Separate metals from organics, yes.[1] Reduce metals, probably not. Reduce means to pull a metal out of its oxide. This is way uphill energetically. It is usually done by heating the oxide to a high temperature in an oxygen-poor environment. The other direction, oxidation, produces energy, and there are some biological processes that use that.

Still, there are some bacteria which manipulate manganese.[2]

> What if atomic-scale manufacturing fundamentally changes our relationship with scarce resources?

I used to know Drexler, the early nanotechnology guy, back when nanotechnology meant pushing atoms around by mechanical means, rather than surface chemistry. Not much came of that. It's hard to apply enough force to break strong molecular bonds apart. IBM did manage to spell out "IBM" with xenon atoms, but xenon is inert and doesn't bond strongly to anything. No strong bonds to break.

Asteroid mining is potentially possible. Somebody will probably try it for gold and platinum within fifty years. It's unlikely to become cost-effective for cheaper metals.

[1] https://www.sciencedirect.com/science/article/abs/pii/S00489...

[2] https://www.cnn.com/2020/07/16/world/metal-eating-bacteria-i...