Most U.S. coral reefs have never been adequately mapped. The agencies of the USCRTF are undertaking a major effort to develop comprehensive and consistent coral reef ecosystem maps for all U.S. reefs (Fig. 103). This is led by NOAA, the National Aeronautics and Space Administration, and the USGS (MISWG 1999).

The USCRTF National Action Plan committed to delineating and digitally mapping all U.S. shallow coral reefs by 2009 using airborne and satellite photography. Mapping and habitat characterization of selected deep reef and bank areas has also begun using multi-beam sonar, submersibles, and remotely-operated vehicles. This information will support more effective fish and coastal zone management, disaster mitigation, research, and restoration efforts.

Detailed and spatially accurate digital benthic habitat maps can be used to design monitoring programs, organize data, and conduct assessments. Digital data and the associated maps delineate major habitat types – seagrass, coral reefs, and mangroves – and can provide a framework for tracking changes in those habitats (Monaco et al. 2001). Other measurements of the ecosystem that correlate with habitat change ¹¹⁶ can be layered onto these maps and perhaps ultimately used to help predict habitat change. Completed maps and related information (discussed in the following subsections) are available on a NOAA web site (Coral Reef Mapping and Monitoring 2002).

Caribbean Shallow-Water Mapping Initiatives – The characterization of marine habitats of Puerto Rico and USVI has been completed, and benthic habitat maps are now available (Coral Reef Mapping and Monitoring 2002). This was a collaborative project¹¹⁷ using visual interpretation of aerial photographs (Fig. 104). NOAA’s National Geodetic Survey acquired aerial photographs for the near-shore waters in 1999.

Working in conjunction with the State of Florida, similar maps are available as a benthic habitat atlas of the Florida Keys (FKNMS Benthic Map 2002). Since this is just for the Keys, about 50% of Florida’s coral reef ecosystem still needs to be mapped.

Pacific Shallow-Water Mapping Initiatives – NOAA is leading an investigation to map the distribution of coral reefs and other benthic habitats throughout the U.S. Pacific islands. Remotesensing technologies, ranging from ships to satellites will be used to create digital maps of marine habitats including coral reefs, seagrass beds, and mangrove forests.

Gulf of Mexico Deep-Water Mapping Initiatives – In 2001, USGS, MMS, and NOAA completed multi-beam sonar mapping of major areas off the Northeastern Gulf of Mexico including the newly-designated Madison-Swanson and Steamboat Lumps Marine Protected Areas. These are important habitats for commercial reef fishes and contain some deep reefs that may rival those in the FGBNMS.

In 2001, NOAA also conducted habitat characterization of deep Oculina coral reefs off the eastern coast of Florida using submersibles and multibeam sonar. Results showed significant habitat damage to protected banks from illegal trawling.

Assess and Monitor Reef Health
The USCRTF’s National Action Plan (2000) called for an integrated nationwide coral reef monitoring system that could provide regular assessments of reef health as well as initiate new monitoring to fill gaps. This will provide the essential information managers need to respond to changing environmental conditions, to assess the effectiveness of management strategies, and identify the need for additional protective measures. Since then, NOAA initiated and is leading a coordinated effort to determine the condition of coral reefs, the causes of coral reef decline, and the impacts of environmental pressures on coral reef ecosystems.

A National Program to Assess and Monitor Coral Reef Ecosystems – In FY99, 50 coral reef managers and scientists prepared an Implementation Plan for A National Program to Assess and Monitor Coral Reef Ecosystems (National Coral Reef Program, Coral Reef Mapping and Monitoring 2002 , fig. 105). In FY00, NOAA held a workshop for 60 coral reef managers to rank environmental threats and prioritize management needs (e.g., biotic inventories, ecosystem monitoring, and assessments of the sources and extent of reef degradation). The managers endorsed the proposed program (the National Coral Reef Program).

Now in its third year of NOAA funding, the National Coral Reef Program has provided cooperative grants to state and island agencies to build local capacity for assessing and monitoring coral reef ecosystems. With this funding, coordinated monitoring is being conducted off Puerto Rico, the USVI, Hawai‘i, American Samoa, Guam, and the CNMI. Another major objective of this program, coral reef ecosystem health indicators, metrics, and a ‘report card’ will be developed to evaluate changes in the condition of benthic habitat, living marine resources, and water quality. NOAA’s National Ocean Service will integrate local assessments into these biennial reports. They will evaluate the effectiveness of activities to conserve reef resources.

