I have limited knowledge and ...

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I have limited knowledge and experience in the area yet felt can help so venturing in with a suggestion.

As far as I understand the colour is because you are using wood, essetially Lignin o why not digest lignin first using an appropriate enzyme.can suggest and demonstrate a natural source as well. The other problem is the issue of hevy metals in the effluent so even for that can suggest Bioremediation.