U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2009–3113

December 2009

Applying New Methods to Diagnose Coral Diseases

Printed on recycled paper

Coral disease, one of the major causes 

of reef degradation and coral death, 

has been increasing worldwide 

since the 1970s, particularly in the 

Caribbean. Despite increased scientific 

study, simple questions about the 

extent of disease outbreaks and the 

causative agents remain unanswered. 

A component of the U.S. Geological 

Survey Coral Reef Ecosystem STudies 

(USGS CREST) project is focused on 

developing and using new methods to 

approach the complex problem of coral 

disease. 

Mitigation of impacts from coral 

diseases and syndromes requires better 

diagnostic techniques to detect the onset 

of disease. Ideally, these techniques 

would be rapid and non-destructive. 

USGS scientists are working on such 

a diagnostic method that is based 

on fluorescence. Reef-building 

corals have symbiotic dinoflagellates 

(zooxanthellae) that contain chlorophyll 

and associated photosynthetic pigments. 

Chlorophyll, associated photosynthetic 

pigments, and some proteins within 

coral have fluorescent properties. 

Images of coral fluorescence can 

be captured in three colors with a 

multispectral camera: green, orange, 

and red (fig. 1). Analyzing the 

natural variability in fluorescence 

intensity for a given species, as well 

as the differences between diseased 

and healthy specimens, enables the 

development of an index relating 

fluorescence to disease. This diagnostic 

tool would provide researchers and 

resource managers with a rapid, noninvasive means to assess coral health. If 

successful, a towable camera system can 

be developed, allowing entire segments 

of the reef to be surveyed rapidly.

Prior research has indicated that coral 

diseases may be due to secondary 

opportunistic infections, rather than 

primary pathogens, making it imperative 

to understand the microbial shifts that 

occur from healthy to diseased corals. 

(Lesser and others, 2007; Sunagawa and 

others, 2009). USGS researchers, in 

collaboration with Lawrence Berkeley 

National Laboratory (Berkeley, 

California), will employ customdesigned microarrays to characterize 

microbial patterns on corals. These 

microarrays are small chips that 

are printed with DNA sequences 

representing 30,000 microbial groups, 

ranging from family to species. If 

bacterial DNA from a coral matches any 

of the microarray DNA spots, a signal is 

Figure 1. (A) Under natural lighting, both the knobby brain coral (Diploria clivosa) and the star coral (Montastraea faveolata) are tan or brown. When 

stimulated to fluoresce with blue light (B), ridges of the brain coral appear red and its valleys are green. The polyps of the star coral fluoresce green, 

punctuating a background of red. In both cases, chlorophyll and a green fluorescent protein are responsible for the red and green fluorescent emissions, respectively. Note the border zone between the two corals is dominated by a filamentous alga that fluoresces red due to its chlorophyll content. 

Ruler squares are 1 centimeter. The red box in (A) indicates the area shown in (B). Photo credit: David Zawada, USGS.

A B
Figure 2. Boulder star coral (Montastraea annularis) affected by white 

plague. The white parts of the colony (indicated by black arrows) are dead. 

The disease has rapidly killed the coral, leaving bare white skeleton behind. 

The apparently healthy parts of the colony are indicated by red arrows. 

Photo credit: Christina Kellogg, USGS.

Contact Information:

Christina A. Kellogg, Ph.D.

Environmental Microbiologist

U.S. Geological Survey

St. Petersburg Science Center

600 4th Street South

St. Petersburg, FL 33701

PH: (727) 803–8747 x3128

FAX: (727) 803–2031

Email: ckellogg@usgs.gov

David G. Zawada, Ph.D.

Research Oceanographer 

U.S. Geological Survey

St. Petersburg Science Center

600 4th Street South

St. Petersburg, FL 33701

PH: (727) 803–8747 x3132

FAX: (727) 803–2031

Email: dzawada@usgs.gov

Figure 3. A closeup view of dark spot lesions (purple areas) on a colony of Siderastrea siderea, 

the massive starlet coral. Photo credit: Julie Olson, University of Alabama. 

generated that can be used to determine the relative 

abundance of those microbes in the sample. Samples 

have been collected for this experiment from healthy 

and white plague-affected Montastraea annularis

(boulder star coral; fig. 2) as well as from healthy 

and dark spot-affected Siderastrea siderea (massive 

starlet coral; fig. 3). This experiment will allow an 

unprecedented comparison of microbial communities 

between healthy and diseased corals, between species 

of coral, and between geographic locations. The 

microarray data generated by this experiment will 

provide a new baseline of information and may 

reveal previously unknown patterns underlying the 

diseased state. 

Initial field tests and sample collection for these 

methods took place in the Virgin Islands National 

Park and the Dry Tortugas National Park in July and 

August 2009. Work will continue in the Florida Keys 

during the 2010 summer field season.

http://coastal.er.usgs.gov/crest/

References:

Lesser, M.P., Bythell, J.C., Gates, R.D., Johnstone, R.W., and Hoegh-Guldberg, O., 2007, Are infectious diseases really killing corals? Alternative 

interpretations of the experimental and ecological data: Journal of Experimental Marine Biology and Ecology, v. 346, 

p. 36-44.

Sunagawa, S., DeSantis, T.Z., Piceno, Y.M., Brodie, E.L., DeSalvo, M.K., Voolstra, C.R., Weil, E., Andersen, G.L., and Medina, M., 2009, Bacterial 

diversity and white plague disease-associated community changes in the Caribbean coral Montastraea faveolata: The ISME Journal, v. 3, p. 512-521.