U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2005-3039

March 2005

Coral Microbial Ecology

INTRODUCTION

Coral microbial ecology is the study of the 

relationship of coral-associated microorganisms to each other, the coral host, and 

to their environment. Just as we humans 

have beneficial bacteria living on our skin 

and in our intestines, corals also have 

co-habitating non-pathogenic (not disease-causing) microbes. These microbes 

include bacteria, archaea, and fungi–

representing all three of the major 

domains of life (Fig.-1). Archaea are 

prokaryotes (cells with no nucleus) like 

bacteria but are genetically and biochemically more similar to eukaryotes (organisms with cells that contain a true nucleus).

Where are these microbes? Coral-associated microorganisms are found in the 

mucus, tissue, and skeleton of corals. 

Corals secrete a surface layer of mucus, 

which functions to keep the coral surface 

clean of sediment and to capture prey. 

Each species of coral has mucus that is 

biochemically unique. When shed, this 

mucus provides a major nutrient source 

for the reef environment (Wild, 2004). 

The tissue of the coral animal is where the 

symbiotic algae, known as zooxanthellae, 

live. Endolithic microorganisms (bacteria, 

fungi, or algae that bore into the coral’s 

calcium carbonate skeleton) are a potential 

source of nutrients to the overlying tissues.

What can we learn from studying coral 

microbial ecology? Why is it important? 

Coral reefs in the Caribbean have been in 

decline for several decades. One of the 

most visible causes is disease. Coral diseases are not well understood, but the few 

that have been characterized are all caused 

by microorganisms. In order to understand 

the diseased state, we must first understand 

the healthy state. Until now, coral biology 

studies have been limited to studies of 

the coral animal, the algal symbiont, or 

the interactions of the two. Coral microbial-ecology studies contribute a missing 

piece of information to the study of overall 

coral biology. It has been speculated that 

coral-associated bacteria benefit the coral 

by fixing nitrogen, breaking down waste 

products, and cycling basic nutrients back 

to the photosynthetic algal symbionts 

(zooxanthellae). Bacteria may also ward 

1. Global Climate Change – Microbial 

Communities as a Diagnostic Tool? 

[Christina Kellogg, Virginia Garrison, 

John Lisle]

Scientists and reef managers are concerned 

about coral reef systems being affected 

by global change and need to understand 

the processes that control their resilience. 

This large, integrated project involves 

collaboration between the USGS, the 

off other potentially harmful microbes by 

producing antibiotics or by just occupying 

the available space. Relative to disease 

studies, it would be helpful to know if the 

infectious agents come from the normal 

microbial flora under certain conditions. 

The field of coral microbial ecology is 

relatively new. What do we know so far? 

• A handful of coral pathogens (microbes 

that are proven to cause a specific disease) have been identified (reviewed by 

Rosenberg and Loya, 2004). 

• Coral-associated microbes are distinct 

from those in the water column (FriasLopez, 2002). 

• Different species of corals have different bacterial communities (Rohwer, 

2002). 

• The coral-associated bacterial community shifts when the coral is stressed 

(Pantos, 2003).

USGS CORAL MICROBIAL-ECOLOGY 

STUDIES

The U.S. Geological Survey (USGS) scientists involved in each study are listed in 

brackets after the project titles.

Figure 1. The molecular “Tree of Life” consists 

of three domains derived from 16S rDNA genetic 

data. 16S rDNA is the gene that codes for ribosomal 

RNA, a key part of cellular reproduction. Eukarya 

includes plants, animals, and fungi.

Bacteria

Archaea

Eukarya

You are

here

Figure 2. Pocillopora eydouxi is one of the coral species being monitored for microbial-community changes in 

Ofu Lagoon, American Samoa. Photo credit: Virginia Garrison, USGS.
University of Hawaii, the Florida Institute 

of Technology, the Wildlife Conservation 

Society, and the National Park Service. 

Studies are underway in the National 

Park of American Samoa to determine the 

internal and external factors that increase 

the ability of a wide variety of corals to 

resist environmental stress. The shallow 

lagoon there contains species of Acropora

and Pocillopora, corals ordinarily prone 

to bleaching (expelling their symbionts) 

at high temperatures (Fig. 2). External 

factors include changes in water temperature, ultraviolet (UV) radiation, dissolved 

oxygen, and water motion. Internal factors 

being investigated include genetic diversity of algal symbionts and the associated 

microbial communities. Because changes 

in the coral-associated bacterial communities echo changes in the health of the coral, 

bacteria are at minimum atuned to their 

host’s metabolism and may play an active 

role in maintaining the overall health of 

the coral. 

