Coral Reef Bleaching: An Ecological and Biological Overview Coral Reef Bleaching: An Ecological and Biological Overview

Coral reefs are central to the biology of our planet, but in the past few decades, they have suffered a severe decline due to a variety of natural and anthropogenic disturbances. On a worldwide scale, the main disturbance is bleaching, which can be defined as the loss of endosymbiotic dinoflagellates and/or of their photosynthetic pigments from their cnidar ‐ ian host; with that, the normal pigmentation of the tissue of cnidarians is generally lost and the white calcium carbonate skeleton becomes visible through the transparent tissue of the host. Coral bleaching can be triggered by multiple factors, but most of the bleach ‐ ing observed in the field is a result of elevated sea surface temperature. It has been widely documented that bleaching is deleterious to coral reefs, significantly altering the biologi ‐ cal and ecological processes that maintain reef communities; yet populations resistant to climate change have recently been identified, and it has been reported that acclima ‐ tization occurs in less than two years. The aim of this review is to provide up‐to‐date information regarding cnidarian‐dinoflagellate symbiosis; causes of coral bleaching; mechanisms underlying this phenomenon; consequences of bleaching; and the survival mechanisms by which coral reefs face this threat.


Introduction
Despite occupying only 0.1% of the ocean, coral reefs play a critical role in marine ecology, and in human sustainability, they are invaluable from a variety of perspectives. They are home to more than a quarter of all the species that inhabit the ocean, provide coastal protection, and support more than 10 millions of people living on tropical coasts [1,2]. Economic goods and ecosystem services of coral reefs are worth more than US $20 trillion annually [3].
Coral reefs are central to the biology of our planet; in terms of biodiversity, they are the most rich, complex, and productive marine ecosystem on Earth. It has been estimated that over 90% of the species inhabiting coral reefs have yet to be described [4]. Therefore, it is not surprising that the organisms that constitute these ecosystems produce a great variety of molecules with unique structural characteristics that exhibit numerous biological activities [5], and are considered a rich source of novel bioactive agents with great pharmaceutical and biotechnological potential [6].
Unfortunately, coral reefs are extremely susceptible to the stress related to greenhouse gas emissions, particularly ocean warming and acidification [7][8][9][10], which provoke disturbances that can seriously affect and break down the homeostatic capacity of coral reefs to overcome stressors [11]. One of these disturbances is the event called "bleaching," in which the tissues of corals and hydrocorals lose their photosynthetic endosymbiotic zooxanthellae (dinoflagellate algae of the genus Symbiodinium) or their pigments, which exposes the white exoskeleton of calcium carbonate [12][13][14].
Numerous studies have shown that bleaching is harmful to coral reefs, since it significantly alters the biological and ecological processes that maintain equilibrium in the reef communities. Bleaching episodes have resulted in massive damage to coral reefs around the world, with serious effects on the maintenance of biodiversity in the marine tropics. Bleaching is also responsible for other declines in reef health, such as the increase in coral diseases, declines in reef calcification, the breakdown of reef framework by bioeroders, and the loss of critical habitat for associated reef organisms [15][16][17][18]. Climate models predict that, if CO 2 emissions continue to rise at the current rate, bleaching events will increase in frequency and severity, threatening the survival of coral reefs. Actually, it has been projected that 90% of coral reefs around the world will be at risk if bleaching events occur annually [15,16,19].
The US National Oceanic and Atmospheric Administration (NOAA) coral reef watch, the Global Coral Reef Monitoring Network (GCRMN), as well as other environmental agencies around the world have been monitoring mass coral bleaching events for more than a decade, in order to understand conditions that cause bleaching and to develop measures to rehabilitate reefs [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20]. On the other hand, academic researchers have addressed the study of this phenomenon employing different approaches, including genomics, transcriptomics, and proteomics to better comprehend the molecular mechanisms that provoke it, its consequences, and the potential adaptive response of cnidarians to this condition [21][22][23][24][25][26][27][28][29]. Undoubtedly, bleaching represents an enormous threat to the survival of coral reefs, as bleached organisms display an increased susceptibility to pathogens, a decreased resistance to predators and bioeroders, declines in reef calcification, depressed growth and reproduction rates, and a lessening of ability to repair damages [15][16][17][18]. In this context, the purpose of this review is to provide updated information regarding cnidarian-dinoflagellate symbiosis; causes and consequences of coral bleaching; the molecular processes underlying this phenomenon; and the survival mechanisms by which coral reefs face this threat.

