Microbial Importance to Coral Reef Health

Introduction: The Invisible Engine of Coral Reefs

Coral reefs rely on small, microscopic organisms called microbes to maintain a functional and healthy ecosystem. Microbes are organisms such as bacteria, fungi, algae, plankton, and even viruses that live in the environment. In coral reefs, microbes participate in nutrient acquisition, metabolic cycling, and protection against disease. Stony corals and sponges specifically form close connections with many types of microbes, termed the holobiont. These microbes are necessary in providing nutrients and energy to corals, as well as protecting corals from pathogens. They allow coral reef ecosystems to thrive in the nutrient-poor environment necessary for coral growth. Microbes respond quickly to disturbances in the environment, and environmental stressors can cause changes in the coral microbiome. It has been shown that in response to increasing ocean temperatures, there has been a shift from beneficial bacteria to opportunistic and potentially pathogenic bacteria. This shift corresponds to an increase in coral diseases and bleaching (Vanwonterghem & Webster, 2020). Coral disease and bleaching have created a shift from coral- to algae-dominated states, a transition that is intensified by microbialization and the DDAM (Dissolved Organic Matter, Disease, Algae, and Microbes) negative feedback loop (Barott & Rohwer, 2012). This article will explore the causes and implications of microbialization and DDAM, explain how they function, and discuss potential solutions to limit these problems in coral reefs.

What is Microbialization?

Microbialization is a process where organisms called microbes (microscopic organisms such as bacteria) take over ecosystems that were originally dominated by larger animals. Some microbes are essential for healthy ecosystems because they help break down waste and recycle nutrients. During microbialization, however, microbes grow too quickly and begin to use more and more of the ecosystem’s energy, leaving less available for those larger organisms like fish and corals. Overall, microbialization means that an ecosystem is becoming less balanced, more microbe-heavy with fewer large animals and more microscopic life.

The DDAM feedback loop explain

Understanding The Holobiont

A holobiont is a composite organism, where intricate interactions and associations between coral or benthic algae macroorganism hosts and their microbial communities function together as one unit. Holobiont associated microbiomes are highly diverse and distinguishable from microbial communities in the surrounding water column and biofilms on other non living substrates. Protists like diatoms and zooxanthellae, as well as bacteria, fungi, and viruses are common microbial players associated with coral and algae. [Barrot et. al]. These microbial players are important physical and physiological components of coral reefs; surface microbes preempt space on the host, providing protection from fouling or pathogens and nitrogen-fixing bacteria microbes provide the host with access to nutrients [Rohwer et al.]

DDAM Model

The [Dissolved Organic Matter (DOM), disease, algae, and microbes] model, or DDAM, hypothesizes a positive feedback loop caused by interactions within its four components impact coral survival and health. Ecologists have conducted field experiments and provided evidence to explain a mechanism in which anthropogenic activity leads to coral mortality. The three main steps of the loop are

Algae releases dissolved organic matter into the water column. Primary producers like algae release dissolved organic carbon and dissolved oxygen into the water as a by product of photosynthesis [ Haas et al. 2011]
Dissolved organic matter facilitates increased respiration and microbial growth. Opportunistic pathogens respond and increase in abundance.
Coral pathogens are more prevalent and often spread very rapidly. Coral becomes increasingly vulnerable to disease, bleaching, stress, land death.

Direct Contact

The DDAM model has been proposed to be expanded to the 3DAM model: DOM, direct contact, disease, algae, and microbes. Direct contact coral-algae interactions directly connect the tissues of the two competitors for potential transfer of DOM, pathogens, and hydrophobic organic matter like allelochemicals. Ecologists expect increases of direct contact between coral and algae on degraded reefs, based on observed increases in macro and turf algae. In response to human activity, reef species compositions may shift to include more turf algae that compete better against coral due to releasing more DOM and hosting more opportunistic pathogens, as well as thicker and increased height of turf algae boundary layers with coral (Barrot et al.)

What Triggers Microbialization?

Why does microbialization occur?

Because holobionts rely on a large and diverse team to function together as one, disturbances and environmental influence can often result in community change that can be disastrous for the macroorganism host. As human activity continues to alter the natural state of ocean ecosystems, stressors like increasing surface water temperatures, acidification, and water pollution can trigger collective responses. When reefs react to these stressors collectively, microbes increase in abundance and biomass which opens the door for opportunistic pathogens to swoop in and overtake the reef, known as reef microbialization (Mohammed et al. 2023).

Bioenergetic mechanisms

When coral neighboring algae release dissolved organic carbon, the reef microbial community shifts to more heterotrophic interactions. Microbial communities with heterotrophic metabolism shift towards communities with more copiotrophic consumers than autotrophic producers. This nets the reef greater oxygen consumptions that creates micro hypoxia at the interface of the coral and the algae. As the number of heterotrophic consumers increases, much more of the available energy is used by the microbial members of the ecosystem which defines microbialization (Mohamed et al. 2023).

