Criteria For Samples Being Archived

Corals that are used in the collection must come from healthy coral colonies. However, visual inspections alone are not sufficient to determine if a coral is healthy (Fig. 1). As with human or veterinary clinical medicine, you have to define health using a number of criteria. Coral health can be defined by criteria that measures aspects of reproduction, growth and regeneration, and clinical laboratory tests.

The Global Coral RepositoryFig 1. Visual triage of the health condition of a coral.  This includes the character of the mucus boundary layer, presence/absence of lesions, and coloration.

Measuring the rate and success of coral recruitment (birth rate) for a reef is one of the most important gauges of population health. In various places in the Caribbean Sea and Pacific and Indian Oceans, one can observe reefs that have large adult coral and are abound in fish and invertebrates. Often, this vitality is an illusion, because many of these reefs have exhibited no coral recruitment in the past 3-6 years. Coral reefs that lack coral recruitment are zombies – they are dead, but just don’t know it. The adults may persist for a decade or more, but eventually, these reefs slowly perish – there is nothing to replace aging adults that are killed by sponges, fish, snails, crown-of-thorns, pollution, pathogen-related diseases, or weather/climate events.

The Global Coral RepositoryFig 2. Collection of coral biopsies for laboratory analytical testing.

Another critical criterion for gauging the health of a coral colony is reproductive viability. If a coral is unable to reproduce, then it cannot contribute to the sustainability of that population (or of the species). Just like in human clinical medicine, reef doctors can take a biopsy of a coral colony (Fig. 2) and determine if its reproductive functions are intact. Sometimes, reproductive organs may be stressed or deformed (Fig. 3), and the gametes are not viable. In other cases, reproductive organs never form, so the coral is considered reproductively incompetent (Fig. 4).

The Global Coral RepositoryFig 3. Histopathology of coral reproductive tissue.  Panel A indicates healthy structure and position of spermaries and oocytes.  Panel B demonstrates a stress condition – pathomorphologies of spermaries, damage to the oocyes, collapse of tissue architecture.(e.g., Downs et al., 2009)

If coral recruitment rates are low, it is difficult to determine what part of the coral life cycle was defective. If a coral is not reproductively viable, reef doctors have a much better idea of where to look for the causes of this pathology, because we know the effect. Drawing upon the vast literature of human and veterinary medicine, as well as invertebrate physiology and pathology, we can begin the process of diagnosing the disease as well as uncovering its etiology – the factors and process that give rise to the disease. This process is also an important aspect of environmental forensics.

The Global Coral RepositoryFig 4. Histopathology of coral reproductive tissue in Acropora palmata. Cuban reference indicates polyps that contain oocytes and spermaries.  Samples collected in the U.S. Virgin Islands at the same time exhibit no reproductive tissue.


When a coral is biopsied, this single tissue sample provides the reef doctor with a myriad of opportunities for diagnostic testing. The laceration that results from the biopsy can also be used in coral diagnostics – to determine the laceration-regeneration rate of the coral colony. Basically, the reef doctor puts a “band-aid” on the wound (Fig. 5), and with a ruler and a camera, measures the rate of the regeneration (Fig. 6; Fisher et al., 2007).

The Global Coral RepositoryFig 5. After a biopsy is taken from the coral, a band-aid using non-toxic modeling clay is used to fill in the laceration.  This prevents sponge and other boring invertebrates from entering the skeleton from the lesion, as well as “leveling” the divet so that tissue can grow over a flat surface rather than a concave structure.


The Global Coral RepositoryFig 6. In the two panels on the left, biopsy lacerations are made in June on two different colonies of the coral, Acropora palmata.  In 1 month, the laceration is re-photographed to determine the surface area rate of regeneration.  The colony series at the top of the panel demonstrates regeneration – an indication of a healthy coral.  The colony series at the bottom of the panel demonstrates expansion of the laceration – an indication of a sick coral.

Healthy corals have a nominal range in their rate of regeneration. In the case of the Caribbean-threatened species, Acropora palmata, regeneration rates of healthy coral are above 1 mm2 per day (Fig. 7). Anything lower than this rate is an indication that the coral is not well. Stress from degraded water quality, abnormal high or low sea temperature, infectious diseases, and predation are all factors that can lower a coral’s regeneration rate. There is an economy to all things. If corals are using their resources to stave off infectious diseases, or tolerate high-temperature, or being poisoned by sewage, it may not have the available resources to regenerate at a nominal rate.

The Global Coral RepositoryFig 7. Laceration regeneration rates for the coral, Acropora palmata. Healthy corals regenerate wounds at a rate of 1 mm2/day or more.  Corals below this rate are stressed.

The coral biopsy can be used for histopathology, as well as looking at cellular and biochemical diagnostic markers. Is a coral experiencing DNA damage either from oxidative stress or from a pollutant, like oil or fuel (Downs et al., 2006)? DNA damage in corals is a pathological process that both slows the regeneration rate, as well as induces reproductive pathologies – the same as in humans and other animals! Reef doctors can run laboratory tests on corals to determine the amount and nature of the DNA damage (Fig. 8; Downs et al., 2011). There are literally hundreds of other laboratory diagnostic tests that can be applied to coral to determine; if they are healthy, or if they are not, and the nature of their pathology.

The Global Coral RepositoryFig 8. Laboratory test on coral biopsy that measures a specific DNA damage product.  Normal levels are between 80 to 140 AP lesions per 105 DNA base pairs.  Above 150 AP lesions, corals are experiencing a significant amount of DNA damage that can affect their immunity against infectious diseases, reproductive viability and effort, or predict mortality.

Once the reef doctor is satisfied that the clinical tests meet the criteria for a healthy coral, the doctor still needs to take into account the condition of the majority of the coral colonies and coral species on a reef (Downs et al., 2005). The reef doctor will conduct an epidemiological assessment of the population to measure the prevalence and incidence of disease signs, recent mortalities, recruitment rate, etc. Once the clinical and epidemiological criteria are met, the coral species and its population on a specific reef are a candidate for being archived.

The final step for a decision to archive samples from a reef community is discussion with the local community and local and regional governments. Is this reef important to the local community that subsists on it? Do they want it preserved? Do they want to have its specimens to be used as a source for restoring other nearby reefs that have deteriorated? Stakeholder input is both the first and final step in the decision process for archiving.

Downs et al.,  (2009)  Cellular pathology and histopathology of hypo-salinity exposure on the coral Stylophora pistillata.  Science of the Total Environment 407:4838-4851.

Downs et al., (2005) Shifting the Paradigm for Coral Reef ‘Health’ Assessment. Marine Pollution Bulletin 51:486-494.

Downs et al., (2006) Cellular-physiological effects of the MV Kyowa Violet fuel oil-spill incident on the coral, Porites lobata. Environmental Toxicology & Chemistry 25: 3171-3180.

Fisher et al., (2007) Lesion regeneration rates in reef-building corals Montastrea spp. as indicators of colony condition. Marine Ecology Progress Series 339:61-71.

Downs et al., (2011) A survey of environmental pollutants and cellular-stress markers of Porites astreoides at six sites in St. John, U.S. Virgin Islands. Ecotoxicology in press.