Search strategy
The literature consulted corresponds to the main reviews and articles explaining the phenomenon of bleaching, which contributes to the understanding of the relationship between the causes, mechanisms, and consequences of bleaching.

Cnidarian-dinoflagellate symbiosis
An important feature of coral reef ecosystems is that most of the 798 reef-forming species have developed a mutualistic symbiosis with unicellular dinoflagellate algae of the genus Symbiodinium, commonly referred to as zooxanthellae (Figure 1). This symbiosis is essential in the formation of large and important structures in coral reefs [30]. The genus Symbiodinium encompasses nine major clades (A to I), most of which were identified based on the ribosomal DNA small subunit [31]. These tiny organisms (8-10 μm in diameter) live within cnidarian cells, inside a host-derived vacuole (symbiosome) located within the gastrodermal cell layer. Under normal conditions, the population density of symbionts ranges from 0.5 to 5 × 10 6 cells per cm 2 of coral surface, although the limits of this range may vary [30,32]. Regulation of symbiont density involves different mechanisms, such as limiting the nutrients delivered from corals to symbionts, digesting photosynthetic algae, expulsing excess symbionts, rearranging excess symbionts into new coral cells, and producing growth inhibition factors [30,[33][34][35].
Symbiodinium algae carry out photosynthesis, but instead of retaining the sugars and amino acids that result from this activity for their own growth and reproduction, they deliver more than 95% of their photosynthetic production to their host. In return, Symbiodinium has direct access to the waste products of coral metabolism, such as carbon dioxide, which is used in photosynthesis. The recycling of nutrients between coral host and its endosymbionts is extremely efficient and allows them to live in nutrient-poor waters [30,35,36]. Endosymbionts translocate molecular oxygen to their hosts and most of their photosynthetically-fixed carbon in the form of glycerol, glucose, amino acids, and lipids. Moreover, the oxygen produced during photosynthesis helps maintain the high levels of ATP required for the calcification process [30]. In exchange, cnidarians afford inorganic nitrogen, phosphorus, and carbon, as well as a lighted environment that provides refuge from herbivores (Figure 1) [36,37]. Signaling molecules regulating host-symbiont interaction have not been fully characterized. It has been suggested that translocation of photosynthetic products may be controlled by host release factors (HRFs) [30,36], some of which are of proteinaceous nature (approximately 10 KDa) [38], although free amino acids and mycosporine-like amino acids have been found to induce the release of photosynthetically fixed carbon [39,40].
Another important characteristic of reef-forming cnidarians is their capacity to produce calcified skeletons. Calcification is a crucial process for building the largest biological structures in the world [38,41]. Despite its importance, the mechanism of calcification, or, more broadly, biomineralization, is little known. The coral exoskeleton is made of aragonite, a crystalline form of calcium carbonate (CaCO 3 ), and it is completely covered by a thin single layer of epithelial cells called calicoblastic epithelium (calicodermis). These cells play an important role in coral calcification, controlling the ionic composition of the medium in which calcification occurs (extracellular calcifying medium, ECM) [38,41,42].
Two hypotheses have been proposed to explain the stimulation of calcification by the presence of dinoflagellate symbionts [38]. One of them considers that absorption of CO 2 and release of O 2 by the symbionts [43] indirectly alter the pH and/or modify inorganic calcium concentration inside the gastrovascular cavity of the cnidarian, which leads to calcification by the precipitation of CaCO 3 [44]. The other hypothesis states that symbiotic algae produce organic molecules, such as nitrogenous compounds, glucose, and glycerol, that carry out the following functions: provide energy for calcification, modify the buffering capacity of the ECM, or are precursors for organic matrix synthesis [38,45].
Colonies of reef-building cnidarians exhibit a great variety of colors due to the different types and concentrations of pigments conferred by the presence of the millions of symbionts found per square centimeter in their tissues [46]. Symbionts can be acquired by either vertical or horizontal transmission. Vertical transmission occurs when symbionts are transferred from parents to offspring through direct inheritance. On the other hand, horizontally transmitted symbionts are acquired from the environment, such is the case of 80% of scleractinian symbiotic corals, whose larvae acquire their symbionts during a nutritional process [47][48][49][50]. The process of the establishment and maintenance of symbiosis comprises six phases: (i) initial contact; (ii) immersion of the symbiont; (iii) dynamic intracellular sorting of the symbionts; (iv) proliferation of symbionts in gastrodermal cells; (v) stabilization dynamics; and (vi) symbiosis dysfunction and breakdown [38]. According to some authors, the recognition of symbionts works in the same way as the recognition of pathogens, i.e., it involves pattern recognition receptors (PRRs) that are able to recognize and bind to specific conserved components of the cell walls of the algae (carbohydrates, lipids, and proteins) [51][52][53].
