Helping the Great Barrier Reef
With a dose of satire, it was recently reported that the Great Barrier Reef is ‘dead.’ This is, of course, false. Roughly 22% of the reef is dead due to coral bleaching; the rest is in need of rescuing.
So what is coral bleaching? Well, most reef-building corals’ primary source of food is derived from photosynthetic unicellular symbionts. These tiny zooxanthellae – small single cell protozoa – provide food and energy for the coral in exchange for protection.
Interesting factoid: Reef-building corals are relatives of the sea jellies and anemones.
A bleaching event occurs when the conditions to sustain these microorganisms are no longer met, resulting in the zooxanthellae leaving the coral. Since these zooxanthellae are photosynthetic, they provide much of the color you see in coral reefs. So, once the zooxanthellae leave the coral, the coral appears white, hence the ‘bleaching’ event. Corals without zooxanthellae lose their primary food source and are more susceptible to disease. Those corals where bleaching has occurred do not survive for very long.
Causes of Bleaching
There are several factors which affect corals ability to host zooxanthellae, including:
- Changes in Temperature
- Oxygen starvation caused by an increase in zooplankton due to overfishing
- Increase in sedimentation due to silt runoff from agriculture
- Changes in salinity
- Cyanide fishing
- Mineral dust from dust storms caused by drought
- Chemicals in sunscreen which are not biodegradable
The leading cause, however, is the increase of ocean temperatures as a result of global warming.
How Researchers can Help the Coral Reefs
It is not too late to save the reef, as recent news would have you believe. Steps are being undertaken by scientists to ensure the survival of the reef for years to come. One of these steps is through analyzing coral DNA.
Genetic diversity is linked to ecological functioning, adaptive capacity and an organism’s risk of extinction. With higher levels of genetic variation within a population, the more resilient species are to the bottleneck effect. That is, when a rapid decrease in population occurs (like a bleaching event), the species is at a greater risk to disease and extinction. If, however, the species has greater genetic diversity, the likelihood of resistance to disease and other negative effects will develop is greater. So, in knowing just how diverse the genetic data is, scientists can better inform policies on conservation efforts for the Great Barrier Reef and corals overall.
DNA Extraction Tips for Coral Reefs
Unfortunately, extracting DNA from coral reefs is extremely tricky, in part because of corals containing polymerase inhibitors, mucopolysaccharides which precipitate with coral DNA, and possible contaminations from preservation techniques.
It is always best to test which preservation methods work best. In previous studies, species-specific differences in preservation quality were found. Thus, preservation comparisons should be done before collection. However, soft tissues stored in salt-saturated DMSO resulted in better PCR, higher DNA molecular weight, and more efficient amplification.
Coral DNA Extraction Protocol
I. Always perform the extra steps as instructed by your kit. For example, if the digestion step takes one to three hours, but has the option to leave overnight, it is best to leave overnight.
II. Be sure to homogenize your samples thoroughly.
III. Freshly collected corals with small polyps should be rinsed in distilled water and frozen at -70 °C
IV. Break up in small pieces and place a small sample with 100 mMEDTA, 10MM Tris (pH 7.5) on ice.
- Agitate slurry periodically for 2 hours
- Centrifuge at 3000 rpm for 10 min
- Remove supernatant
- Suspend pellet in a lysis buffer and proceed with normal DNA extraction methods
V. Freshly collected corals with large polyps should be rinsed with distilled water. Dissect polyps from the skeleton and proceed as normal.
VI. Use a kit with a CTAB extraction buffer:
- 2% CTAB (hexadecyltrimethylammonium bromide)
- 100 mM Tris-HCl (pH 8)
- 20 mM EDTA
- 1.4 M NaCl
- 0.2% β-mercaptoethanol
- 0.1 mg/mL proteinase K
Put your new-found knowledge to good use, and help save the reef!