Science-Based Strategies for Sustaining Coral Ecosystems 

Coral ecosystems and their natural capital are at risk. 

Greenhouse gas emissions, overfishing, and harmful land-use 

practices are damaging our coral reefs. Overwhelming scientific 

evidence indicates that the threats are serious, and if they are 

left unchecked, the ecological and social consequences will 

be significant and widespread. Although the primary stressors 

to coral ecosystems are known, science-based strategies 

are needed to more accurately explain natural processes 

and forecast human-induced change. Collaborations among 

managers and scientists and enhanced mapping, monitoring, 

research, and modeling can lead to effective mitigation plans. 

U.S. Geological Survey scientists and their partners assess 

coral ecosystem history, ecology, vulnerability, and resiliency 

and provide study results to decisionmakers who may devise 

policies to sustain coral resources and the essential goods and 

services they provide. 

Introduction

Nearly 25 percent of all marine life is linked directly to 

coral ecosystems, often in complex biogeochemical pathways 

and food webs (fig. 1). Moreover, millions of people rely on 

coral ecosystems for the food, shoreline protection, income, 

recreation, and cultural values that these diverse, productive 

marine communities can supply. The provision of such natural goods and services is often taken for granted, but if trends 

observed over the past 30 years persist, the natural capital 

inherent in our coral ecosystems–worth hundreds of billions of 

dollars–will be lost over the coming decades. An estimated 20 

percent of the world’s coral reefs are already damaged, perhaps 

beyond restoration, and recent assessments of reef health show 

continued downward spirals (Carpenter and others, 2008).

Coral ecosystems include shallow, sunlit coral reefs in 

tropical regions (which are the focus of this Fact Sheet) and 

deepwater or cold reefs. Shallow coral ecosystems, which 

include coral reefs and associated mangrove and seagrass 

habitats, are vulnerable to a variety of stressors. At the local 

to regional level, corals and their associated plant and animal 

communities show the effects of disease and degradation from 

overfishing, coastal developments, and changing land-use 

practices within watersheds that introduce sediment runoff and 

other pollutant discharges. On a global level, atmospheric emissions of greenhouse gases are causing ocean temperatures to 

increase, pH levels to decrease (resulting in ocean acidification), 

and sea levels to rise, according to the U.S. Global Change 

Research Program (Karl and others, 2009). Most corals are 

intolerant of increased temperature and lower pH. Depending on 

the rate of sea-level rise, the growth of coral reefs may not keep 

pace with rising sea levels. Business-as-usual scenarios that 

project increasing carbon dioxide concentrations in the atmosphere and oceans from burning fossil fuels and deforestation 

Figure 1. A healthy reef requires moderate water temperatures, 

clear and clean water, and a complex suite of interacting microbes, 

plants, and animals, including herbivorous and predatory species. 

Healthy coral reef ecosystems provide essential goods and 

services. Photograph by Gary Brewer, USGS.

portend unprecedented changes in the distribution, abundance, 

and survival of coral communities and life in the global oceans 

(Intergovernmental Panel on Climate Change, 2007).

Working with Partners to Identify Research Priorities

U.S. Geological Survey (USGS) scientists work with other 

Department of the Interior bureaus, other Federal agencies, the 

U.S. Coral Reef Task Force, academic institutions, and nongovernmental organizations to guide research directions and 

prioritize studies. The USGS coral ecosystem research priorities 

are described in a Strategic Coral Plan (USGS, 2007). USGS 

scientists organize workshops with partners to set research 

priorities, and they help plan and conduct field and laboratory 

analyses (fig. 2). The results of such carefully designed research 

are shared with partners and resource managers so they can 

manage and plan for environmental change. 

The USGS applies these data through models and forecasting tools that enable managers to test hypotheses and create 

simulations for areas beyond studied coral reefs. Modeling 

enables researchers to extrapolate results and draw reasonable 

inferences about the causes and consequences of environmental 

change. When these models are combined with hydrodynamic, 

climatic, and socioeconomic models, robust forecasts can 

be made of how various management scenarios might affect 

biological and human communities. Models, in combination 

with ongoing research and monitoring, provide scientists 

U.S. Department of the Interior

U.S. Geological Survey Printed on recycled paper

Fact Sheet 2009–3089

September 2009
and managers with the means to “experiment” with different 

management options, make refinements, and respond adaptively 

as environmental conditions change. Such research requires 

diverse mapping, monitoring, and field and laboratory research 

to adequately explore the structure, function, and natural history 

of coral ecosystems, the ability of such ecosystems to tolerate 

stressors and climatic change, and the complex ecological 

relations of indicator species living on the reefs.

