Stony corals (Order Scleractinia) are found in clear, shallow (<100 m) ocean waters between 30o N and 30o S latitude. These animals live in a symbiotic relationship with dinoflagellates (phytoplankton) of the genus Symbiodinium. This symbiosis provides sufficient food-energy for the coral host to lay down a CaCO3 skeleton with species-specific morphology. The large CaCO3 skeletons produced by millions of tiny coral polyps then become sites in and on which other organisms such as fish, snails, fleshy algae, and coralline algae can find places to live and eat. Coral reefs, therefore, are some of the most diverse places on Earth; one study estimates that they are home to ¼ of all marine fish species.

It is estimated that, each year, coral reefs produce 1 billion metric tons (or over 2 trillion pounds) of limestone and provide billions of dollars in services and revenue for governments and businesses. These services and revenue include protection of coasts from waves, fish and invertebrates as a food source, and income from tourists. However, coral reefs are currently facing the combined threats of physical destruction, nutrient loading, increased sea surface temperatures, and ocean acidification, all of which are strongly linked to human actions (i.e., anthropogenically caused). It is this last threat, ocean acidification, which we are studying in the Environmental Biophysics and Molecular Ecology Lab and Marine Biogeochemistry and Paleoceanography Group (

The burning of fossil fuels and cutting of trees since the Industrial Revolution have led to increasing atmospheric CO2. Some of this CO2 dissolves into the ocean where it reacts with water and decreases ocean water pH. It has been projected that decreasing ocean pH (i.e., ‘ocean acidification’) will make it harder for corals to calcify (or make more of that 2 trillion pounds of limestone each year) and/or lead to large-scale dissolution of existing coral skeleton. 


Figure 1. Vertical cross section of a generalized coral polyp showing oral and aboral ectoderm and endoderm, symbiotic dinoflagellate cells (yellow spheres), and aragonite skeleton precipitated below each polyp in a species-specific morphology. Figure from: Veron, JEN, 1986. Corals of Australia and the Indo-Pacific. Univ. of Hawaii Press, Honolulu, HI. 644 pp.

Our group is focusing on the molecular mechanisms of coral calcification, and by extension, whether and how this mechanism is being affected by ocean acidification. We use molecular, biochemical, bioinformatics, and geochemical tools to study coral calcification at the protein and cellular level (Figure 1). We are also conducting advanced physical chemistry research on the atomic-level reactions that take place during calcification. By understanding the coral calcification at these scales, we hope to improve predictions for the fate of stony corals in the coming decades and centuries.


Figure 2. Relief contrast, confocal and SEM images of S. pistillata protopolyp. (A) 72-h old proto-polyp (magnification 406x). (B) Z-stack of a proto-polyp at 12 d. The Symbiodinium sp. cells are seen by chlorophyll florescence and animal cells are revealed by GFP fluorescence. (C) SEM of 12 d old proto-polyp cell organization, and (D) extracellular precipitation of aragonite crystals associated with proto-polyp. Figure and legend from: Mass et al. 2012. Aragonite precipitation by ‘‘proto-polyps’’ in coral cell cultures. PLoS ONE 7(4): e35049.

We use cell cultures of two stony corals, Stylophora pistillata and Pocillopora damicornis, to study the effects of ocean acidification at the cellular level. We are able to maintain cultures of these two species in a seawater-based nutrient-rich medium for up to one month. Dermal cells, symbiont-containing cells, and stinging cells are present in the culture and arrange themselves into a 3-D structure over the course of just a few days (Figure 2 A, B). Within 3 days, the cultures begin to produce aragonite crystals that reach 10’s of microns (<1/64 inch) in 10 days (Figure 2 C,D). We plan to study these coral cell cultures at various CO2 concentrations and in different media to understand how environmental factors external to the cells affect the calcification reaction.


Figure 3. SEM images of the different types of extracellular matrix monolayer of adherent cells from Montipora digitata. [Scale bar is 10 m.] Figure and modified legend from: Helman et al. 2008. Extracellular matrix production and calcium carbonate precipitation by coral cells in vitro. Proceedings of the National Academy of Sciences 105(1): 54-58.


Figure 4. Multiple sequence alignment of coral acid-rich protein (CARP) 4-like proteins from various stony corals. Figure from Drake et al. 2013. Proteomic analysis of skeletal organic matrix from the stony coral Stylophora pistillata. Proceedings of the National Academy of sciences 110(10): 3788-3793.

We have recently taken a proteomics approach toward characterizing the proteins secreted by corals between their aboral endodermal cells and recently formed CaCO3 skeleton or other substrate (Figure 3). We used liquid chromatography and tandem mass spectrometry, along with a draft genome for Stylophora pistillata, to sequence proteins extracted from S. pistillata skeleton. The sequences suggest that structural (eg., collagen), adhesion (eg., cadherin), and highly acidic proteins remain occluded in the coral skeleton and may be important in the calcification process. Additionally, we have described a novel family of highly acidic Coral Acid-Rich Proteins (CARPs) that are only found in stony corals and exhibit a high degree of sequence conservation across coral families (Figure 4).


Moving forward, we plan to study the effects of increased CO2 on the ability of coral proto-polyps to produce skeletal proteins and to form CaCO3 crystals. We are also working on immunolocating several of the more interesting skeletal proteins in coral cell cultures, intact polyp tissue, and skeletons. In the coming months, we and other members of our group will be examining the physical chemistry of the biomineralization process and its effects on geochemical proxies.


Dr. Paul G. Falkowski, Principle Investigator on the Biochemical Mechanisms of Coral Calcification 


Dr. Tali Mass, Post-doctoral Researcher


Liti Haramaty, Laboratory Researcher


Jeana L. Drake, PhD Candidate