The state of coral: A mini-review

Coral reefs are one of the main harbingers of the climate crisis.  As such, there have been numerous studies, TED talks, Blue Planet episodes, podcasts, et cetera, about the state of corals. I’ve condensed a select few research findings for a mini-review to highlight some of the most recent results. This is by no means a comprehensive review of the coral literature, obviously.  I will, no doubt, egregiously fail to mention some rock stars who are making great strides in coral biology and conservation.  It’s a big group – both of scientists and of species.

A quick background on coral endosymbionts

Shallow water corals are considered holobionts, comprised of the host coral, endosymbiotic dinoflagellates (often referred to colloquially as zooxanthellae), bacterial and archaea communities. The endosymbionts provide the fixed carbon for the coral via photosynthesis.  When water temperature increases above average for a prolonged time, the endosymbionts are expelled from the coral polyps, leaving bleached coral behind. Corals can rely upon heterotrophy to get their nutrients and fixed carbon, but this is not sustainable over long stretches of time. They can reuptake endosymbionts and recover if temperatures return to normal in a short enough time span.  Most corals obtain their endosymbionts from the environment (horizontally) either during their larval stage in the water column or shortly after settling. Others inherit endosymbionts vertically from their parents. The most reported and studied coral endosymbionts historically have belonged to the genus Symbiodinium, but a recent revision has split the several clades within the genus into seven distinct genera.

A study looking at two species of corals with contrasting modes of endosymbiont inheritance (vertical vs horizontal) measured the heritability of the endosymbiotic communities of each. A heritability of zero would suggest that there is no genetic influence from the coral host on the pattern of endosymbionts found in the holobiont.  A heritability of one would indicate that the endosymbiont pattern is completely governed by host genetics.  Surprisingly, in the case of horizontal capture of endosymbionts, host genetic influences accounted for 29% of phenotypic variation, suggesting that endosymbiont capture from the environment is not completely random, there is a heritable component that selection can act upon. In the vertical transmission scenario, the host genetic influences accounted for only 62% of phenotypic variation, suggesting a fair amount of environmental influence (38%).  This finding is important when considering how best to engineer coral to survive bleaching events (see “super coral” below). Non-zero heritibilities mean coral can be bred or cultivated to pass along these favorable traits. Heritibilities less than one also indicate that these traits won’t strictly “breed true” and other environmental factors play a role in what endosymbionts are captured and maintained by the coral host.

How is current day bleaching different from historical events of bleaching?

Prior to the 1980s, bleaching didn’t happen. Post-1980s, bleaching was regionally localized and triggered by El Niño events with decadal gaps. The first global bleaching event occurred in 1998 and was the first time the Great Barrier Reef (GBR) bleached. It happened again in 2002. Since 2014, it has been occurring more frequently without sufficient recovery time for coral. Now bleaching occurs throughout ENSO cycles including cooler La Niña years, which are now warmer than El Niño years 30 years ago. 


Figure from NOAA’s climate.gov site. alert 1 = coral bleaching is likely. alert 2 = widespread bleaching and significant mortality of corals are likely. Severe coral bleaching was reported in areas circled in white. 

A recent paper looking at patterns of coral cover and recruitment on the GBR between the late 1990s and 2016-17 reported major taxonomic shifts in the recruitment larval pool. For the first time, brooding corals (those that release larvae that spent a short time in the water column before settling locally) produced more recruits than the usually dominant acroporids, which are spawners (those that release eggs and sperm into the water column and drift in the water column for longer time periods). Overall, larval recruitment suffered an 89% decline in 2018 compared to historical levels. Clearly, massive ecological shifts are happening at large scales.

Can deeper coral reefs be refugia?

