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Context: Humans have escaped a a super-bacteria, similar in situation to the Bubonic Plague, that they could not create a cure for. They've done this by engineering gargantuan trees and adapting to lower oxygen levels.

However, I'm not sure my explanation of "the bacteria cannot survive in lower oxygen levels" makes sense because, well, trees produce oxygen, and it's supposed to be super-adaptive.

What's a plausible reason a bacterial plague couldn't survive in higher atmospheric conditions, or could only exist closer to the planet's surface? Open to any changes here including changing disease type. If there isn't one, I'll work on switching up the premise.

Edit for additional information: The planet itself is much larger than our own, and the layers of the atmosphere are wider to match. The original idea was that the bacteria somehow could not mutate to live in even marginally lowered oxygen levels, I'm talking the difference between sea level/airplane cruising altitude here. Worldbuilding-wise there is a heavily monitored quarantine layer between society and freefall to the surface. It's clear I need more research in general on atmospheric layers and oxygen production, the question is just if there's a different reason a bacteria could only survive close to the surface of a planet. Unfortunately I don't have numbers to give you, but continuing an Earth parallel the trees themselves would need to be at least 30,000ft.

Edit 2: The trees are genuinely actual wood trees. The question of how they grew them is currently not something I need scientifically answered for various worldbuilding reasons, or at least it's not the focus here. Assume these insanely massive trees are just a given.

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    $\begingroup$ How high are the trees? Gotta be pretty darn tall to have noticably different oxygen levels. Tall enough for greater UV, maybe, though that's something that can be produced artificially... $\endgroup$ Oct 27 '19 at 21:53
  • $\begingroup$ Are the gargantuan trees really made of wood? Or what do you mean with the engineering? $\endgroup$
    – PSquall
    Oct 28 '19 at 0:13
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Just about any Acheles heel in the bacteria will be one exploitable by Humans.

So there is a Bacterium which is highly infectious, and deadly within humans. To the point where it makes the Black Death look like hay fever. Yet somehow enough humans survived, yet did not become immune in the process. So quite likely the living humans were the ones who were not infected in the first place.

Where were the humans that did not get infected?

They were capable of engineer a huge forest. This speaks of industrial capacity, but limited in terms of inputs. Scientific knowledge, skills, and training.

What makes the canopy of a huge forest preferably to say the side of a mountain? Mt. Everest is 29,029ft (8,840m) above sea level. There is significantly less oxygen up there (from a human point of view). The canopy being this high might be the reason - The height was needed but oxygen levels needed altering. What else does 30000ft have?

  • Slightly less gravity
  • its above some forms of weather.
  • higher uv.
  • no ground to speak of.

That last point is probably it. The microbe survives quite happily in soil, and does not survive very long outside of it (or a human). Removing humans from soil keeps the humans relatively safe, with very occasional outbreaks that quickly dissipate as quarantines are enforced. The occasional outbreaks might be from bad dust storms (which usually do not plume so high), from a bird with soil on its feet, or some small amount of soil pushed up by the trees themselves.

This would also explain the few places where you might get the survivors. At sea in ships, in rocky regions with zero soil, near volcanos, large industrial complexes that long ago cast the ground in cement. They would be resource starved, as most resource sources would require encountering soil.

Over-engineering trees is interesting. It would have taken no small amount of ingenuity. Trees pose a problem in that they need soil to grow in. So of course they need to be tall enough so that any bacterium lifted by their roots are dead by the time they reach the leaves and are transpired or otherwise transmitted to the humans living at the top. Though this was probably not the reason for selecting trees as the solution.

The trees were probably selected as a massive antibiotics administration device. Trees often enter into chemical warfare. Surely humans capable of strengthening Lignin to permit such tall trees, can also tweak them to administer massive amounts of any anti-biotic of choice in the hopes of killing off the source of the plague.

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UV light

As you go higher, the amount of UV light increases

If the bacteria is sensitive to UV, the increased elevation could kill it

At high elevations, the atmosphere thins and is less able to absorb U.V. radiation. With every 1000-foot increase in height, according to the National Institutes of Health, U.V. levels increase by about 4%. So, in Denver, “the Mile High City”, U.V. radiation is about 20% stronger than a location at sea level at the same latitude. Heading up into the Rocky Mountains, where peaks can reach above 14,000 feet, the U.V. intensity soars even higher.

http://www.weathergamut.com/2014/08/12/why-u-v-intensity-increases-with-elevation/

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Have a carrier for your disease. When reading your question, I immediately thought of dust mites, because they cannot live in altitude. But it seems it's actually because they hate cold and dry places, and mountains are usually cold and dry.

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