These aren't formed nodules like other seabed metals, this is mud with higher than normal amounts of rare earths present. What isn't clear from the article is

These aren't formed nodules like other seabed metals, this is mud with higher than normal amounts of rare earths present. What isn't clear from the article is if they plan on dredging the top layer, which would entirely disrupt the ecosystem, or somehow pump up mud from under the seabed itself. If it is the latter, the ecosystem is unlikely to have a dependency on the rare earths in the mud itself; at that depth you don't have plants with deep roots or anything transecting the layers. You will certainly have surface deformation which will be disruptive, but not so much as dredging would be.