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ReefLink Database

Microorganisms

Microorganisms

Microorganisms are microscopic plants or animals, such as cyanobacteria and disease-causing pathogens that live in coral reef ecosystems.

CMap

Applied chemicals are chemicals applied to lands, vehicles, buildings, or during manufacturing for a variety of purposes, including maintaining pests, improving soil quality, or cleaning surfaces. Cultural services are the nonmaterial benefits people obtain from ecosystems through spiritual enrichment, cognitive development, recreational opportunities, aesthetic experiences, sense of place, and educational and research opportunities. Cyanobacteria (also known as blue-green algae) obtain their energy through photosynthesis. Discharge limitations are responses to regulate and control the discharge of pollutants and the use of chemicals. Discharges are the intentional or unintentional distribution of chemicals, debris, or other pollution, into the environment as a consequence of human activities. Ecosystem monitoring and restoration refers to responses to directly alter the condition of the reef ecosystem through restoration or remediation activities, setting limits on degradation through biological criteria or water quality criteria, or improving knowledge through monitoring, mapping, and scientific research. Ecosystem services are the benefits people obtain from ecosystems . Light is the level of visible and ultraviolet solar radiation that penetrates the water column. Microorganisms are microscopic plants or animals, such as cyanobacteria and disease-causing pathogens that live in coral reef ecosystems. Nutrients are essential elements needed by plants and animals for growth and primarily include nitrogen, phosphorous, and potassium, as well as minor nutrients such as calcium, magnesium, or zinc. Pathogens are disease-causing microorganisms, including bacteria, viruses, and fungi. The Reef Ecosystem includes a suite of abiotic variables that form the physical and chemical environment. Pressures are human activities that create stress on the environment. Provisioning services are the products or ecosystem goods obtained from ecosystems, including seafood, genetic and biochemical resources, pharmaceuticals, ornamental resources, and water resources. The state of the Reef Ecosystem is the condition, in terms of quantity and quality, of the abiotic and biotic components including physical, chemical, and biological variables. Reef Habitat is the abundance, distribution, and condition of the benthic components of the reef ecosystem. Reef Inhabitants are all of the motile components of the reef ecosystem, including fish, invertebrates, marine reptiles and mammals, and are quantified by their abundance, distribution, and condition. Reef Life is the abundance, distribution, and condition of the biological components of the coral reef ecosystem. Regulating Services are benefits obtained from ecosystem processes that regulate the environment, including erosion regulation, natural hazard regulation, and climate regulation. Responses are actions taken by groups or individuals in society and government to prevent, compensate, ameliorate or adapt to changes in Ecosystem Services or their perceived value. Sea temperature is a measure of the warmth of ocean waters, and depends on water depth, solar radiation, water circulation patterns, and atmospheric temperatures. Sediment includes dirt, sand, silt, clay, and small rocks that form soil on land or soft substrate in marine habitats, and may be transported by water, wind, or human activities. Socio-Economic Drivers include the sectors that fulfill human needs for Food & Raw Materials, Water, Shelter, Health, Culture, and Security, and the Infrastructure that supports the sectors. Supporting services are ecological processes that indirectly benefit humans by maintaining a functional ecosystem for the production of other ecosystem goods and services. Waterborne discharges include direct and indirect discharges of pollutants into the aquatic environment, including chemicals, nutrients, sediment, and pathogens. A wetland is an area of land whose soil is saturated with moisture either permanently or seasonally.

CMap Description

Biological inputs of pathogens through wastewater discharges can cause disease in native species. Pathogen growth and disease outbreaks may be accelerated in elevated sea surface temperatures. Periodic cyanobacteria blooms may be related to elevated nutrient levels, and can alter light availability or produce toxic chemicals. Changes in reef condition can affect the availability of goods and services. Many of the same socio-economic sectors that benefit from reef ecosystem goods and services also create pressures on reefs through wastewater discharges. Monitoring and scientific research can be used to track blooms and disease outbreaks, and to better understand their impact on reef species. Discharge limitations can control the intensity and frequency of discharges, reducing inputs of nutrients and potential pathogens into the environment.