Linking Science with Management Needs: 

A Multiscale Approach

Concerns exist that local coral reef conservation efforts 

(reducing overfishing, pollutants, contaminants, and habitat 

losses) may be overwhelmed by global factors beyond local 

control (ocean temperature increases, sea-level rise, and ocean 

acidification). These concerns underscore the need for scientists 

to provide data at various scales for managers to use in designing holistic solutions. While mitigation of global factors 

requires larger scale societal changes at longer time scales, local 

management changes can be designed to promote resiliency 

by managing for a healthy ecosystem, potentially allowing 

some species to adapt to climate change. Science can help local 

communities and resource managers address and reduce overfishing, harmful land-use practices, and watershed impacts that 

reduce biodiversity, damage coral habitat, and disrupt fundamental biogeochemical pathways such as those that affect the 

food web. If the resiliency threshold has not been crossed, some 

restoration may be possible, although recovery may take much 

longer than degradation took.

The USGS aims to provide scientific understanding 

of the natural processes and human activities that influence 

the development and sustainability of U.S. coral reefs. The 

USGS promotes partnerships and collaborations among 

marine scientists, social scientists, environmental economists, 

and resource managers, thereby informing and enabling 

decisionmakers with knowledge, forecasts, and decision-support 

tools. 

Figure 2. USGS scientists monitor changes in reef communities.

Photograph by Caroline Rogers, USGS.

USGS Researchers Address Broad Topics

As societies at local, regional, and global levels address 

questions about climate change and resource sustainability, 

coral-reef ecosystems are particularly well suited for study 

as indicators for understanding links between human activities and resource management. Coral reef structures record 

historical environmental conditions and provide clues about 

how human activities influence the ocean’s physical and 

chemical properties, including relative sea level and trends in 

ocean temperature, pH, currents, nutrients, and anthropogenic 

contaminants. These properties, together with the variable use, 

extraction, and protection of reef resources, will largely determine the future of coral ecosystems. USGS researchers seek 

to understand such complex interactions and the interrelated 

global- to local-scale management issues and information needs 

described below.

Carbon sequestration.—The global problem of increasing 

greenhouse gas emissions has inspired USGS scientists to assess 

the feasibility of capturing and sequestering carbon dioxide. 

These efforts include evaluating (1) biological techniques to 

remove carbon from the atmosphere by increasing photosynthesis with the growth of more plants and trees and (2) physical 

techniques that capture carbon dioxide (such as that from coaland gas-fired powerplants) and inject it permanently into natural 

subterranean reservoirs. Marine systems, and particularly coral 

reefs, will be increasingly susceptible to unchecked greenhouse 

gas emissions that raise ocean temperatures and sea level while 

lowering ocean pH levels. Corals represent an early-warning 

system for gaging incipient and long-term climate change 

impacts.

Ocean temperature.—USGS scientists are exploring the 

relations among high water temperatures, coral bleaching, 

and coral disease. USGS and National Park Service biologists 

documented a severe coral bleaching event in the fall of 2005, 

coincident with the warmest ocean waters ever recorded in 

the Caribbean. Coral bleaching results in the breakdown of a 

symbiotic dependency between corals and colorful microscopicsized algae. The algae live within the coral tissue, providing 

corals with nutrition they derive from photosynthesis. The 

bleaching occurs when the corals expel the algae, leaving white 

coral tissues visible (fig. 3). Over 60 percent of the living coral 

cover was lost within the Virgin Islands National Park to an 

outbreak of diseases that followed the 2005 bleaching event 

(Miller and others, in press). Scientists continue to monitor 

the long-term response of bleached and diseased elkhorn coral 

(listed as threatened under the Endangered Species Act) and 

other species in the U.S. Virgin Islands. Ongoing research in the 

Virgin Islands and American Samoa will help explain why some 

corals bleach and others do not; in general, bleaching is variable, even within the same species at the same location. USGS 

scientists are exploring the mechanisms (such as genetic adaptation, physiological acclimatization, microbial interactions) 

by which some corals and their algal symbionts tolerate high 

temperatures and high levels of sunlight. Such knowledge is 

fundamental to protecting the most tolerant coral colonies and 

sustaining coral reefs in the future. Natural resource agencies 
Figure 3. Elkhorn coral colonies in the U.S. Virgin Islands showing (A) normal coral and (B) bleached coral. Photographs by Gary Brewer, USGS.

