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.
That's why my other comment pointed to the autotrophs with the simplest requirements, and the (unknown but complexity-bounded) origin of life.
> pace of biological activity is a lot slower than industrial ones
Bacterial replication times can be under an hour.
What something like E. Coli can do in a well bioreactor is the ideal case, and even then most of what they produce is the bacteria themselves. On Earth this isn’t a problem at all, but as a means of husbanding every joule because you don’t know when or where the next one is coming from, I think it might matter.
It’s also probably a genuinely hard problem keeping your organisms viable without a constant supply of food, a means to get rid of mutants, or some hitherto unknown means of preservation that could handle the extreme time spans involved between “awakenings”.