During their life cycle, Symbiodinium cells interchange between a vegetative cyst, which is the dominant form in the endosymbiotic state, and a motile zoospore that possesses thecal plates and two flagella, one transverse and one longitudinal [54]. The current hypothesis about the establishment of symbiosis between host cnidarians and Symbiodinium states that in the first phase, lectins, secreted by the host cell, induce symbionts to progress to cyst stage [30,53]. Subsequently, lectins on the host cell surface attach to glycoproteins present on the surface of non-motile Symbiodinium cysts, which are subsequently phagocytized and carried into an early endocytic compartment by Rab5 proteins. Afterward, cells that were successfully recognized end up in a symbiosome, whereas damaged symbionts are digested by fusion with lysosomes after transiting through the late endocytic compartment. This traffic takes place through Rab7 and Rab11 proteins [30]. The relationship between cnidarians and symbiotic algae is regulated by environmental and physiological conditions of the host [30,55].
It is clearly evident that establishment and maintenance of cnidarian-Symbiodinium symbiosis are critical to preserve homeostasis in coral reef ecosystems. On one side, algal symbionts obtain from their hosts protection and inorganic compounds, which are essential for their metabolism. On the other hand, cnidarians receive from their symbionts a great percentage of their energy demand and a balanced pH and precursor molecules needed for the calcification process. Undoubtedly, disruption of this symbiotic relationship can trigger numerous adverse effects, not only for the reef-forming organisms, but also for the great variety of organisms that depend on coral reefs.

Coral bleaching: causes and global episodes
Bleaching has been described as a visual effect of the stress that occurs when the symbiosis between reef-forming cnidarians and their symbiotic algae breaks down (Figure 2). It comprises the loss of pigmentation in coral reefs due to decreased Symbiodinium population, reduction in the concentration of their photosynthetic pigments, or both [12,17,56,57]. Up to now, at least four general cellular mechanisms of algal loss have been proposed: in situ degradation, symbiont (intact or degraded) expulsion, host-cell detachment, and host-cell death [58,59].
It has been widely documented that several factors can induce coral bleaching, including reduced salinity [60]; amplified or reduced solar irradiation [61][62][63][64]; elevated [62,65] or low water temperature [66,67]; and the presence of chemical contaminants in the sea water, such as herbicides, pesticides, and cyanide [68]. However, field and laboratory investigations have indicated that elevated temperature is the principal cause of bleaching. Some of these studies are listed below.
(a) Hoegh-Guldberg and Smith (1989) studied the conditions required to achieve experimental bleaching of Stylophora pistillata and Seriatopora hystrix; they found that exposing fragments of these species to 32°C for 7 h caused a rate of expulsion of zooxanthellae 1000 times greater than in the control, which was kept at 27°C [62].
(c) Lesser et al. (1990) showed that increases in temperature significantly reduced the total number of zooxanthellae per polyp of the class Anthozoa. At the same time, temperature, solar radiation, and ultraviolet radiation independently increased the activities of superoxide dismutase (SOD), catalase, peroxidase, and ascorbate in the symbionts of Palythoa caribaeorum [69].  (e) Eakin et al. (2005) reported that the most serious bleaching event that affected Caribbean and Atlantic coral reefs happened in 2005, the warmest year ever documented in the Northern Hemisphere. Whitening of coral reefs provoked mortality of living reef-forming organisms by up to 40% [71].
Among the other environmental factors that can cause bleaching, besides thermal stress, solar radiation [17] has the most significant influence. This stressor can act independently of, or synergistically with, elevated sea water temperature [14,72]. Fitt and Warner (1995) found a substantial reduction in symbiont photosynthesis in the coral Montastraea annularis after exposure to ultraviolet and blue light [73], whereas Gleason and Wellington (1993) demonstrated that bleaching occurred more readily when corals were exposed to high energy, short wavelength solar radiation [61]. Other studies have confirmed that exposure to high temperature and ultraviolet light exacerbates the stress on the symbiont population, contributing to bleaching [74,75]. Along with increased temperature and high irradiance, elevated atmospheric CO 2 concentration is also affecting coral reefs by lowering ocean pH levels, which decreases calcification, increasing the rates of erosion that exceed the capacity for accretion of the reefs in tropical and subtropical zones [76][77][78].
