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what exactly is habitat engineering?

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I assume you are asking about the mitigation of environmental impacts of civil engineering projects on the natural environment.

Civil engineering projects often have significant impacts on the natural environment, and these impacts can adversely affect species at and around the project site.

Projects are often required to mitigate these impacts, especially if the project uses public funds or is on or near public lands.  Mitigation efforts often include either constructing habitat from scratch or rehabilitating distressed habitat nearby. 

For example, a road project that fills in a portion of distressed wetland may include an effort to improve the wetland and other nearby wetlands in order to mitigate negative impacts of the road project on local fish and amphibians.  Wetlands can be improved by restoring more natural flows of water into and through the wetland, generally by changing the effects of previous construction projects that have harmed the wetland.  For example, a culvert under an existing road may be altered to remove a drop that prevents fish passage.