The microbial-ecology portion of this 

project seeks to answer the following 

questions: (1) Does the coral-associated 

bacterial community shift on a seasonal 

basis? We are using molecular methods 

to analyze and compare “fingerprints” of 

the total bacterial community quarterly for 

one year. 

(2) If the microbial community does 

change, do the changes correlate to 

physical changes like temperature, water 

flow, amount of UV, or other extrinsic 

factors? That is, are the changes in the 

microbial community indicators of certain 

types of stress? 

(3) Can changes in the microbial community be used as “early warnings” of 

bleaching or disease? A few studies have 

shown that coral-associated bacterial communities change when the coral bleaches 

or becomes infected. Maybe that shift is 

detectable before the macroscopic signs of 

distress are apparent in the coral. 

(4) If microbes can be used as a diagnostic tool, can the samples be non-invasive, 

meaning only the mucus layer is sampled, 

not the coral tissue? There are different 

microbes in the thin layer of mucus covering corals and inside the coral tissue. If 

the microbial community in the mucus is 

responsive enough to the coral’s metabolism, we may be able to test the mucus 

alone. Over the course of the larger study, 

corals under different stress conditions on 

the reef will be evaluated for acclimatization, adaptation, and (or) susceptibility to 

disease. The results of these investigations 

may play an important role in choosing the 

most effective Marine Protected Areas to 

mitigate the effects of global warming on 

coral communities.

2. Discovering Archaea Associated 

With Corals [Christina Kellogg]

Many studies have shown that coral mucus 

hosts a diverse bacterial community. 

Archaea (formerly called archaebacteria) 

are the third domain of life (Fig. 1). 

Superficially, they look like bacteria, but 

genetically and biochemically, they are 

very different. For years, archaea were 

found only in extreme environments, such 

as hot springs or deep-sea hydrothermal 

vents. More recent studies, however, have 

uncovered archaea in temperate coastal 

waters. Archaea have also been detected 

in marine sediment and as symbionts 

2

Figure 3. Sequencing means using a chemical reaction to determine the order of the four nucleotide bases (A, 

G, C, T) that make up DNA. Each “species” of microbe will have a unique combination of bases, sort of like a 

bar code. In this example of a DNA sequence chromatogram, each of the four nucleotide bases is coded in a 

different color.

Figure 4. The colorful landscape and incredible diversity of a deep-sea reef in the Aleutian Islands. Photo 

credit: Alberto Lindner, NOAA Fisheries.
Bay Laboratory have been documenting deep-water coral and sponge reefs 

in waters off these islands (Fig. 4). The 

deep-sea corals that make up the Aleutian 

reefs are mainly gorgonians (soft corals). 

The diversity and abundance rival those 

seen in tropical coral reefs. During a 2004 

cooperative research cruise, three types of 

gorgonians were collected with the Delta

submersible for microbial analysis. Live 

bacteria and fungi have been cultured from 

these samples (Fig. 5), and total microbial 

DNA was extracted so that molecular 

techniques could be employed to identify 

archaea and uncultured bacteria and fungi.

3b. Study Site: Gulf of Mexico

The deep-water coral Lophelia pertusa is 

globally distributed but is most common in 

the Atlantic Ocean. This hard branching 

in sponges. Archaea remain difficult to 

cultivate in the laboratory, so most current 

research is based on detection of archaeal 

DNA sequences, which are used to 

identify different types of archaea.

To determine if there were archaea 

associated with tropical corals, mucus 

was collected from three species of reefbuilding corals in the U.S. Virgin Islands: 

Montastraea annularis complex, Diploria 

strigosa, and Diploria labyrinthiformis. 

Total microbial DNA was extracted 

from the coral-mucus samples, purified, 

and analyzed by molecular techniques. 

