Leaching, the recovery of copper from the drainage water of mines, as a method of the extraction of minerals, it was well established as early as the eighteenth century, but until about 25 years ago miners did not realize that bacteria take an active part in the process.
as a method of the extraction of minerals, it was well established
as a method of the extraction of minerals well established
was a well-established method of mineral extraction
was a well-established method of extracting mineral that was
had been a method of mineral extraction, well established
(E) inappropriate tense.
if the past perfect is used to describe a state or description of something (as opposed to an action verb), it should generally be used to describe a state/description that is no longer the case. since leaching is presumably still an extraction method (this is not the sort of thing that is subject to change), the past perfect is inappropriate.
also, the modifier (starting with "well established") shouldn't be a nonessential modifier, i.e., it shouldn't be set off by commas.
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