Life as we know it relies on a complex and interdependent ecosystem, and complex life relies on countless other organisms to support us. Without plants we absolutely couldn’t survive, without microorganisms we can’t survive. Without ample supplies of food, water and oxygen we can’t function.

Generally speaking the pace of biological activity is a lot slower than industrial ones too. We might make up for the pace with scale, but then you’re back to the hard problem of dependencies and “fuel”.

I’m not sure that the problem of beneficiation changes because the system is biological rather than industrial. Edit: Without carrying whole ecosystems with the probe at least.