Citations

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Citation Year Study Location Study Type Database Topics

Management Options

Management Option Description Sources Database Topics
Agriculture & Aquaculture: Livestock Waste Storage and Utilization Confined animal facilities often produce large amounts of animal waste. This waste can be stored and disposed of in a variety of ways, and it is important to consider how rainwater may carry these wastes in groundwater. Wastes can be kept in temporary storage ponds, storage structures, or treatment lagoons. Once composted, these wastes may be applied to agricultural land in an environmentally acceptable manner in place of other fertilizers. Site selection, timing of application and rate of application must be properly managed to reduce the potential for degradation of ground water. Additionally, this practice may increase microbial action in the soil surface, which helps keep pesticides and other pollutants in place. Environmental Protection Agency Office of Water. 1993. Guidance Specifying Management Measures For Sources Of Nonpoint Pollution In Coastal Waters. EPA/840/B-92/002, US EPA, Washington, DC.

Agriculture; Agriculture, Aquaculture, & Forestry Policies; Discharge Limitations; Discharges; Food & Raw Materials; Microorganisms; Non-point Source Controls; Non-point Source Runoff; Nutrients; Pathogens; Waterborne Discharges
Agriculture & Aquaculture: Composting Composting involves the controlled aerobic decomposition of manure or other organic material by micro-organisms into a biologically stable organic material that is suitable for use as a soil supplement. Composting should be part of nutrient management plans because it reduces the pollution potential of organic wastes. Smaller scale household composting may reduce the amount of material that enters the waste stream, where again it may have greater pollution potential. Larger volumes of material may require construction of containment facilities to ensure pollutants aren't able to enter runoff water in high concentrations. Natural Resources Conservation Service. 2011. National Handbook of Conservation Practices. U.S. Department of Agriculture.

Agriculture; Agriculture, Aquaculture, & Forestry Policies; Carbon Storage & Cycling; Discharge Limitations; Discharges; Landscaping & Household Services; Littering; Microorganisms; Non-point Source Runoff; Nutrient & Contaminant Processing; Nutrients; Solid Waste Disposal; Waste Management; Waste Management Policies; Waterborne Discharges
Monitor & Research: Biological Status and Trends Monitoring This activity produces long-term comprehensive information on sanctuary-wide status and trends of biological resources. Data that could be collected on coral reef communities includes but is not limited to species abundance and density, biodiversity, benthic cover, coral condition, growth, recruitment, predation, and grazing. Mangroves and seagrasses should also be monitored. With adequate baseline data, changes in community structure and biocriteria can be identified and restoration or protection efforts can be taken. NOAA Marine Sanctuary Program. 2007. Florida Keys National Marine Sanctuary revised management plan. National Ocean Service, Key West, FL.

Algae; Anemones & Zooanthids; Apex Fish Predators; Aquaculture; Aquarium Stock; Biochemical & Genetic Resources; Biocriteria; Biological Harvest; Biological Monitoring & Restoration; Biological Monitoring, Mapping, & Scientific Research; Bivalves; Calcareous Macroalgae; Contact Uses; Coral; Coralline Algae; Cyanobacteria; Decision Support; Echinoderms; Ecosystem Monitoring & Restoration; Finfish & Shellfish Stock; Fish; Fishing Sector; Food & Energy Policies; Hydrocoral; Invasive Species; Invertebrates; Large Herbivorous Fish; Lobster, Crab, & Shrimp; Mangroves; Marine Birds; Marine Products; Marine Vertebrates; Marine Worms; Microorganisms; Molluscs; Octocoral; Octopus & Squid; Ornamental Jewelry & Art; Pathogens; Pharmaceuticals & Cosmetics Sources; Physical Damage; Primary Production; Provisioning Services; Resource Use Management; Sea Turtles; Sea Urchins; Seagrasses; Seastars; Skeletal Coral; Small Herbivorous Fish; Snails & Conch; Sponges; Stony Coral; Tunicates; Wetlands; Whales & Dolphins
Resource Use Management: Develop Regulations for Sponge Fisheries Sponges play a vital role on reefs, providing structure, food and filtration. Depending on the method of removal, this process can be very destructive to other reef fauna and habitat. Research is needed to compare impacts of different sponge fishing methods in different areas. NOAA Marine Sanctuary Program. 2007. Florida Keys National Marine Sanctuary revised management plan. National Ocean Service, Key West, FL.

