual selection universe. So the order of things can change because its purposely very vague if they make another game in the universe. The arctic dlc can bring more light to whats going on.
So...we know that after a while, your PDA tells you that you are infected, and you find out the planet was stopping some out break called the "Kharaa". (Due note this is a name change from the devs, it was called 'Carar' in before the game launch). You become infected and as time passes, you see the changes, even developing bulbs on your skin.
You eventually find a way to cure the disease (Enzyme 42), and turn off the planetary defenses, allowing you to finally escape the planet and head back to civilization. The Sea Emporer's children is free in the safe shallows, spreading Enzyme 42, so all should be good right? Perhaps not....think about the bigger picture now, with N.S.2 in it. Here are things to think about...
1) The whole point of the Precursers putting up the Quarantine was to make sure that NOTHING got off the planet that was infected, or onto the planet to leave with it, hence why it shot down ships too close. By deactivating the the gun, you get off planet and go home (to your total amount of creds you owe Alterra totalling 1 Trillion...good luck paying that off), but now that means OTHER ships can now go to said planet without being shot down. Yes, lives are spared, but now they could go into areas that the Kharaa has not been cleansed of by Enzyme 42.
2) With that, what's to stop someone else from going to the planet, doing some exploring and what not for another company or Alterra, and leaving, but becoming infected...NOT knowing about Enzyme 42 like the player character. We don't know exactly how it's spread, whether it's by food, contact, or heck if it's even air born and breathable. This could lead to the spread of the disease...which leads us to...
3) Natural Selection 2 from what I understand, takes place many years later, with the Frontier Men battling the mutations aptly named the Kharaa. They share similar traits to what we see on the water planet. What exactly? The 'Nest' or "Nexus" of the creature side....is a giant glowing, orange bulb. What grows on your player character or creatures in Subnautica? Green glowing bulbs. There are defensive tentacles that shoot at the Frontier's Men that look almost identical to the Tiger Planets on the water planet as well. Coincidence? Possibly not.
4) The logo on the Frontier's Men weapons has the "Alterra" logo. So not only do you know they're involved with the player character in Subnautica, but also supporting the equipment for the Frontier's Men in N.S. 2. What's to say that Alterra hasn't had a hand in trying to study the disease for their own interests?
That's my 2 cents at least, and this is just based on the theory vids putting everything together, which, frankly to me, makes a HELL of alot of sense.