A B

need reliable models that forecast shifts in the abundance and 

distribution of plants, animals, invasive species, and pathogens 

in response to changing water temperatures. 

Ocean acidification.—Coral polyps use calcium from seawater to create their hard skeletons in a process called calcification. Experimental and modeling studies indicate that increases 

in atmospheric carbon dioxide will significantly affect coral 

reef growth during this century because of increasing ocean 

acidification (lower pH) and the resulting decrease in calcification rates by reef organisms. By using incubation chambers and 

other analytical equipment in reef study areas, the USGS and 

partnering agencies are measuring baseline rates of calcification, metabolism, growth, and accretion/dissolution of selected 

corals and coral communities. The goal is to estimate future reef 

conditions under elevated levels of carbon dioxide, lower pH, 

and higher temperatures that were forecast by the Intergovernmental Panel on Climate Change (2007). 

Sea-level rise.—Warming oceans and melting land ice contribute to rising sea levels. Understanding rates of sea-level rise 

and rates of coral reef growth will allow scientists to estimate 

whether corals will keep pace with rising seas. With sea level 

rising, coral reefs that protect shorelines and human infrastructure from storm waves and erosion may no longer be effective. 

Communities that inhabit low-lying islands and coastlines may 

have few options other than relocation. As noted above, USGS 

scientists are studying how the growth of coral reefs responds 

to changing temperatures and pH. In addition, our scientists use 

high-resolution bathymetric and topographic maps and knowledge of subsidence and uplift to describe and forecast shoreline 

change and associated ecosystem and human vulnerabilities. 

Reef history.—As corals grow, they record environmental 

data in their skeletons. USGS scientists use long-lived corals 

and coral fossils to reconstruct past environmental conditions 

that put recent coral reef declines in historical context and 

enable the development of reliable forecasting tools. The physical characteristics (such as growth bands) and chemical composition of coral skeletons record changes in ocean temperatures, 

salinity, pH, productivity, sedimentation, and rates of sea-level 

change. Combined with climate models, these records are 

providing clues to understanding the future condition of marine 

systems broadly and coral reefs specifically. 

Atmospheric dust.—Billions of tons of soils are eroded 

from the Earth’s surface each year, transported sometimes thousands of miles by prevailing global wind systems, and eventually deposited at downwind locations. This natural process 

fertilizes both ocean and terrestrial ecosystems with growthenhancing nutrients, but the dust also carries living microorganisms, as well as pollutants and contaminants, some of which 

are synthetic and new. Hotter and dryer conditions related to 

climate change in Africa, Asia, and other source regions may 

be increasing rates of soil erosion and downwind deposition. 

USGS scientists and collaborators are studying how these 

complex mixtures of soil particles, microbes, and chemicals 

influence coral reef processes. Potential relations between coral 

disease and algal growth in response to various constituents in 

the dust (including microbial pathogens and micronutrients such 

as iron) are of particular interest.

Land-derived impacts.—Coral reefs are affected by 

the runoff of sediments and associated chemicals and pollutants from nearby landmasses (fig. 4). To understand linkages 

between land-use changes in watersheds and their effects on 

runoff and adjacent coral reefs, USGS researchers and colleagues used an integrated approach to study the reefs of 

Moloka`i, Hawaii, combining geology, oceanography, and biology. These efforts resulted in a landmark publication (Field and 

others, 2008), which includes insights about watershed management. The approach used in the Moloka`i study is now being 

applied to other sites in Hawaii and the Pacific that have similar 

management needs. 
Figure 4. Image of Moloka`i, Hawaii, showing runoff from the land; 

sediments, pollutants, and contaminants in the runoff degrade coral 

reefs. Image by Susan Cochran (USGS) from a data image supplied 

by the National Aeronautics and Space Administration (NASA). 

