Fish populations and ecosystems are definitely on that will be very hard to recover. Many scientists think we have destroyed fish habitats so much, that they may not recover. Check out the article for more info.
I think there are several forests, both rain and regular, that have been completely clearcut and destoryed of its natural beauty and all the goodness that they offered. Like plant diversity and animal habitat, that took dozens or hundreds (in some cases perhaps thousands) of years to grow to the state that it became before it was buldozed down.
I think marshlands and swamps are the hardest hit and perhaps the most vital ecosystems destroyed by mankind. Delta regions throughout the world are used by the planet as filtering systems and are home to many unique forms of life. Through development and/or pollution these regions have been abused to their breaking points.
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