Coral reefs are some of the most biologically diverse and important ecosystems in the ocean, but they are also fragile and particularly sensitive to environmental changes, such as rising ocean temperatures, acidity, and pollution levels. As such, an estimated 33-50% of coral reefs are classified as degraded, which puts approximately a quarter of all marine species at risk of extinction.

Threat Of Excess Nitrogen To Coral Reefs

One of the most significant threats to coral reefs comes from anthropogenic nutrient runoff. Corals, typically, thrive in an oligotrophic, or nutrient-poor environment, and any change to nutrient levels within the sea water can severely affect the coral ecosystem. Humans often fertilize their fields to put more nutrients into the soil in order to grow better crops, but if this is done irresponsibly, such as before heavy rainfalls, these nutrients can be washed out into the ocean where they affect the delicate balance of coastal ecosystems. Improperly treated sewage is also another source of anthropogenically-derived nitrogen that affects these coastal systems.

Although nitrogen is an essential nutrient and critical for coral growth, high levels of fixed nitrogen in the ocean is problematic for reef ecosystems, as it can trigger algal blooms. Algal blooms are harmful to surrounding marine life because they create dense mats of algal growths that limit sunlight penetration through the water column and deplete the water of oxygen. This causes the corals to become stressed and can result in bleaching.

Natural Buffers Against High Nitrogen Levels

Coral reef health relies on the intricate relationships between the corals, the zooxanthellae (or photosynthetic algae with which corals have a symbiotic relationship), and a complex microbial community. This microbial community is made up of microscopic organisms, such as bacteria, archaea, fungi, and viral associates, and is collectively referred to as the holobiont. This holobiont is thought to contribute to the coral’s ability to survive in nutrient-poor environments, as it influences and maintains the delicate nutrient balance essential for the survival of life on the reef.

Nitrogen In The Ocean Water And The Role Of Microbes

Nitrogen does occur naturally in the ocean, although at much lower concentrations than those caused by excessive nutrient runoff. Within the natural system, there are two main microbial-driven processes which affect the availability of fixed nitrogen in the ocean. The first of these is nitrogen fixation, which is the conversion of inert N2 gas to a more readily available form, known as ammonium (NH4+), which can be absorbed by the corals and used to produce proteins. Cyanobacteria, or blue-green algae, are largely responsible for nitrogen fixation in tropical reefs and other surface waters. The other process, known as denitrification, is the loss of fixed nitrogen from the water column, and is usually associated with anoxic systems, or systems with very low levels of oxygen.

The Science

So, what does the coral microbial community and the nitrogen cycle have to do with keeping coral reefs healthy?

Well, researchers from the Massachusetts Institute of Technology (MIT) and the Woods Hole Oceanographic Institute (WHOI), together with marine biologists and oceanographers in Cuba, have found that the slimy biofilm, or mucus, secreted by many corals, creates regions of low-oxygen environments that provide the right set of conditions for microbes that scrub the nitrogen out of the water column to thrive. According to this media release by MIT News, These nitrogen-scrubbing microbes may potentially be able to protect coral reefs by lowering nitrogen levels, thus preventing algal blooms caused by excess nutrient runoff.

In order to investigate the potential of coral-associated microbes to denitrify the ocean water, Andrew Babbin and his team of researchers set off to the protected Jardines de la Reina, or Gardens of the Queen, marine national park in Cuba. The park is a marine protected area and one of the last refuge for Caribbean coral reefs. The research findings, published in ISME Journal show that the site was fairly low impacted and helped the scientists establish a baseline of what kind of nitrogen cycle dynamics are associated with healthy coral reef ecosystems, so that they can understand how the nitrogen cycle is affected in more anthropogenically impacted areas.

Using Isotopes To Trace Nitrogen Pathways

Within the park, researchers collected small samples of five different commonly found coral species on the reef, and placed them into their own individual containers with some of the surrounding seawater. The corals were then incubated, and the seawater was injected with 15 N tracers. This is a slightly heavy isotope of the nitrogen found naturally in seawater and allows researchers to trace the path of nitrogen within the incubation containers using mass spectrometry. Depending on the molecules of nitrogen produced or consumed within the container, the researchers could estimate the rate of denitrification, or production. Containers with corals showed an order of magnitude higher rates of denitrification than containers with just seawater – indicating that the nitrogen was being reduced by something associated with the corals.

Identifying Denitrifying Microbes Using Genetics

The researchers then swabbed the coral surfaces and grew the bacterial isolates in a marine growth medium overnight. DNA was then extracted from these bacterial samples and used to identify genes that are known to be associated with anaerobic denitrification, thus confirming that there are microorganisms with the ability to respire nitrate anaerobically present in the coral holobiont.

Different Species Cycle Nitrogen At Different Rates

The rate of nitrogen cycling varied among the different species of corals collected by the researchers, most likely because the microbiomes are likely to differ slightly between them. The highest rate of nitrogen cycling was found to be associated with the Diploria, or brain coral, a generally hardy coral compared to the Acropora, which had minimal rates of nitrogen cycling and is generally in poor shape throughout the Caribbean.


Babbin and his team of researchers have provided evidence that the coral holobiont contains nitrogen-scrubbing bacteria, which may potentially act as a buffer against the high levels of nitrogen pollution threatening coral reefs. They have shown that just like the human microbiome drives our health so too is there a connection between the health of the coral microbiome and the rest of the coral ecosystem.