What are the other ways (if they exist) that atoms can gain or lose electrons that aren't bonding?
My question rather concerns if electrons are ever lost or gained naturally.


Yes, they can!

Here are two examples of natural processes by which atoms can gain or lose electrons "naturally":

Electron Capture

In the natural radioactive decay process known as electron capture the nucleus captures an inner-shell electron, K- or sometimes L-shell. This results in a proton being converted to a neutron, and the emission of a neutrino. The atom has lost an electron, but conveniently a proton as well, so it remains neutral but with a deep vacancy. 

Auger Process

If the vacancy is filled by a higher shell electron falling into it this can result in the emission of a photon, or in the emission of yet another electron. That emission is referred to as the Auger process.



See Electron capture; Reaction_details for examples.

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