Anthropogenic Activities

Along with anthropogenically induced climate change, fishing pressure can also contribute to microbialization of coral reef ecosystems. When reef fish, like parrotfish. that scrape algae off of rocks, are removed, it reduces the pressure on the macroalgae. This allows macroalgae to rapidly increase in abundance and trigger the DDAM loop by releasing more DOC into the surrounding seawater (Mohamed et al. 2023). This mechanism further underscores the importance of whole ecosystem conservation management strategies; the fish, coral, microbes, and other creatures and intrinsically linked and work together to maintain a delicate equilibrium of healthy

Measuring the Shift: Where Scientists Come In

Coral reefs are complex food webs, and one subtle sign of trouble is a shift in who is consuming the energy. Microbialization, as you have learned from reading this article, is when tiny microbes start hogging the reef’s energy budget at the expense of the bigger organisms like fish. To track this hidden shift, scientists and researchers developed something called the microbialization score. This score essentially asks in layman terms: out of all the energy being used by fish and microbes on the reef what percentage is being used by the microbes? In practice, it’s like calculating what fraction of the reef’s “metabolic pie” is eaten by bacteria instead of fish. A 2012 study by Tracey McDole and colleagues introduced this metric and showed it’s a telling indicator of reef health (McDole et al., 2012). The higher the microbialization score, the more the reef’s energy flow has shifted into the microscopic realm, which is often a sign of disturbed or unhealthy reef (Haas et al., 2016). What does that look like in numbers you might ask? On an intact, remote reef with very minimal human impact, microbes might only account for around 8% of the combined metabolism, with fish and other big creatures doing most of the energy processing. But on heavily impacted reefs near people, the tables turn dramatically. In the main Hawaiian Islands, for example, some reefs showed microbialization scores between 75% to 98%. O’ahu, one of the islands, had the highest scores of about 98%, which means microbes were consuming virtually the entire energy budget, while fish were barely contributing. Furthermore in O’ahu reef, surveys found that although fish made up 94% of the living biomass by weight, they were only responsible for 3% of the combined predicted metabolic rate because the microbes had far outpaced them in energy use. This imbalance was closely linked to human influence: reefs with more fishing pressure and pollution tended to have higher microbialization scores. So our impact, like overfishing and nutrient runoff, often lead to energy being diverted into microbial loops instead of supporting fishes and corals. The microbialization score gives scientists a single number to quantify this shift, and it has proven to correlate strongly with human disturbance levels on reefs . It’s a bit like a “fever thermometer” for reefs, as higher scores signal an ecosystem under stress and a food web out of balance (McDole et al., 2012).

How do scientists actually measure this shift?

They combine field surveys with lab measurement to get a full picture. Key indicators that researchers monitor include:

Fish biomass and activity: Teams of marine scientists, often scuba divers, perform visual censuses on reef fish. This includes counting fish, estimating their sizes, and identifying species. From this data, they calculated fish biomass per area and used established metabolic rates(bigger fish and active species use more energy) to estimate how much energy the fishes use. Healthy reefs typically have lots of fish, which indicates much of the energy is tied up in those larger animals instead of microbes(McDole et al., 2012). Low fish biomass or the removal of key grazers(via overfishing) can tip the balance toward microbes by allowing algae and microbes to flourish(Too much algae – and too many microbes – threaten coral reefs 2016). So fish surveys are crucial as a lack of fish often foreshadows microbial takeover.
Dissolved Organic Carbon (DOC) levels: This is essentially the amount of liquid food available for bacteria in the water. Corals and algae naturally leak sugars and other organic molecules into the seawater. Scientists collect water samples above the reef and analyze the DOC concentration to see how much of this microbial fuel is around. Changes in DOC can signal a shift in the reef’s balance. Interestingly, one counterintuitive finding is that reefs overgrown with fleshy algae often show lower DOC levels in the water column than one might expect. The reason being is that microbes respond so fast that they gobble up the algal DOC almost as soon as it’s produced. In effect the water is too clean of DOC because bacteria are eating it continuously. So, a drop in measurable DOC alongside a blood in algae can actually be a red flag, as it indicates a massive microbial appetite is at work. On coral dominated reefs by contrast, microbes have less to eat, so DOC lingers at higher baseline levels. By tracking DOC, researchers get insights into this unseen food supply and how it’s being utilized (Haas et al., 2016).
Microbial abundance and activity: Perhaps the most direct way to gauge microbialization is to count the microbes themselves. Scientists take water samples and use methods like microscopy to measure the concentration of bacterial cells in the reef water. They also sometimes assess microbial respiration, how fast those microbes are consuming oxygen or organic carbon. High microbial counts and high respiration rates indicate the reef’s microbial engine is revving high. In algae-rich, disturbed reefs, studies have found significantly elevated bacterial abundances compared to healthy coral-dominated sites (Haas et al., 2016)(McDole et al., 2012).