Accidental & Illegal Harvest; Biochemical & Genetic Resources; Biological Harvest; Biological Monitoring, Mapping, & Scientific Research; Boring Sponges; Commercial Fisheries; Contact Uses; Culture; Cyanobacteria; Educational & Research Opportunities; Encrusting Sponges; Finfish Harvest; Fisheries & Hunting Policies; Fishing & Harvesting Management; Fishing Sector; Invertebrate Harvest; Live Collection; Marine Products; Microorganisms; Nutrient & Contaminant Processing; Pharmaceuticals & Cosmetics Sources; Physical Damage; Resource Use Management; Scientific Research; Sponges; Tourism & Recreation; Tourism & Recreation Policies; Trawling & Fishing Gear Damage; Tube, Barrel, & Finger Sponges
Restoration: Reintroduce Indigenous Living Corals The approach reviews the policies and regulation regarding the re-introduction of living corals indigenous to a specific geographic location that were propagated in the lab. The concern about reintroduction of organisms from the lab and aquaria revolves around the possibility of introducing exotic or foreign strains of diseases to natural coral. Also, there is concern about introducing defective genetic material as well. One viable solution may be to reintroduce corals reared in in-situ coral nurseries. NOAA Marine Sanctuary Program. 2007. Florida Keys National Marine Sanctuary revised management plan. National Ocean Service, Key West, FL.

Biological Addition; Biological Monitoring & Restoration; Biological Monitoring, Mapping, & Scientific Research; Coral; Decision Support; Ecosystem Monitoring & Restoration; Microorganisms; Reef Habitat; Security & Public Administration Policies; Special Use Permitting; Stony Coral; Wetland & Reef Restoration
Water Quality Management: Reduce Pollution & Discharges from Marinas & Live-Aboards This management option strives to reduce and eliminate the discharge of wastewater and pollution within zones near corals. In many instances, "no-discharge" zones already exist and are simply poorly enforced. In other instances the discharge limits are not stringent enough. Successful regulation requires marinas to be equipped with the proper infrastructure to support transfer of wastewater from vessels to shore-side for treatment. This infrastructure includes: pump-out facilities and mobile pump-out services. NOAA Marine Sanctuary Program. 2007. Florida Keys National Marine Sanctuary revised management plan. National Ocean Service, Key West, FL.

Biological Addition; Boating Activities; Boating Regulations; Coastal Engineering; Cyanobacteria; Discharge Limitations; Discharges; Docks & Marinas; Health; Health Policies; Marine Debris; Microorganisms; Nutrient & Contaminant Processing; Nutrients; Pathogens; Physical Damage; Point & Mobile Source Controls; Point Source Discharges; Ports & Harbors; Resource Use Management; Sewage Treatment; Solid Waste Disposal; Waste Management; Waste Management Policies; Wastewater Discharge; Waterborne Discharges
Water Quality Management: Pet Waste Cleanup Ordinance & Education In residential areas, pet waste can contributes to the large amount of nutrients and pathogens that enter the water through stormwater runoff. This is especially useful in regions such as Gu�nica, Puerto Rico where there are a lot of stray dogs. Education for pet-owners and possible ordinance would help decrease harmful pathogens reaching corals through stormwater runoff and reduce eutrophication. Center for Watershed Protection. 2008. Guanica Bay watershed management plan.

Natural Resources Conservation Service. Animal Waste Collection. Urban BMP's - Water Runoff Management Accessed 3/18/2011.

Clary, J., Leisenring, M., and Jeray, J. 2010. International Stormwater Best Management Practices (BMP) Database. Pollutant Category Summary: Fecal Indicator Bacteria. Wright Water Engineers.

Aquarium & Pet Trade; Biological Addition; Chemical Variables; Cultural Policies; Cultural Services; Culture; Cyanobacteria; Discharge Limitations; Discharges; Domestic Animal Waste; Environmental Education & Outreach; Health; Health Policies; Invasive Species; Landscaping & Household Services; Microorganisms; Nutrients; Pathogens; Shelter; Solid Waste Disposal; Stormwater Management; Waste Management; Waste Management Policies; Water; Water Resources; Water Utilities Policies; Waterborne Discharges

Laws

Legal Citation Purpose of Law Management Organization Database Topics
Clean Water Act of 1974, 33 United States Code § 1252. To restore and maintain the chemical, physical, and biological integrity of the Nation's waters

