Portuguese term (edited): produção... por rota biotecnológica

Sugiro tirar o "rota", que não agrega muita coisa, e inverter a estrutura:

produção de enzimas por rota biotecnológica
= biotechnological production of enzymes

Ex.:
http://cdn.intechopen.com/pdfs/27381/InTech-Microorganism_pr...
Perspectives for biotechnological production of enzymes...

Portuguese term (edited): produção de enzimas oxidativas por rota biotecnológica

Alternative (more literal but less idiomatic): production of enzymes by the biotechnology route.
(Explanation: Typographical error. Author probably meant to write "produção de enzimas oxidativas por ruta biotecnológica". Thus, "ruta", not "rota".)
(The typo interpretation makes much more sense than the interpretation "for the biotechnology sector". In the first place, "rota" does not mean "sector" in ordinary expository Spanish. In the second place, from a technical standpoint there would be very little enzyme content from agricultural wastes and the like that could be "produced" for the biotechnology sector -- ordinarily enzymes might be extracted from agricultural wastes but not "produced"!)

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Note added at 46 mins (2018-03-22 01:00:51 GMT)
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NOTE: I was preparing my answer when Freitas's answer appeared, and I never saw it. Therefore I hope people will credit me with a time of answering equivalent to his.

Or 'using biotech methods'.