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There are tons of soil, rock, etc. being dug up, dug into, and moved all around the world each day. Paleontologists likewise regularly excavate fossils and both buried and frozen specimens, and biologists take samples of permafrost, soil and underground bodies of water.

Given all of the upheaval of these ancient and underground substrates and specimens, I'm wondering what the odds are that we unearth a superbug?

  • by superbug, I mean an otherwise unknown microorganism that modern medicine does not have a way to kill.

I understand that this is likely too broad of a question to be answered here (but feel free to try!), so I will break this down into a more relevant set of questions to inform my research.

  1. How many microbes (# of species and/or density) typically exist in a cubic meter of soil? (or some other volume)

  2. Do these microbe abundances and diversity change with depth?

  3. What is the deepest place in the crust that has been found to harbor life?

    • This article from 2010 suggests almost 1400 meters. Have we found deeper?
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What is the deepest place in the crust that has been found to harbor life?

The deepest living animal:

  • That award goes to the "Devil Worm" (Halicephalobus mephisto), a nematode that has been found living at 3.6 km below the surface!!

Halicephalobus mephisto is tiny (only 0.5mm long), and represents the deepest multicellular organism ever found.

  • The original paper can be found here: Borgonie et al. (2011)

    • I should note, that the paper found definitive Halicephalobus mephisto at 1.3km depth, but found rRNA gene sequence belonging to a specimen of Monhysteridae at the deep 3.6km depth.

Do these microbe abundances and diversity change with depth?

According to Inagaki et al (2015), microbe density is very low at low depths:

By counting the cells of these microbes, they also conclude that it is a small community, with just one cell in a cubic centimetre of sediment in some sections of the sediment

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It's an interesting question and I hope this answer doesn't seem flippant, because that is not my intention. The odds of finding a microorganism that has never encountered humans (or any mammal) but has evolved the ability to infect them seem rather low, in my opinion. For an organism to be pathogenic it must have the means evade the host immune system. This is an adaptive trait requiring co-evolution with the host. You can find a textbook discussion of pathogens in Molecular Biology of the Cell. Importantly, there's a section titled Pathogens Have Evolved Specific Mechanisms for Interacting with Their Hosts which answers your question rather well:

In contrast [to the normal microbial flora], dedicated pathogens do not require that the host be immunocompromised or injured [to cause an infection]. They have developed highly specialized mechanisms for crossing cellular and biochemical barriers and for eliciting specific responses from the host organism that contribute to the survival and multiplication of the pathogen.

In order to survive and multiply in a host, a successful pathogen must be able to: (1) colonize the host; (2) find a nutritionally compatible niche in the host body; (3) avoid, subvert, or circumvent the host innate and adaptive immune responses; (4) replicate, using host resources; and (5) exit and spread to a new host. Under severe selective pressure to induce only the correct host cell responses to accomplish this complex set of tasks, pathogens have evolved mechanisms that maximally exploit the biology of their host organisms.

Also keep in mind that the appearance of superbugs is due to intense selective pressure by the use of antibiotics. Such a scenario is not applicable to organisms we've never encountered before.

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