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I've seen Taq polymerase being marketed as either "native" or "recombinant". I understand that the recombinant version is produced by specially modified Escherichia coli strains that have the gene for polymerase production spliced in them, but I am wondering about the "native" variant. I imagine that Thermus aquaticus is rather difficult to culture in a medium; is it thus true that the archaeans have to be extracted from the springs they came from for producing "native" polymerase?

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There are protocols on how to culture T. aquaticus, but I don't see any on how to get any decent expression of Taq pol. Maybe it expresses extremely well anyways? It still seems asinine that companies charge a mere ~10% price premium on the native vs. recombinant protein; probably why a startup that is sharing our building is able to carve themselves out a market. – Nick T Dec 15 '11 at 15:10
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@Nick: 1969?! Wow, the protocol hasn't ever been modified since then? – user132 Dec 15 '11 at 15:17
It certainly has been, that's just an example demonstrating it's ability to be artificially cultured. Biotech companies that produce native Taq probably have all sorts of tricks and optimizations that they'd never share. – Nick T Dec 15 '11 at 15:22
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@nico I don't know, clearly someone wants them or they wouldn't be offered. I've only done a couple PCR reactions, and only with Phusion (Pyrococcus derived; "50X" fidelity) – Nick T Dec 15 '11 at 16:37
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About why you would want a native enzyme: the answer is on this site. Essentially, you want to use the native enzyme when you don't want any E. coli genome DNA contaminants in the reaction mix. – Naofumi Kagami Dec 22 '11 at 1:10
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For recombinant Taq polymerase, industrial-scale production produces liters of highly concentrated enzyme in a single run. It comes in such small, dilute quantities when sold that only a few preps a year would be necessary to satisfy research lab demand.

I don't know the Thermus aquaticus protocol, but considering the achievements in yield for E. coli, and the minimal price difference between the two enzymes, I'd imagine that yields are similar there. That would say to me that nobody's farming hot springs for T. aquaticus.

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