Also a part of the NOAA National Mapping and Monitoring Network, complementary monitoring is being conducted off Puerto Rico, Florida, and Hawai‘i. NOAA sponsored additional work through cooperative grants from pass-through appropriations in FY00-02 to the Department of Natural and Environmental Resources of Puerto Rico, the National Coral Reef Initiative (NOVA University Florida), and the Hawai‘i Coral Reef Initiative (the University of Hawai‘i). With the USEPA and NOAA, the FKNMS Water Quality Protection Program monitoring continues in the Florida Keys. Specific monitoring of ecosystem process and functional changes that result from the implementation of fully protected marine reserves is also underway.

Regional Assessment and Monitoring Activities
Most of the U.S. coral reef ecosystem monitoring is conducted by State, Commonwealth, and Territory agencies, at times in conjunction with Federal agencies or with local non-governmental organizations. The following is a summary of FY00-01 activities in each jurisdiction.

Florida – In the Florida Keys, fish and benthic habitat assessments and monitoring were conducted and an integrated molecular biomarker system was used to assess ecosystem health. Four cruises performed baseline surveys of the Tortugas Ecological Reserve to determine the influence of Reserve status on fish communities, the food web, and habitat structure and function (FKNMS 2002.

Puerto Rico – Puerto Rico established a Commonwealth- wide network of monitoring sites where sessile-benthic organisms, reef fish, motile invertebrates, and water quality were surveyed (Fig. 106). They also conducted a baseline characterization of bio-optical properties, surveyed three coral reef locations to gain baseline information, and assessed the effects of establishing a no-take zone at the Luis Peña Natural Reserve on Culebra Island. Additionally, a baseline characterization of the fish and motile and sessile benthic invertebrates inhabiting coral reef and sea grass habitats was conducted at 15 sites on Vieques Island.

U.S. Virgin Islands – The USVI Department for Planning and Natural Resources has partnered with the University of the Virgin Islands, the National Park Service (NPS), and the USGS to start filling gaps in monitoring and establishing a Territorywide Monitoring Network
(USGS 2002, Coral Reef Mapping and Monitoring 2002).

Hawai‘i – In the NWHI, monitoring and assessment techniques were developed as part of an overall effort to inventory the shallow-water reef biota and map benthic habitats around each of the 10 remote islands and atolls
(Hawaii DLNR 2002). Initial survey data assessed the impact of bottom fishing on the Raita and West St. Rogatien Banks in the NWHI Coral Reef Ecosystem Reserve. State-wide monitoring of coral reef habitats, algae, invertebrates, fish, marine mammals, and sea turtles of the Main Hawaiian Islands continued (CRAMP 2002).

American Samoa – American Samoa hired two fisheries biologists in the Department of Marine and Wildlife Resources. They are conducting fish census surveys of commercial fish stocks and a creel survey of market species. Water quality monitoring is currently limited to 12 beaches on Tutuila and the Manu’a group, but is being enhanced with new instrumentation.

Guam – A monitoring program for the recently created MPAs has been initiated (University of Guam MPA Research Group 2002). These activities complement ongoing inshore and off-shore island-wide creel surveys, weekly water quality tests, freshwater hydrology and contaminant testing and the University of Guam’s benthic transect surveys. They monitor for disease and coral bleaching (Guam DAWR 2002).

Commonwealth of the Northern Mariana Islands – CNMI hired a marine biologist to coordinate its coral reef monitoring program (CNMI DEQ 2002). Biweekly monitoring surveys are conducted on Saipan, Tinian, Rota, and Aguijan. The USFWS conducted its annual coral reef monitoring of Farallon de Medinilla reefs and provided monitoring assistance to the U.S. Navy by monitoring for impacts of military training activities.

Pacific Remote National Wildlife Refuges – The USFWS continued surveying and monitoring coral reef ecosystems in its Pacific Remote Islands National Wildlife Refuges of Howland, Baker, Jarvis, Palmyra Atoll, and Kingman Reef (Fig. 107). The USFWS participates in the Northwestern Hawaiian Islands Reef Assessment and Monitoring Program with followup surveys and continues to conduct surveys at Midway Atoll National Wildlife Refuge.