Mesophotic Coral Ecosystems (MCEs) occur between 30 and 150 m of water, where less light penetrates, often in close proximity to shallow reefs. However, some taxa that occur at shallow water reefs also occur at these deeper reefs. One hypothesis is that MCEs could act as refugia where coral remain unbleached, then reseed the shallower waters after the thermal event. For this hypothesis to hold, MCEs need to have been refugia from thermal stress in the past. Also, if impacted, MCEs should be able to sufficiently recover between events to maintain high coverage and functionality. To explore this hypothesis, a recent study looked at coral coverage and bleaching along with water temperature from 2005-2013 at shallow, upper mesophotic, and lower mesophotic Orbicella spp. reefs in the US Virgin Islands. The authors found that corals in the mesophotic zone have lower bleaching threshold temperatures, suggesting that cooler environments are not  protective. Furthermore, many of the deeper coral that suffered bleaching in the 2005 thermal event had not recovered by 2013. Their results indicate that MCEs will be just as vulnerable as their shallow water counterparts as temperatures rise.

Another study conducted in the western Atlantic (Bermuda and Curaçao) and the Pacific (Philippines and Pohnpei) demonstrated that both coral and their fish assemblages showed high beta diversity with respect to turnover between shallow and mesophotic reefs, illustrating a lack of shared species between sites.  Previous studies may have over-estimated shared species between shallow and deeper reefs because they relied upon historical depth range reports.  Additionally, the authors show that mesophotic reefs often suffer from anthropomorphic and environmental stressors such as hurricane sedimentation, fishing damage, and pollution run-off as much as their shallow water counterparts. Their results provide further evidence that mesophotic reefs are distinct and individual communities and they are likely not a panacea for the rescue of shallow water corals or their associates.

How about creating  “Super Coral”?

Efforts to identify coral either resistant to bleaching or able to fully rebound after a thermal event or both are ongoing globally.  A coral holobiont’s ability to adapt to higher thermal stress is affected by acclimatization to its environment, its host species and its genetic makeup, the type of endosymbiont and its acclimatization, and its microbiome. Many researchers are working on ways to maximize these parameters in laboratory settings to create tolerant “super corals”. For example, a common garden experiment using 800 coral fragments from 80 different colonies of four species was conducted in American Samoa from 2014 to 2017 that happened to coincide with two bleaching events. The best predictors of thermal tolerance were response to experimental heat stress, location on the reef, and thermal microclimate. Also, colony genotype and endosymbiont genus were important in predicting bleaching. The results showed that selecting for both host and endosymbiont resilience led to a multi-species coral stock that withstood two bleaching events.

Breeding and out-planting super coral to mitigate bleaching in the wild is referred to as “assisted evolution”. Adaptation in the wild takes many generations (in most cases) and anthropogenic drivers are outstripping nature’s capacity to evolve higher thermal tolerance.  Identifying resistant colonies in the wild, then bringing them into captivity to protect them and crossing them with other resistant colonies to maximize resiliency of host and symbiont speeds the adaptation process that otherwise could take 1000s of generations. Work continuing in the late Ruth Gate’s lab has involved identifying non-bleached coral neighboring affected colonies off the Hawaiian Islands and bringing segments of those into a controlled laboratory setting to use for cultivation.  The aim is to find optimal rearing conditions, coral genotype(s), and symbiont type(s) that confer increased thermal tolerance to offspring.  Out-planting these “super coral” back into the environment could stabilize vulnerable reefs. 



Eight week time lapse between the left and right photos in French Polynesia, 2019. Photos kindly provided by Dr. Luiz Rocha (@CoralReefFish).

The genotypes mentioned above refer to neutral markers – SNPs or microsatellites or both scattered throughout the genome.  They are molecular tags that identify the more tolerant strains, but are not necessarily directly involved in conferring the thermal/bleaching tolerance. Scientists are obviously interested in knowing which genes are directly involved in the holobionts’ thermal stress response. There have been numerous transcriptome surveys of corals and symbionts that have looked at which genes are up or down regulated as a response to thermal stress and bleaching. Knowing the mechanism and genetic pathways responsible for resistance can guide and quicken the assisted evolution efforts. A recent study employed the genetic editing machinery CRISPR-Cas9 to induce loss-of-function mutations in three genes in the coral Acropora millepora. Mutations were observed in ∼50% of individuals screened, and were maintained through several cell cycles. This proof-of-concept experiment paves the way for engineering coral larvae with optimized sets of gene variants that maximize thermal tolerance.

