Predicting the coral microbiome in a changing environment

Written by Evan Quinter

Corals are known as the backbone of reef ecosystems because they are home to a wide diversity of marine organisms. They also host much smaller creatures like microbes, who aid corals with an array of functions, including nutrient cycling and energy production. Although they can catch their own food, corals depend on their photosynthetic micro-residents for 90% of their energy consumption. We can look at it this way, corals uphold the reef environment but the microbial community upholds them. However, these tiny organisms are susceptible to a changing environment, and with the possibility of an oncoming massive bleaching event, we need to improve our understanding of environmental impacts on coral microbial community structures. Fortunately, a recent paper, authored by PhD candidate Lais Lima at San Diego State University and peers, proposes a model that could predict microbial responses to one of the major environmental influencers –  temperature.

Fig. 1 Microbes are microscopic organisms such as bacteria, viruses, fungi, algae and protozoa. This diagram shows the different microbes that interact with a coral host. You can see how each one has a role or relationship with the coral and a relationship with each other. Resource: Peixoto et al 2017,

Microbes are sensitive to environmental conditions, many of which, like pH levels and eutrophication (over-enriched with nutrients), are heightened by climate change. The full extent of each factor’s impact is still unclear, but temperature fluctuations clearly impact the microbe’s functionality and physiology.  In addition to these external influencers, the interactions and networks between microbes play key roles in shaping coral microbial communities. The study attempts to understand these influences on the coral microbiome, and proposes, “…a dynamic model to determine the microbial community structure associated with the surface mucus layer (SML) of corals using temperature as an outside factor and microbial network as an inside factor.” By looking at factors outside and inside the coral community, the model could predict the coral SML community structure in a given environment. To test the model, the team went to collect field samples in the Bermuda archipelago.

Bermuda Outer Reef Snorkeling - The Best Corals And Big Fish ...
Fig. 2 Barrier reefs in the Bermuda archipelago. Photo credit to the Bermuda Zoological Society

The team extracted SML samples from six Pseudodiploria strigosa coral colonies on the inner and outer reefs. A coral colony contains three distinct microhabitats: the coral SML, tissue, and skeleton, each with their own microbial community. The SML is the outermost layer of the coral microbiome, like a slimy windbreaker for corals, and thus is the most influenced by the surrounding habitat. The microbe community abundance and biodiversity were identified through shotgun metagenomics, a sequencing tool designed to derive a broad picture of a sample’s genetic information. When compared, the model’s theoretical results were not significantly different from the Bermuda reef samples, which means the model can be a valid predictor of coral SML community abundance.

6 The coral surface mucopolysaccharide layer and coral tissue layers with associated microbial consortium. The microbes (viruses and prokaryotes) are not to scale in relation to the cell layer and endosymbiotic dinoflagellates. The surface mucopolysaccharide layer is depicted containing eukaryotic and prokaryotic viruses and bacteria. Viruses are seen further infiltrating the ectodermis and endodermis coral tissue layers with filamentous virus-like particles infecting the endosymbiotic dinoflagellates. 
Fig. 3 The various layers of a coral polyp. Photo credit to William N.S. Arlidge

By investigating the impacts of temperature and the microbial network, the study not only demonstrates the influence of external and internal factors on coral microhabitats, but also that temperature is a primary formulator of the SML community. Their results support past literatures findings and could serve as a predicting tool for sensing coral microbiome dysbiosis, which is a shift or loss in coral micro-community structures. Additionally, the model could expand to test other reef environments’ reaction to temperature and other stressors like light availability, pH levels, and nutrient concentrations. It’s quite difficult to understand the complex effects of habitat change on the coral microbiome, but this model begins to uncover this relationship.

Our world is a vibrant and volatile place, a constantly changing space where our actions contribute to its instability. Coral reefs, and their residential micro communities, are prone to degradation by environmental factors; their conservation largely depends on our understanding of coral colonial responses to their habitat. This paper demonstrates the impact of temperature and microbe community interactions on the SML layer, and offers a potential model to predict future community adaptations to environmental conditions. As we continue to pursue knowledge on coral’s complex micro-ecosystem, let’s remember that modeling is a crucial tool in bridging the gap between field and lab studies. 

If you’d like to learn more about the coral microcosm and how cool mucus is for coral colonies, follow the links below!

Dinsdale Lab(authors of the study): 

The Coral Microbiome from iBiology: 

The Global Coral Microbiome Project:

The role of coral mucus 101:

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