Pathogens and disease.—Although disease is known to 

be a major cause of coral mortality (fig. 5), the transition from 

healthy to distressed and diseased states in corals is poorly 

understood. Specialists have characterized many coral diseases, 

but few pathogens have been proven as causative agents. The 

USGS is comparing coral-associated microbial communities in 

healthy and diseased colonies and testing how various disease 

states may relate to physical, chemical, and biological stressors 

that potentially include high temperatures, pH, pollutants, contaminants, predators, and parasites. 

Overfishing and ecological integrity.—Unsustainable 

fishing activities are recognized as severe threats to the integrity 

of coral reefs; such activities include overfishing and practices 

that destroy reef structure, remove keystone species (predators 

and herbivores), and damage coral communities (and connected 

mangrove and seagrass habitats). The concept of ecological 

integrity has been variously defined but may be quantified in 

terms of basic reef structure, functions, and processes such as 

Figure 5. White plague disease affecting coral in the U.S. Virgin 

Islands. The disease has killed many reef-building corals in Florida 

and the Caribbean. Photograph by Caroline Rogers, USGS.

reef growth, calcification, photosynthesis, and respiration; plant 

and animal abundance and biodiversity; biomass production; 

rugosity; and measures of ecosystem services. Quantifying reef 

health in terms of such functionality is an important aspect of 

ongoing monitoring and research by the USGS and its collaborators. This topic also relates directly to ongoing studies of the 

role and function of marine reserves (designated no-fishing or 

limited-fishing zones) being conducted by the USGS in partnership with the National Park Service. These efforts, in turn, relate 

to understanding reef status and trends, ecological linkages 

and dependencies (such as for sea turtles and as fish nurseries), 

habitat connectivity, herbivore and predator/prey interactions, 

resiliency, and recovery from disturbance. Such comprehensive 

information is being acquired at targeted study sites in Hawaii, 

American Samoa, Palmyra Atoll, Florida, Puerto Rico, and the 

U.S. Virgin Islands. These primary study sites will allow scientists to compare reef function in areas having various kinds and 

levels of human disturbance and, ultimately, to identify environmental thresholds and tipping points when a reef’s ecosystem 

becomes so severely compromised that recovery is prevented. 

References Cited

Carpenter, K.E., and others, 2008, One-third of reef-building 

corals face elevated extinction risk from climate change 

and local impacts: Science, v. 321, no. 5888, p. 560–563, 

doi:10.1126/science.1159196.

Field, M.E., Cochran, S.A., Logan, J.B., and Storlazzi, 

C.D., eds., 2008, The coral reef of south Moloka`i, 

Hawai`i; Portrait of a sediment-threatened fringing reef: 

U.S. Geological Survey Scientific Investigations Report 

2007–5101, 180 p. (Also available at http://pubs.usgs.gov/

sir/2007/5101/.)

Intergovernmental Panel on Climate Change (IPCC), 2007, 

Climate change 2007; Synthesis report; Contribution of 

Working Groups I, II and III to the Fourth Assessment 

Report of the Intergovernmental Panel on Climate Change 

[core writing team, Pachauri, R.K., and Reisinger, A., eds.]: 

Geneva, Switzerland, IPCC, 104 p. (Also available at http://

www.ipcc.ch/.)

Karl, T.R., Melillo, J.M., and Peterson, T.C., eds., 2009, 

Global climate change impacts in the United States: New 

York, Cambridge University Press, 188 p. (Also available at 

http://downloads.globalchange.gov/usimpacts/pdfs/climateimpacts-report.pdf.)

Miller, J., Muller, E., Rogers, C., Waara, R., Atkinson, A., 

Whelan, K.R.T., Patterson, M., and Witcher, B., in press, 

Coral disease following massive bleaching in 2005 causes 

60% decline in coral cover on reefs in the US Virgin Islands: 

Coral Reefs, doi:10.1007/s00338-009-0531-7.

U.S. Geological Survey, 2007, Strategic science for coral 

ecosystems, 2007–2011: Reston, Va., U.S. Geological 

Survey, 22 p., available at http://marine.usgs.gov/coral-plan/

coralplan2007.pdf.

Banner on p. 1: Collage by Gary Brewer, USGS.

Contact Information

For further information about USGS coral ecosystem research 

programs, contact Dr. Gary D. Brewer at gbrewer@usgs.gov or 

visit http://marine.usgs.gov.