However, the fact that coral are holobionts adds a level of complexity to considering how best to cultivate resistant corals.  The components of the holobiont interact in complex ways, so finding a host strain that maximizes coral transcripts associated with thermal tolerance, for example, may not pan out when including the genotypic interactions of its entire biological community.  For example, in one study, host corals had more similar transcriptome profiles if they shared the same endosymbiont types than if they shared the same thermal profile.

A potential wrench in the assisted evolution efforts is the decreasing length of time between bleaching events. In 2016, 50% of more susceptible, branching coral species were killed on the GBR. The remarkable aspect of the 2016 event was the instantaneous mortality of the coral.  The expectation after a bleaching event is for the corals to slowly starve to death if temperatures don’t decrease fast enough.  Alarmingly, the instantaneous deaths showed that the corals cooked, preventing acclimatization to new conditions. Should this trend continue, a more effective conservation tactic may be long term laboratory culturing until CO2 levels are brought down and controlled.

How does ocean acidification fit in?

Bleaching affects corals that live in the photic zone – the upper layers of the ocean where light penetrates and fuels photosynthesis.  Below 200 meters is darkness and yet there are vast swaths of deep sea corals world-wide.  In fact, last year an 85-mile long Lophelia pertusa reef was discovered 160 miles off the coast of Charleston, South Carolina, 800 meters below the surface. Cold water coral capture their food from the water column and do not rely on symbionts for fixed carbon so bleaching is not an issue.  Ocean acidification, on the other hand, is a threat to all organisms with calcium carbonate shells (CaCO3) or skeletons (i.e. calcifiers), in shallow and deep water. When CO2 reacts with ocean water it forms carbonic acid, decreasing the amount of carbonate ions available to marine organisms such as bivalves, corals, snails, and many types of plankton. Aragonite saturation state (ΩA) is a common measurement of ocean acidification because aragonite is one of the more soluble types of CaCO3 and used by many marine calcifiers.  The aragonite saturation horizon is where ΩA=1 in the water column and the level of saturation tends to decrease with depth.  A value greater than three is ideal and less than one will dissolve most shells/skeletons. As CO2 gets added to ocean water, the horizon creeps upward.  A NOAA model of past and future aragonite saturation levels predicts that in the year 2100, assuming atmospheric CO2 of 950 ppm (2017’s average was 405 ppm), most of the ocean will be at ΩA between one and two with the polar regions already below one. In fact, negative consequences have already been recorded in the Southern Ocean where researchers recorded extensive dissolution of pteropods as upwelled water came into contact with undersaturated surface water. Though live deep sea corals have been found  at ΩA levels near or below saturation, dissolution of dead coral structures that provide critical settling habitat for coral larvae was documented.  

The situation is dire for corals and those that depend on them.  However, there is controversy concerning how alarmist scientists should be when engaging with the media and public.  With regard to communicating about the growing climate crisis, there seems to be a Catch-22 where optimism breeds complacency or denialism, while alarmism will lead to immediate capitulation with little room for nuance or complexity. To add to the anxiety, sometimes we find ourselves science ambassadors when we least expect it (cocktail parties, Thanksgiving dinners, riding to the airport) and can feel ill-equipped. I hope this collation of recent work on the front line of climate change and its effect on coral reefs leaves you with a healthy dose of alarmism with a dollop of hope.  Substantial global effort is going into conservation of susceptible coral species and while the work is innovative, important, and necessary, there is strong scientific consensus that drastically decreasing global atmospheric CO2 emissions is by far the most effective way to save these ecosystems.

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