Application to Coral Reefs:The Act can be used to establish water quality standards for the disharge of pollutants into surface waters. Section 101 (3) stated that it will be the national policy that the discharge of toxic pollutants in toxic amounts will be prohibited. The legislation employs a variety of regulatory and nonregulatory tools to reduce direct pollutant discharges into waterways, finance wastewater treatment facilities, and manage polluted runoff. The tools are employed to achieve the broad goal of restoring and maintaining the chemical, physical, and biological integrity of the nation's waters so they can support "the protection and propagation of fish, shellfish, and wildlife and recreation in and on the water."

Legislative Actions:During the late 1980's, the program shifted from program-by-program, source by source, pollutant-by-pollutant approach to more holistic water-shed strategies. Under the watershed approach equal emphasis is placed on protecting healthy waters and restoring impaired waters. Also during the 1980's, voluntary programs for nonpoint runoff and regulatory programs for wet weather point sources began to be addressed.

Comments:The Federal Water Pollution Contrl Act Amendments of 1972, PL 92-500, replaced the previous language of the Act entirely, including the Water Quality Act of 1965, the Clean Water Restoration Act of 1965, and the Water Quality Improvement Act of 1970, all of which had been amendments of the Water Pollution Control Act first passed in 1956. The 1977 amendments, PL 95-217, further amended PL 92-500. 		US Environmental Protection Agency

Jurisdiction:
United States; US Territories 		Agriculture, Aquaculture, & Forestry Policies; Biocriteria; Collaboration & Partnering; Construction Codes & Projects; Corporate Responses; Drinking Water Supply; Economic Markets & Policies; Energy Policy & Development; Hydrologic Management; Improved Technology; Mangroves; Microorganisms; Non-point Source Controls; Nutrient & Contaminant Processing; Nutrients; Physical & Chemical Water Quality Criteria; Point & Mobile Source Controls; Point Source Discharges; Political Pressure; Public Administration; Remediation; Resource Use Management; Seagrasses; Sewage Treatment; Waste Management Policies; Wastewater Discharge
Coral Reef Conservation Act of 2000, 16 United States Code § 6401 (2000). To preserve, sustain, and restore the condition of coral reef ecosystems, to promote the wise management and sustainable use of coral reef ecosystems, to benefit local communities and the Nation, to develop sound scientific information on the condition of coral reef ecosystems and threats to the ecosystems, to assist in the preservation of coral reefs by supporting and financing conservation programs including local and non-governmental programs, establish a formal mechanism for collecting and allocating monetary donations from the private sector to be used for coral reef conservation projects

Application to Coral Reefs:Allowed the development of programs and projects, and provided financing for developing sound scientific data to preserve and restore coral reefs. Continued the Coral Reef Task Force and Coral Reef Initiative started under Executive Order 13089 (1998).

Legislative Actions:Provided funding for matching grants, encouraged education and outreach, encouaged cooperative conservation and management through partnerships with other federal, state, regional and local partners including citizen groups.

Comments:The Act is administrative, not regulatory. It established four major programs; (1) The National Coral Reef Action Strategy established goals for research, monitoring and conservation, (2, 3) The Coral Reef Conservation Program and Coral Reef Conservation Fund provided financial assistance for coral reef projects, (4) the National Program facilitated cooperative work between federal, state and regional efforts that work to improve coral reef ecosystems. The National Program also enhanced the public awareness of coral reefs through educational programs. The Act incorporated Executive Order 13,089 and provided coordinated funding activities through twelve federal agencies and seven states. 		National Oceanic and Atmospheric Administration

Jurisdiction:
United States; US Coral Reefs 		Biocriteria; Biological Monitoring, Mapping, & Scientific Research; Corporate Responses; Education & Information; Environmental Education & Outreach; Environmental Monitoring, Mapping, & Scientific Research; Fishing & Harvesting Management; Food & Raw Materials; Funding & Incentives; Marine Debris; Marine Protected Areas; Microorganisms; Public Administration; Remediation; Utilities
Fish and Wildlife Coordination Act, 16 United States Code §§ 2901-2911. To provide financial and technical assistance to the states for development, revision and implementation of conservation plans and programs for nongame fish and wildlife, and to encourage federal agencies to utilize their statutory and administrative authority to conserve and to promote the conservation of nongame fish and wildlife and their habitats.

