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The key strategies used in reef protection include reducing the impact of stressors and key threats, increasing the use of management planning and effectiveness, using measurable goals for coral restoration, implementing management training and community involvement in Marine Protected Areas (MPAs), and developing new techniques for monitoring reef health and species.

Purpose
The purpose of coral reef protection is to sustain the assets the reef provides, and prevent further destruction of the physical structure of the reef. It takes approximately 10 thousand years for coral polyps to form a reef, and between 100,000 and 30 million years for a fully mature reef to form. The unique ecosystem provides a habitat to over 9 million species of organisms, and approximately one fourth of marine life. The three dimensional framework of the coral polyp itself is what creates the structure of the habitat for the species of the ecosystem.

Biodiversity
The three dimensional structure of the reef allows it to become a shelter and habitat to different species. The difference in exposure to wave patterns creates a range and variety of habitat types. Millions of marine life species interact and live within the branches of the coral, and use it as a shelter, hiding place, and a food source. Single celled algae inhabit the coral polyps. The coral need a mutualistic symbiotic relationship with zooxanthellae algae in order to build a reef. The ocean water contains relatively little beneficial nutrients that the coral can utilize. The single celled algae derive their nutrients by using photosynthesis, and the coral provide shelter to the algae in return for some of the nutrients. Coral receive their vibrant colors from the different species of zooxanthellae that inhabit them. Zooxanthellae populations can die with changing environmental conditions, causing the coral to lose color, known as coral bleaching.

Medicine
Coral reef ecosystems are home to a variety of species of plants and animals that produce chemical compounds that are isolated and then used in medicines. Due to the genetic diversity of the reef ecosystem, research has allowed for the discovery of potentially beneficial chemical compounds. As early as the 14th century, the medical properties of coral reef dwelling species have been utilized. Antiviral extracts and tonics used as traditional medicine continue to be studied and researched, and toxic compounds such as neurotoxins discovered in coral reefs have proven beneficial as painkillers. The limestone skeleton of coral has also been tested and used for human bone grafts, due to its porous nature, and has a lower rate of rejection than artificial bone graft materials.

Restoration
The aim of coral restoration is helping coral adapt to changing environments and to improve their recovery time. The NOAA's Coral Reef Conservation Program and Damage Assessment, Remediation, and Restoration Program approaches restoration using methods including responding to and restoring physically damaged reefs, preventing the loss of environment, implementing coral conservation projects, focusing on restoring endangered coral species, and controlling excessive amounts of invasive species. The Coral Restoration Foundation has restored over 100 genotypes of staghorn corals (Acropora cervicornis) using coral nurseries, and also maintains research goals of determining ecological success of coral reefs, ideal restoration locations and how surrounding organisms affect restoration success.

Coral Nurseries
Using coral aquaculture, the process of using coral nurseries to restore the world's reefs, is a project that is capable of improving biodiversity, structural integrity and coral cover of the reef. Coral nurseries are used to rehabilitate areas of reef decline or physically damaged areas. In this process, coral gametes are harvested and grown in a laboratory environment and then replanted when they are larger in size. This allows the coral to grow safely in controlled amounts within lab conditions before being transplanted. Nurseries can also begin as small patches of rescued coral colonies, and may be salvaged and restored before transplantation. In 2009, The Nature Conservancy began to grow over 30,000 young coral in underwater nurseries in Florida and the Caribbean to be transplanted.