The resulting archaeal DNA fragments 

were sequenced (Fig. 3) and identified 

by comparison to known sequences in 

GenBank, an international repository for 

sequence information. A diverse archaeal 

community was detected in each of the 

mucus samples. Most of the coral-associated archaeal sequences were most closely 

related to archaea previously detected in 

marine waters. The remaining sequences 

were similar to archaea detected in marine 

sediment and hydrothermal vents. A 

few sequences were distinctive enough 

to be considered novel. Unlike previous 

bacterial studies, which found specific 

associations between certain bacterial and 

coral species, this study found that archaea 

seem to be generalists, with the main types 

detected being observed in all three coral 

species tested. Finding archaea, with their 

varied (and, for the uncultivated specimens, mostly unknown) metabolic capabilities, adds to the likelihood of unique 

biogeochemical processes occurring in the 

microbial communities associated with 

corals. This work was done in cooperation 

with the Virgin Islands National Park and 

was published in the journal Marine Ecology Progress Series (Kellogg, 2004).

3. Microbial Ecology of Deep-Sea 

Corals [Christina Kellogg]

Most people are familiar with tropical 

coral reefs, located in warm, shallow 

waters. However, corals also exist 

hundreds and even thousands of meters 

below the ocean’s surface where it is 

cold and completely dark (Fig. 4). In 

the last few decades, scientists have 

discovered and photographed incredible 

gardens of deep-sea corals off the 

coasts of North America, Great Britain, 

Europe, Scandinavia, Australia, and New 

Zealand. These corals survive without 

algal symbionts (because there is no light 

for photosynthesis) and may take a long 

time to grow. Thus the potential role of 

coral-associated microbes is even more 

interesting. It is possible that the microbes 

are helping to feed these corals, similar to 

the chemosynthetic bacterial symbionts 

that feed hydrothermal-vent worms. The 

microbial communities of these coldadapted corals are also likely to contain 

novel organisms, which will not only 

increase our understanding of microbial 

diversity but could also be a source of new 

enzymes or pharmaceuticals.

3a. Study Site: Aleutian Islands

The Aleutian Islands are a string of 

volcanic islands stretching from Alaska 

toward Russia, dividing the North Pacific 

from the Bering Sea. Since 2002, National 

Oceanic and Atmospheric Administration 

(NOAA) fisheries scientists from the Auke 

3

Figure 6. Lophelia coral in the Gulf of Mexico provides a complex habitat for many organisms, including the 

rosefish, squat lobsters, and sea urchin seen here. Photo credit: Christina Kellogg, USGS.

Figure 5. Bacteria, isolated from deep-sea corals, 

are grown on dishes of nutrient agar for identification and further study. Photo credit: Christina 

Kellogg, USGS.

Figure 7. Submersibles, like Harbor Branch Oceanographic Institute’s Johnson-Sea-Link, are essential 

to deep-sea coral collection missions. Photo credit: 

Cheryl Morrison, USGS.
coral forms bushes or thickets that provide 

extensive reef habitat for fishes and 

invertebrates (Fig. 6). The USGS has 

partnered with the Minerals Management 

Service (MMS), NOAA, and the 

University of North Carolina to determine 

the biology and ecology of Lophelia reefs 

that have been discovered in the Gulf of 

Mexico. Using a submersible to collect 

samples and environmental data at depths 

to 800 meters (Fig. 7), USGS scientists 

are determining the relationship between 

Lophelia and the reef’s microbial flora; 

Lophelia’s genetics, growth, metabolism, 

and reproduction; and food-web 

relationships of reef-associated organisms 

through the analysis of stable isotopes. 

Many of these Lophelia clumps are located 

near natural hydrocarbon seeps in the 

ocean floor, so it is of particular interest 

to determine if hydrocarbon-utilizing 

microorganisms are the link between the 

coral and the seeps. Samples of Lophelia

were collected for microbial experiments 

in the summer of 2004, and additional 

samples will be collected in 2005. 

4. Microbial Wars: Mucus-Associated 

Bacteria Fend off Coral Pathogens 

[John Lisle]

Most coral-disease pathogens that have 

been identified are bacteria (reviewed by 

Rosenberg and Loya, 2004; Richardson, 

1998). Although some microbes have 

been successfully linked to specific coral 

diseases, the mechanisms by which they 

establish infections are not understood. 