Application to Coral Reefs:

Legislative Actions:

Comments: 		Federal Agencies

Jurisdiction:
United States 		Finfish & Shellfish Stock; Finfish Harvest; Funding & Incentives; Microorganisms; Point & Mobile Source Controls; Public Administration
Identification of impaired surface waters, 62-303 Florida Administrative Code Annotated (2002). The Chapter established a methodology to identify surface waters of the state that will be included on the state's planning list of waters that will be assessed pursuant to subsections 403.067(2) and (3), Florida Statutes. It also establishes a methodology to identify impaired waters based on representative data that will be included on the state's verified list of impaired waters, for which the Department will calculate Total Maximum Daily Load (TMDLs), pursuant to subsection 403.067(4), F.S., and which will be submitted to the United States Environmental Protection Agency pursuant to paragraph 303(d)(1) of the Clean Water Act (CWA).

Application to Coral Reefs:By regulating the amount of pollutants that will be allowed to be discharged into major waterbodies of the state, the amount of pollutants reaching estuarine and then marine environments, and eventually coral reefs, will assist in protecting the reefs and other habitats.

Legislative Actions:The planning list of impaired water bodies has been completed. Data on each water bodies has been collected. DEP is in the process of calculating TMDLs for each water body.

Comments: 		Florida Department of Environmental Protection

Jurisdiction:
State Coastal Waters 		Agriculture, Aquaculture, & Forestry Policies; Construction Codes & Projects; Corporate Responses; Designated Uses; Fertilizer & Pesticide Use; Finfish & Shellfish Stock; Forestry; Irrigation; Landscaping & Household Services; Landuse Management; Metals, Electronics, & Machinery Products; Microorganisms; Mining; Non-point Source Runoff; Nutrient & Contaminant Processing; Nutrients; Oil & Gas Research & Exploration; Point Source Discharges; Sewage Treatment; Solid Waste Disposal; Waste Management Policies; Wastewater Discharge; Wood, Plastics, & Chemical Products
Marine Protection, Research, and Sanctuaries Act of 1972, 33 United States Code § 1401. To regulate the dumping of all types of materials into ocean waters and to prevent or strictly limit the dumping into ocean waters of any material which would adversely affect human health, welfare, or amenities, or the marine environment, ecological systems, or economic potentialities. To regulate (1) the transportation by any person of material from the United States and, in the case of United States vessels, aircraft, or agencies, the transportation of material from a location outside the United States, when in either case the transportation is for the purpose of dumping the material into ocean waters, and (2) the dumping of material transported by any person from a location outside the United States, if the dumping occurs in the territorial sea or the contiguous zone of the United States.

Application to Coral Reefs:The Act has been historically used to regulate dumping of dredged materials and sewage sludge into the marine environment. The law intends to improve the conservation, understanding, management, and wise and sustainable use of marine resources, enhance public awareness, understanding, and appreciation of the marine environment, and to maintain for future generations the habitat, and ecologigal services, of the natural assemblage of living resources that inhabit those areas. Because permits are required, it can be assumed that dumping would not be allowed if the material would be dispersed into a sensitive habitat such as coral reefs.

Legislative Actions:EPA may assess an administrative civil penalty up to $50,000 per person. Higher penalties can be assessed for dumping medical waste (up to $125,000). Each day in violation constitutes a separate offense. Continuing violations can suffer criminal penalties with fines and up to five years imprisionment possible.

Comments:The Act has played a major role in regulating the disposal of dredged material into the ocean environment. However, medical and radioactive wastes, industrial wastes, as well as sewage sludge, are also regulated in the law. 		United States Environmntal Protection Agency