As of early 2002, the USFWS established 38 permanent coral reef monitoring transects, most with the cooperation of NMFS, at Baker, Howland, Jarvis, Johnston, Kingman, Palmyra, Rose, and Swains in the remote U.S. Pacific Islands and Midway, Pearl and Hermes, Maro, and French Frigate Shoals in the NWHI.

Pacific Freely Associated States – The USFWS has completed reports on its biennial inventory of significant marine species at U.S. Army Kwajalein Atoll in the Republic of the Marshall Islands.

National Survey of Monitoring Capacity
To determine gaps in ongoing coral reef monitoring programs, NOAA launched its Survey of U.S. Coral Reef Monitoring Projects in FY99. This comprehensive survey inventoried a total of 439 ongoing programs and projects assessing and monitoring coral reef ecosystems. The information gathered by this survey is now available in a GIS and metadata database (Coral Reef Mapping and Monitoring 2002, Fig. 108).

Survey results indicate that significant geographical disparities exist in the quantity and quality of monitoring projects conducted around the United States and its associated territories (Ascher and Turgeon in press, Fig. 109). A series of environmental problems occurred in the early 1990s involving the Florida Bay aquatic ecosystem and plans for ‘re-plumbing’ the Everglades. Therefore historically, most of the U.S. coral reef monitoring support had focused on the Florida Keys. Since 2000, U.S. agency efforts have focused on building island capacity for long-term monitoring and other coral reef conservation activities.

The National Coral Reef Monitoring Network
NOAA has made considerable progress in the development of a web-based data management and information system for the nation-wide integration of monitoring and mapping data. A large team of coral reef scientists and information technology specialists was brought together and is developing a NOAA single-point-of-discovery information management system for coral reef data and information (CORIS). CORIS provides direct access to coral reef data and information, including relevant NOAA Library holdings (CORIS 2002).

Coral Reef Watch Program
To predict bleaching events, NOAA’s Coral Reef Watch Program combines real-time environmental monitoring data from satellites and the in-water Coral Reef Early Warning System (CREWS) sensors (Fig. 110). Near real-time bleaching alert systems are now available on the web (NESDIS 2002). New CREWS systems continue to be installed worldwide with 20 domestic systems expected to be in place by 2007.

Volunteer Monitoring Programs
A variety of volunteer monitoring programs collect information on coral reef ecosystems. These provide data and related information to the National Coral Reef Monitoring Network and enhance the monitoring being conducted by agency and non-governmental scientists. These programs differ widely in scope, methods, and parameters measured, and may have issues regarding the quality of data. However, all provide the opportunity to educate the public, engage them in coral reef monitoring, and get basic information with minimal expense.

Global Coral Reef Monitoring Network (GCRMN) – This global network consists of 15 independent networks (nodes) in six regions around the world (GCRMN 2002). It focuses on regional databases used in national reports on reef status. The National Coral Assessment and Monitoring Program supports regional GCRMN activities and contributes regional reports to GCRMN for its biennial report on the Status of Coral Reefs of the World.

Reef Check – Initiated in 1997, Reef Check is a protocol for rapid assessment of reefs specifically designed for non-professionals and volunteers (ReefCheck 2002). It evaluates the effects of human impacts on coral reefs. Annually it engages a large cadre of volunteer SCUBA and free divers in over 50 countries to survey selected harvested species, classify benthic substrates using the pointintercept method, and report coral reef damage from bleaching and other stresses. The GCRMN designated Reef Check as its community-based monitoring protocol (Westmacott et al. 2000).

Reef Environmental Education Foundation (REEF) – Since 1990, this nonprofit organization has educated the public about marine resources and engaged divers and snorkelers in long-term monitoring (REEF 2002). REEF surveys fish distributions in the tropical western Atlantic, along the U.S. and Canadian West Coast, in the tropical eastern Pacific¹¹⁸, and off Hawai‘i (Fig. 111). With NOAA, REEF evaluates the effectiveness of management zones in protecting fish resources in the FKNMS (Jeffries et al. 2000).

