Biomarkers: diagnosing stress and predicting success

By Melissa Naugle

Figure 1. Visibly stressed coral polyps show bleaching (loss of symbionts).

When corals turn pale white in color, we can be pretty confident that they are stressed. While this is often due to high water temperatures, sometimes other stressors such as fluctuating pH, elevated nutrient levels, or plastic pollution also play a role. Despite the stark appearance of bleaching, we can’t always tell how stressed corals are or specifically which of the possible stressors is causing that bleaching at any given time. This is where biomarkers come in. Biomarkers—molecules, processes, or other substances that behave predictably in response to a particular stressor—can be used to diagnose causes of stress that aren’t readily apparent.

What are biomarkers?

Biomarkers are naturally occurring, and we can use them as tools to learn more about coral’s internal physiology. There are multiple types of biomarkers including gene expression biomarkers, protein biomarkers, and epigenetic biomarkers, among others. These biomarkers have the potential to provide valuable information to reef managers about coral physiology. For example, they may be used to predict bleaching events, determine which corals have the greatest potential to exhibit resilience, and identify the sources of long-term stress on reefs. Biomarkers also are also time- and cost-efficient since they can be used on reefs in real time and don’t require time-consuming physiological tests while in the field—instead, they can be measured from a small tissue sample.

Gene expression biomarkers

Gene expression biomarkers are valuable for their ability to tell us what a coral is doing on a physiological level. All living organisms have between hundreds and thousands genes in their genetic code, but not all of those genes are being used all the time. In fact, different parts of our bodies turn on and off different genes depending on what they need to accomplish. Corals do the same thing—they often change which genes they turn on and off depending on their environment. So, we can dig deeper into how corals are responding to stress in their environment by looking which genes they are expressing, or which genes are turned on and off. Though all of the organism’s genes are contained in its DNA, only genes transcribed into RNA are being expressed. The entire set of expressed genes is known as a transcriptome, and proteins that the organism needs can be made from genes that are available in the transcriptome (Fig 2).

Figure 2. The central dogma of genetics. DNA, contained in the genome, is transcribed into RNA, making up the transcriptome, which is then translated into proteins.

By using gene expression biomarkers, scientists can monitor genes that are expressed under stress in order to determine the coral’s stress level. Since changes in gene expression are often proportional to stress intensity, this method appears to be promising for measuring short-term stress, such as during bleaching events (Kenkel et al 2014). For longer-term stress, gene expression biomarkers may also be used to assess reef health and determine resilience potential for future bleaching events. For example, in response to long-term thermal stress, corals may adjust their expression of genes involved in growth, changing how they allocate their resources (Kenkel et al 2014).

Protein biomarkers

In addition to gene expression biomarkers, there are also protein biomarkers: these measure levels of proteins that correlate with stress, such as heat-shock proteins. For example, Downs et al (2005) has developed protein biomarkers for Boulder Star Coral (Montastraea annularis) in the Florida Keys. Under stress, corals produced higher levels of proteins called Superoxide Dismutases (SODs) and their symbionts produced higher levels of heat shock proteins. While these biomarkers are promising, they also may be difficult to standardize between batches since the lab methodology relies on antibodies, which can be highly variable (Baker 2015, Kenkel et al 2014, Parkinson et al 2018).

Now what?

Despite their promise, biomarkers are still a relatively new tool. More research is needed to find common responses among coral species and corals in different regions in order to develop biomarkers that can be used universally. In order to address these limitations, Parkinson et al (2018) suggests a framework that includes validation of existing biomarkers, field trials, and an implementation plan. Once more standard biomarkers are developed and tested, reef managers can integrate this technology into their reef monitoring surveys alongside more traditional methods like visible bleaching data, coral diversity indices, and coral growth. Altogether, this data provides scientists with a stronger understanding of how coral reefs are responding to climate change and what this means for their future. Additionally, by using biomarkers to monitor long-term stress, coral propagation programs to target the most resilient individuals on these reefs for cloning, rearing and outplanting back onto the reef (Fig. 3). These potential benefits are what makes biomarker research so exciting and promising!

Figure 3. A coral nursery growing Staghorn Coral (Acropora cervicornis).  

Further Reading

Baker M (2015) Reproducibility crisis: blame it on the antibodies. Nature 521:274

Downs, C. A., Mueller, E., Phillips, S., Fauth, J. E., & Woodley, C. M. (2000). A molecular biomarker system for assessing the health of coral (Montastraea faveolata) during heat stress. Marine Biotechnology2(6), 533-544.

Kenkel, C. D., Sheridan, C., Leal, M. C., Bhagooli, R., Castillo, K. D., Kurata, N., … & Matz, M. V. (2014). Diagnostic gene expression biomarkers of coral thermal stress. Molecular ecology resources14(4), 667-678.

Liew YJ, Zoccola D, Li Y, Tambutté E, Venn AA, Michell CT, Cui G, Deutekom ES, Kaandorp JA, Voolstra CR, Forêt S, Allemand D, Tambutté S, Aranda M (2018) Epigenomeassociated phenotypic acclimatization to ocean acidification in a reef-building coral. Sci Adv 4:eaar8028

Morgan, M. B., Vogelien, D. L., & Snell, T. W. (2001). Assessing coral stress responses using molecular biomarkers of gene transcription. Environmental Toxicology and Chemistry20(3), 537-543.

Parkinson, J. E., Baker, A. C., Baums, I. B., Davies, S. W., Grottoli, A., Kitchen, S. A., Lajeunesse, T.C., Matz, M.V., Miller, M.W., Shantz, A.A., Kenkel, C. D. (2018, November 4). Molecular tools for coral reef restoration: beyond biomarker discovery.

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