Using these approaches, scientists can quantify the subtle shift toward microbial dominance. They might plot something like algal cover vs. microbial metrics to visualize the trend. In one global survey, researchers led by Andreas Haas in 2016 showed that sites with more fleshy algae had far more bacteria in the water and surprisingly depleted DOC levels, supporting a model dubbed “DDAM” (Dissolved organic carbon, Disease, Algae, Microbes). This model describes a feedback loop where algae fuel microbes (with DOC), microbes contribute to coral disease and oxygen stress, and the resulting coral declines let algae grow even more. The data across 60 reefs bore this out: as algae cover went up, bacterial counts shot up, and the water’s DOC was often found stripped of evidence of microbes actively consuming the algal exudates. Here is a figure showing this produced by Andreas Hass et. al study. a,b, Correlation of percentage of algal cover and DOC water column concentrations (a) and percentage of algal cover and log10-transformed microbial cell abundances (b) with 95% confidence interval. r and P values are given for each ocean system.(https://www.nature.com/articles/nmicrobiol201642/figures/2)

Those microbes also shifted to a “high power” metabolism, burning through the organic carbon less efficiently but faster, which produced more carbon dioxide and led to lower oxygen levels around the reef. In plain terms, the reefs became microbial pressure cookers, as bacteria rapidly used energy in ways that don’t support the larger food web. By monitoring parameters like DOC and microbial cell counts alongside fish populations, scientists can detect these early warning signs of microbialization. It’s a prime example of how researchers come in with measurements and models to make the invisible visible, diagnosing the reef’s health beyond what the eye can see! It is worth noting that for years, much of this monitoring focused on the classic scenario of algae overgrowth (often due to overfishing and pollution) driving microbial changes. The microbialization score itself was born from studies comparing near pristine vs impacted reefs and showed that human impacts shift energy into microbial hands. But recently, marine biologists have started asking: are there other routes to microbialization besides algae blooms? In particular, with climate change causing more coral bleaching, could stressed corals themselves kick off similar microbial surges.

Consequences of Microbialization

Reduced Energy Flow

One major consequence of microbialization is that it disrupts the natural flow of energy through the reef ecosystem. Normally, energy moves from small producers like algae to larger animals like Blue Tang, Barjack, and Nurse Sharks, passing through several layers of consumers along the way. But when microbes take over, they absorb a large portion of the energy and nutrients, acting like a “dead end”. Although some small organisms do eat microbes, this food web is less efficient: microbes are hard to catch, use up a lot of energy themselves, and often don’t support enough of the right middle organisms to pass energy on to larger animals. As a result, even the energy gets stuck at the bottom, which limits the growth and survival of larger reef organisms.

Increased Sensitivity to Stress

Microbialization also makes coral reefs more sensitive to environmental stress, like ocean acidification, eutrophication, and rising temperatures. This is because microbial communities are able to respond and change quickly when their environment shifts. For example, unlike larger animals, microbes can grow or die off in hours or days. When conditions change, pollution or rising temperatures, or both for example, microbial populations can viciously increase or shift to types of microbes that may be more harmful, like those that cause disease or use up extra oxygen. The ability to rapidly change may be good for the microbes, but at the cost of making the whole reef system less stable. This can cause the reef to suddenly tip into an unhealthy state that is hard to recover from. Increased Hypoxia Another serious effect of microbialization is a drop in oxygen levels, a condition called hypoxia. Microbes use oxygen to break down waste, and when their numbers increase they can use up oxygen faster than it can be replaced. This means there is less oxygen available for fish, corals, and creatures that need it to survive. Ultimately, hypoxia can lead to the death of important reef species and make it harder for reefs to recover.

Solutions and managements strategies The best way to solve and prevent microbialization and the DDAM negative feedback loop is to address their underlying causes. These causes include climate change, coral bleaching, overfishing, and eutrophication. These factors all have an impact on the amount of algae, particulate organic carbon, and particulate nitrogen released by corals and microbes. There are many steps that humans can take to assist in bettering these conditions. Pollution and greenhouse gas emissions are the main causes of climate change and ocean warming, which causes coral bleaching. Switching to renewable energy sources and reducing waste are simple and effective ways to begin to reduce microbialization and DDAM in coral reefs. These solutions will help limit ocean acidification and nutrient runoff, reducing warming and bleaching events. Addressing the underlying environmental causes for coral reef degradation will help reduce the harmful cycles associated with them.

Conclusion

Microbialization and the DDAM feedback loop highlight the shift in coral reef ecosystems under stress. As coral reefs experience disturbances such as ocean acidification, overfishing, and nutrient runoff, macroalgae increases, releasing higher amounts of DOC. This DOC promotes the growth of pathogenic and opportunistic microbes that cause coral disease and bleaching (Sparagon et al., 2024). The resulting decline in coral cover allows algae to increase further, strengthening this deadly cycle. The DDAM feedback loop and microbialization drive reef degradation by promoting the growth of harmful bacteria and creating an algae-dominated ecosystem. Understanding and addressing the relationship between microbialization, the DDAM feedback loop, and coral reefs is necessary to find solutions and management strategies that will support coral reef recovery and health despite environmental pressures.

Citations

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