Atlantic and Gulf Rapid Reef Assessment (AGRRA) Program – Since June 1998, over 22 large-scale rapid ecological assessments on the condition of reef-building corals, algae, and fishes have been completed
(AGRRA 2002). In 2001, a joint AGRRA and REEF project surveyed the FGBNMS; the data collected were used as part of the evidence that these reefs are in excellent condition.

Caribbean Coastal Marine Productivity (CARICOMP) Program – This program was initiated in 1985 to better understand regional phenomena¹¹⁹ that potentially control Caribbean coastal ecosystems (CARICOMP 2002). It is a regional network of greater Caribbean marine laboratories, parks, and reserves, with over 25 sites in 18 countries. It is dedicated to discriminating between human disturbance and natural variation within the reefs and reef-related habitats.

In 1991, CARICOMP instituted a synoptic, standardized monitoring program of coastal ecosystems that has centralized data management and communications. Members hold regular regional training workshops and facilitate directed research programs that involve members of the network and out-side investigators.

Reef Ecosystem Condition (RECON) – Initiated in 2000 by the Ocean Conservancy and the USEPA, RECON trains recreational divers to collect information on key environmental parameters, assess the condition of stony corals and seafans, and record the presence of certain key organisms and obvious human-induced impacts (RECON 2002). The program is currently being tested in the Florida Keys, Puerto Rico, USVI, and the Bahamas.

Recent observations of increased algal abundance highlight the need to improve water quality monitoring and assess currents and water circulation. The monitoring should include studies on algal populations, coral diseases, and extend to deeper coral reef communities. The great distance of the Sanctuary offshore makes surveillance and enforcement more difficult. Currently, the Sanctuary does not own a boat and relies on charter vessels to get to the area. Recent observations are that the Banks may be important spawning areas for several grouper species and this highlights the need to create a marine reserve to protect the biodiversity.

The level of research and monitoring in the Florida Keys increased markedly after the declaration of the FKNMS. Seven years of data on water quality, seagrasses, and coral reef and hard bottom communities provided Sanctuary managers with trend information on the health of the coral reef ecosystem. In addition, there are 5 years of data on ecological changes associated with the implementation of the first network of marine reserves in the U.S. Those on the southeast coast of Florida and the Middle Grounds are not as well studied, but are being mapped and given some monitoring. Most of the information on these areas, however, continues to be anecdotal with some reefs appearing healthy although there was some bleaching similar to levels seen in the Florida Keys during the massive 1997-1998 event. There is little information on the status of benthic communities at the Florida Middle Grounds.

There is no comprehensive and systematic monitoring program for the reefs of Florida’s East Coast, but one is needed to provide a baseline. Site selection should ensure that representative habitats and unique sites are mapped and monitored. This will require that a selection committee of academic, county, state, conservation and fishing groups, and decisions rapidly disseminated for public discussion. The reef fish communities from seagrass and mangrove habitats of Port Everglades and the Intra-coastal Waterway also remain a mystery. Reefs along the southeast coast and Middle Grounds banks should also
be mapped.

Current monitoring in the Sanctuary has focused largely on detecting changes in
designated no-take zones and establishing the status and trends in corals, seagrasses, and water quality. Such monitoring must continue in the short-term until solid baseline data are obtained. This baseline will assist in detecting possible long-term changes in communities that may result from management practices (e.g. zoning) or from massive restoration efforts soon to be implemented in the south Florida Everglades.

Restoration at grounding sites has taken a variety of forms in order to enhance recovery (Jaap, 2000). While it is impossible to instantly replace an injured coral reef resource, steps can be taken to promote recovery. The typical scenario is to salvage all detached coral and cache them for subsequent reattachment. It is desirable to remove loose injury-generated rubble to expose the reef foundation (limestone rock) and to eliminate a source of material that could be mobilized and create additional injury in future storm events. If the reef framework is fractured to a significant extent, concrete, native limestone boulders and fiberglass rods may be needed and have been used to stabilize the fractured foundation. After the reef has been cleared of rubble and the foundation made stable, corals are reattached based on microhabitat requirements (e.g., orientation to light and waves). In cases where the reef was rendered flat by severe hull injuries, the topographic relief can be enhanced using native limestone, concrete and prefabricated rock structures. These are often secured with concrete and reinforcement rods.