One of the recent investigations of bacterially induced coral diseases concluded that 

a bacterium commonly found in aquatic 

environments and human feces, Serratia 

marcescens, is the cause of white-pox 

disease in the elkhorn coral Acropora 

palmata (Patterson, 2002). Previous 

studies that have isolated alleged coral 

disease-causing microbes from infected 

tissues have done so from the perspective 

of the pathogen being introduced from the 

sea water, with no consideration of the 

role played in the infection process by the 

native bacteria within the coral’s mucus 

layer. This aspect is important to consider 

because the mucus layer provides a barrier 

between the water and coral tissues. 

To determine if native bacteria living in 

coral mucus are capable of providing an 

anti-bacterial defense against outsider 

microbes, mucus samples were collected 

from healthy corals in the Florida Keys. 

Bacterial isolates recovered from these 

mucus samples were screened for antibacterial activity against a strain of S. 

marcescens (a known coral pathogen), and 

Escherichia coli (a bacterium commonly 

found in human feces). Approximately 5 

percent of the screened isolates exhibited 

antibacterial activity, where inhibition of 

growth was the criterion (Fig. 8). These 

native bacterial isolates were characterized 

by biochemical tests and gene sequencing 

in collaboration with University of South 

Florida microbiologist Valerie J. Harwood. All of the isolates were identified 

as belonging to the genus Vibrio. These 

data indicate that coral-associated bacteria 

residing in the mucus layer provide a first 

line of defense against the establishment of 

potentially pathogenic bacteria in corals.

CONCLUSION

There is no doubt that we live in a microbial world. Bacteria, archaea, fungi, and 

algae participate in all the fundamental 

biogeochemical processes that allow life 

as we know it to exist. Coral microbial 

ecology is just beginning to address the 

importance of microbes to the health and 

function of coral reefs.

For more information, 

please contact:

Christina Kellogg

600 4th Street South

St. Petersburg, FL 33701

phone: 727-803-8747 x3128

fax: 727-803-2030

ckellogg@usgs.gov

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

REFERENCES

Frias-Lopez, J., A.L. Zerkle, G.T. Bonheyo, 

and B.W. Fouke, 2002, Partitioning of 

bacterial communities between seawater 

and healthy, black band diseased, and 

dead coral surfaces. Applied and Environmental Microbiology, v. 68, p. 2214-2228.

Kellogg, C.A., 2004, Tropical Archaea: 

diversity associated with the surface 

microlayer of corals. Marine Ecology 

Progress Series, v. 273, p. 81-88.

Pantos, O., R.P. Cooney, M.D.A. Le Tissier, 

M.R. Barer, A.G. O’Donnell, and J.C. 

Bythell, 2003, The bacterial ecology of a 

plague-like disease affecting the Caribbean coral Montastrea annularis. Environmental Microbiology, v. 5, p. 370-382.

Patterson, K., J. Porter, K. Ritchie, S. 

Polson, E. Mueller, E. Peters, D. Santavy, 

and G. Smith, 2002, The etiology of 

white pox, a lethal disease of the Caribbean elkhorn coral, Acropora palmata. 

Proceedings of the National Academy of 

Sciences, USA, v. 99, p. 8725-8730.

Richardson, L. L., 1998, Coral diseases: 

what is really known? Trends in Ecology 

and Evolution, v. 13, p. 438-443.

Rohwer, F., V. Seguritan, F. Azam, and N. 

Knowlton, 2002, Diversity and distribution of coral-associated bacteria. Marine 

Ecology Progress Series, v. 243, p. 1-10.

Rosenberg, E. and Y. Loya, 2004, Coral 

Health and Disease. Springer-Verlag, 

Berlin, Germany, 488 p.

Wild, C., M. Huettel, A. Klueter, S.G. 

Kremb, M.Y.M. Rasheed, and B.B. Jørgensen, 2004, Coral mucus functions as 

an energy carrier and particle trap in the 

reef ecosystem. Nature, v. 428, p. 66-70.

Figure 8. A bacterial-inhibition experiment. Serratia 

marcescens is spread over an agar plate (its growth 

is visible as a orange haze on the colorless agar); 

then native bacteria are spotted on top of it (visible 

as the circles on the plate). Native bacteria that do 

not resist S. marcescens are grown over (orange 

circles), but white circles indicate antibacterial 

activity. Those spots are colorless because the S. 

marcescens could not grow there. Photo credit: 

John Lisle, USGS.