Jurisdiction:
US Territorial Waters; US Federal Waters; Designated Marine Areas 		Ballast Discharge; Biocriteria; Boating Regulations; Complex Habitat & Resources; Designate Protected Species; Designated Uses; Environmental Education & Outreach; Environmental Monitoring, Mapping, & Scientific Research; Fishing & Harvesting Management; Mangroves; Marine Debris; Marine Protected Areas; Microorganisms; Non-point Source Controls; Oil & Gas Research & Exploration; Physical & Chemical Water Quality Criteria; Point & Mobile Source Controls; Political Pressure; Remediation; Resource Use Management; Seagrasses; Sediment; Sewage Treatment; Solid Waste Disposal; Tourism & Recreation Policies; Transportation Policies; Waste Management Policies; Wastewater Discharge
Marine Sanitation Devices (MSDs); Regulations to establish a No Discharge Zone (NDZ) for State waters within the boundary of the Florida Keys National Marine Sanctuary,Code of Federal Regulations § 40 CFR Part 140, 67 FR 35735. US EPA established a no discharge zone within the boundaies of the FKNMS pursuant to section 312 (f) (4) (a) of the Clean Water Act.

Application to Coral Reefs:Prohibition of waste discharges protects reefs system from eutrophication by the nutrients in waste (particularly nitrogen and phosphorus) as well as the debris and sediment in the waste.

Legislative Actions:

Comments: 		US Environmental Protection Agency

Jurisdiction:
US Coral Reefs; US Federal Waters; State Coastal Waters; Designated Marine Areas 		Algae; Ballast Discharge; Commercial Fishing Boats; Cruise Ships; Large Ships; Marine Debris; Nutrient & Contaminant Processing; Nutrients; Oil & Gas Tankers; Pathogens; Petroleum Spills; Physical & Chemical Water Quality Criteria; Small Boats; Waste Management Policies; Wastewater Discharge
National Environmental Policy Act of 1969, 42 United States Code §§ 4321-4377. Requires analysis, public comment, and reporting for environmental impacts of federal actions. It stipulates the factors to be considered in environmental impact statements, and requires that federal agencies employ an interdisciplinary approach in related decision-making and develop means to ensure unqualified environmental values are given appropriate consideration, along with economic and technical considerations.

Application to Coral Reefs:Requires an Environmental Assessment(EA), and potentially an Environmental Impact Statement (EIS) if the project review finds there will be a significant impact. The EIS must detail the environmental impacts of the proposed action, unavoidable adverse environmental impacts, and alternatives to the proposed action. The resulting studies could protect sensitive environmental ecosystems, including coral reefs.

Legislative Actions:The Act potentially could protect coral reefs if the proposed federal project could have a significant impact on the reef.

Comments:The Act is completely procedural; it does not include specific regulations. The Council on Environmental Quality (CEQ) was created by the Act. CEQ is part of the Executive Office of the President and one of the CEQ directives is to ensure that federal programs comply with NEPA. The puprose of the EIS is to disclose to the public and resource managers the probable long- and short-term impacts of the proposed project as well as consideration of less environmentally damaging alternatives to the recommended course of action. 		Federal agencies

Jurisdiction:
United States 		Agriculture, Aquaculture, & Forestry Policies; Biocriteria; Biological Monitoring, Mapping, & Scientific Research; Boating Regulations; Construction Codes & Projects; Decision Support; Designated Uses; Economic Markets & Policies; Energy Policy & Development; Environmental Monitoring, Mapping, & Scientific Research; Fishing & Harvesting Management; Landuse Management; Marine Debris; Microorganisms; Non-point Source Controls; Permitting & Zoning; Physical & Chemical Environment; Physical Variables; Point & Mobile Source Controls; Political Pressure; Public Administration; Reef Habitat; Reef Inhabitants; Reef Life; Remediation; Resource Use Management; Sectors Filling Human Needs; Security; Socio-Economic Drivers; Transportation Policies; Waste Management Policies; Wetlands
National Park Service Organic Act of 1916, 16 United States Code § 1. The Act was created to start the National Park Service within the Department of Interior for the purpose of promoting and regulating the use of federal areas such as national parks and monuments.

Application to Coral Reefs:

Legislative Actions:Created the National Park Service to be supervised by a Director.

Comments: 		National Park Service

Jurisdiction:
United States 		Boating Regulations; Collaboration & Partnering; Construction Codes & Projects; Designated Uses; Environmental Education & Outreach; Environmental Monitoring, Mapping, & Scientific Research; Fishing & Harvesting Management; Invasive Species; Landuse Management; Marine Protected Areas; Microorganisms; Permitting & Zoning; Political Pressure; Public Administration; Remediation; Resource Use Management; Tourism & Recreation Policies; Transportation Policies

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