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List of Threats, with links to articles for more information

World Resources Institute: Coral Reefs Classified By Potential Threats From Human Activity

CLIMATE:
Reef Base

CORAL BLEACHING:
Coral Reef Ecology
Environmental Protection Agency
International Coral Reef Network
NOAA's "A Reef Manager's Guide To Coral Bleaching"
Oceans Alive
Odyssey Expeditions
Reef Base

CORAL FISH TRADE:
Reef Base
Global Trade and Consumer Choices: Coral Reef Crisis
National Public Radio: Coral Reefs in the Balence
Conservation International: Ravaging The Reefs
Researcher Finds Way To Raise Tropical Fish in Lab, Saving Coral Reefs

CORAL MINING:
Reef Base
International Coral Reef Information Network

DESTRUCTIVE FISHING PRACTICES:
Conservation Science Institute
Marine Conservation Biology Institute
Reef Base
The World Bank Group: Blast Fishing In Indonesia

DISEASES & BIOLOGICAL INFESTATIONS:
Diseases of Coral Reefs
Global Coral Reef Alliance: Mysterious New Diseases Devastate Coral Reefs
Reef Base Diseases
Reef Base Biological Infestations

EUTROPHICATION: 
Global Coral Reef Alliance: Eutrophication
Reef Base

EXOTIC SPECIES:
Reef Base
Community Environmental Research in the Pacific Islands: Crown of Thorns Starfish

HABITAT LOSS FROM DEVELOPMENT:
Threats to Coral Reefs: Human Development
World Resources Institute: Reefs threatened by human activity

MILITARY/NUCLEAR TESTING:
Reef Base

OVER HARVESTING:
Barbara Best & Alan Bornbusch: Global Trade and Consumer Choices: Coral Reefs in Crisis
Coral reefs doomed, study says centuries of overfishing killing ecosystems
Reef Base
World Resources Institute

PHYSICAL IMPACTS: Ship Groundings & Anchor, Pipeline and Cable Damage
Groundings on coral reefs and seagrass beds
Ship groundings smashing holes in Lauderdale coral reefs

POLLUTION:
Reef Base Industrial Pollution
Reef Base Marine Pollution

SEDIMENTATION:
Reef Base Manmade
Reef Base Natural
Threats to Coral Reefs

TOURISM:
The Negative Effects of Tourism on the Ecology of Jamacia
UNEP Tourism's Impact on Coral Reefs