While there are few detailed studies comparing recovery of restored sites with unrestored injury areas, it is clear that there have been some successes. Coral reattachment has been a useful method. A number of monitoring studies off Broward County have demonstrated very high Scleractinian coral reattachment success (80-95%) (Continental Shelf Associates, 2000; Gilliam et al., 2001, Gilliam et al., 2003; Thornton et al., 2002). After approximately three years, recruitment of coral (octocoral and scleractinian corals) is very common. For example, there are restored areas off Miami-Dade County where measurements of percent cover, density, and diversity of sessile benthic organisms exceed those at a nearby reference site (Miami-Dade County, 2003).

The FKNMS enabling legislation requires a comprehensive water quality status and trends monitoring program with three major components: water chemistry, seagrass, and coral reefs (U.S. DOC, 1996). The protocols and sampling strategies were developed in collaboration with EPA in 1994-95. Water chemistry and seagrass monitoring are conducted by Florida International University; coral reef monitoring is conducted by the FFWCC’s Fish and Wildlife Research Institute. The two institutions began collecting data in 1995-96.

A spatial framework for water quality management was proposed on the basis of geographical variation of regional circulation patterns (Klein and Orlando, 1994). Quarterly sampling of more than 200 stations in the Sanctuary and on the Shelf, as well as and monthly sampling of 100 stations in Florida Bay, Biscayne Bay, and the mangrove estuaries of the southwestern Florida coast, provide a unique opportunity to explore the spatial variability in water quality measures in South Florida’s coastal waters (Figure 7.10). Details on water chemistry sampling strategy, field sampling methods, laboratory analyses, and data processing are available on-line at http://sefrc.fiu.edu/wqmnetwork/ (accessed 1/31/05).

FISH

Fishery-Dependent Monitoring

Various programs that collect data directly from Florida fisheries are summarized in Table 7.16.

Florida Fish and Wildlife Conservation Commission

The FFWCC has collected commercial food fish landings since 1986 and commercial marine life fishery statistics since 1990. NOAA Fisheries (U.S. DOC, 2003) collects landings data for commercial and recreational food fisheries, and for recreational charter boats, headboats, private boats and shore fishing. Commercial and recreational spiny lobster fishing effort is reflected by the number of licenses issued (Figures 7.22 and Figures 7.23).

Methods
The NOAA Southeast Fisheries Science Center’s reef fish visual census (RVC) method has used non-destructive visual survey methods to assess reef fish communities and habitat associations in the Florida Keys since 1979. The goals of the method are to monitor trends and habitat associations of the entire reef fish fauna, and to monitor changes in various MPAs and specifically in FKNMS marine reserves following their establishment in 1997 and 2001. A stationary, centrally located diver in a random 7.5 m-radius plot assesses reef fish composition, abundance (density), and size structure. All species observed for five minutes are listed, counted, and their sizes estimated. Habitat features and depth are also recorded. Details on reef fish monitoring field methods and data processing and analyses are published in Bohnsack and Bannerot (1986) and Bohnsack et al. (1999).

Methods
In 1997, the FKNMS established multiple no-take marine reserves, or "sanctuary preservation areas." Annual underwater visual surveys have been conducted to assess changes in reef fish populations in areas open and closed to fishing compared to baselines established between 1994 and 1997.

The Reef Environmental Education Foundation (REEF) is a nonprofit organization that trains amateur divers to conduct standardized volunteer surveys of reef fishes in an effort to monitor species distributions and changes in reef fish occurrence.

Methods
Volunteers used a roving diver technique (Schmitt and Sullivan, 1996) to develop a comprehensive species list from a dive site and multiple surveys to calculate percent frequency-of-occurrence from a dive site. For each dive, observed species are scored in abundance categories based on what a diver observed. Between 1994 and 2004, over 55,595 individual surveys have been conducted in the Tropical Western Atlantic Ocean. A total of 11,105 surveys were collected in the Florida Keys through 2002. Details of methods are available at http://www. reef.org/ (Accessed 01/23/05).

REEF fish monitoring involves expert REEF divers (members of the Advanced Assessment Team) that visit certain sites to do repeated fish surveys. Figure 7.29 shows trends in sighting frequency for Nassau grouper at no-take reserves and comparable fished sites in the FKNMS. Figure 7.30 shows trends for four angelfish species.