What if scientists were able to study the parasite which doesn’t breathe at all and use their findings to tweak the human genome to require less, or no, oxygen? Humans could then survive underwater, or in space, without oxygen or requiring much less.
The technology to edit DNA already exists, and it isn’t a large jump to alter the mitochondrial DNA that affects respiration. There are numerous ethical questions for this to be anything other than a distant-future story, or alternate reality, but there could be multiple uses for humans with these edits.
This could provide the basis for people who live underwater, calling upon legends of Atlantis.
The presence of cloud cities isn't out of the question, though how a city could be suspended in the air would have to be addressed. Magnetism, low orbit might be the answer for this.
Or, humans could live deep underground, needing less fresh air to survive.
An interesting series of novels could be if these three populations, in caves, water, and the sky, already existed and went to war with each other over a scarce resource.
Alternatively, there could be a thriller where the main character is able to escape into the mountains, using their maintained stamina to gain an advantage over their pursuers. It would be especially satisfying if the character had an unknown past, an orphan, and found out they were in fact from people who came from high elevations.
There are some recently published articles which make these scenarios no so unlikely
A parasite that is known for infecting fish, Henneguya salminicola, doesn’t need to breathe at all. Their existence is spent underwater so there would be little chance for them to use oxygen at all. When scientists studied their DNA, they were shocked to discover that not only do they not breathe, there is no trace of the genes used for respiration.
This is the first, and only, known animal to be missing these genes.
These genes are found in mitochondrial DNA inside all animal cells (other than the parasite). Uniquely, this parasite doesn’t have any mitochondrial DNA at all.
The scientists guess that the parasite evolved without mitochondrial DNA so they could reproduce faster and infect more hosts.
Another animal, the Himalayan wolf, has evolved to require less oxygen than nearby gray wolf populations. Their genes are responsible for the Himalayan wolf’s stronger heart and increased oxygen utilization.
Similar genes are found in Tibetan people who call the higher altitudes home.