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Scientists of the U.S. Geological Survey have developed methods for measuring metabolic rates (productivity) of benthic communities such as coral reefs, seagrass beds, and other hard and sand bottom communities. Research efforts have focused on examining the potential for using benthic community metabolism as an indication of ecosystem health. By examining ecosystem health in terms of system processes or function, comparisons can be made between ecosystems in different geographic locations that might be characterized by different species of organisms. Monitoring efforts have begun in Biscayne National Park, Hawaii, Florida Bay, and Tampa Bay. Productivity (photosynthesis, respiration, and calcification) was measured on a seagrass bed, patch reefs, and bare sand in Biscayne National Park for 24-hour periods of time (day, night cycles) using a Submersible Habitat for Analyzing Reef Quality (SHARQ, Figure 1). Figure 1. The Submersible Habitat for Analyzing Reef Quality (SHARQ) is a large-scale underwater incubation chamber designed to isolate a mass of water over the ocean bottom. This enables scientists to measure changes in water chemistry that result from benthic community metabolism and to calculate metabolic rates associated with different types of benthic habitats.

Productivity measurements of benthic communities in Biscayne National Park as an indication of ecosystem health