Bleaching of coral reefs was first recorded in the 1870s [79,80], and since 1980, coral reef bleaching and mortality episodes linked to elevated temperatures have been monitored. Ever since 1979, nine major coral bleaching episodes have affected coral reefs around the world, with an alarming rise in scale and frequency. At first, the phenomenon was regarded as linked to El Niño Southern Oscillation (ENSO) events [77,81], which caused a high mortality in colonies of Millepora platyphylla in the Eastern Pacific coral reefs. However, since the early 1990s, it is known that bleaching is correlated in near real time with anomalously high satellite-derived sea surface temperature (SST) [81]. This relationship was clearly observed in the Caribbean basin during the 1980s and 1990s, when annual coral bleaching increased logarithmically with SST anomalies [82]. A minimal rise of only 0.1°C in regional SSTs caused a 35% increase in the extent and intensity of bleaching, while when SST was increased by 0.2°C and above, massive bleaching events took place [15].
The GCRMN (with support from more than 30 countries, the IOC-UNESCO, UNEP, IUCN, and the World Bank) has provided annual reports on the state of coral reefs. The report from 1997 to 1998 indicated the occurrence of an unprecedented global episode of mass coral bleaching. Before 1998, GCRMN surveys reported a 9.5% loss of corals in six regions. During 1998, one of the hottest years on record, these regions lost an average of 17.7% of their live reef-building corals [83]. The 1998 record was surpassed in 2005 and again in 2010 [71,84]. However, 2014 [71,85] and 2015 were considered the hottest years ever recorded, and 2016 continued this tendency, which has led to the longest and most damaging global coral bleaching event officially documented [86].
A summary of the major bleaching events reported since the 1980 is shown in Table 1.
Unfortunately, anthropogenic activities that affect environment have provoked that coral bleaching events increase in frequency and severity, which represents a very serious threat to coral reefs worldwide. Reef-forming organisms have survived to mass extinction events in the past; however, it is unknown if they will be able to adapt fast enough to cope with rapid environmental change.

Molecular mechanisms underlying bleaching
It has been shown that, under elevated sea water temperatures and high solar radiation, Symbiodinium photosynthesis leads to intense oxidative stress in the two partners of the mutualistic symbiosis between reef-forming cnidarians and dinoflagellate endosymbionts [35,87]. Oxidative stress involves the production and accumulation of reactive oxygen species (ROS), which can damage lipids, proteins, carbohydrates, and DNA [7,52]. ROS play a key role in signal transduction of cell damage mediators and in processes such as apoptosis, autophagy, and necrosis [35,88,89] intensity and duration [17,35]. Moreover, it has been proposed that bleaching itself is a control mechanism to minimize the harmful effects caused by the metabolic imbalance in cnidarian-algal symbiosis [56].
Photosynthetic damage in Symbiodinium spp. has been proven using non-invasive chlorophyll fluorescence techniques, which demonstrated a significant loss of PSII photochemical efficiency during bleaching [70,92,93]. Elevated temperatures and high radiation cause photoinhibition and damage to the chloroplasts and the photosynthetic apparatus of the symbionts, through at least three pathways: • Damage to the D1 protein, a core component of PSII, which is involved in the photolysis of water. This hypothesis proposes that, under stress conditions, the CO 2 fixation is limited and the electrons of PSI are transferred to O 2 . This results in the formation of superoxide, which is quickly converted into H 2 O 2 by superoxide dismutase (SOD). H 2 O 2 hinders the repair of PSII by impairing the synthesis of the precursor D1 protein (pre-D1) [91]. During bleaching, the rate of photoinhibition and damage of D1 protein exceeds the rate of the PSII repair cycle [87].
• Inactivation of ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco), one of the key enzymes of the Calvin-Benzon cycle [94]. This mechanism was proposed when Bhagooli (2013) found that inhibition of the Calvin-Benson cycle by glycolaldehyde induced photoinhibition and coral bleaching, even at optimal temperatures [95].
• Injury of the thylakoidal membranes by ROS, which elicits an energy decoupling of the electron transport in both PSI and PSII, resulting in diminished ATP and NADP production [52]. The excess electrons reduce oxygen instead of NADPH with the subsequent generation of superoxide ion, which is reduced by SOD to H 2 O 2 . This last molecule reacts with ferrous ion and yields, the even more reactive, hydroxyl radical. Furthermore, excess electrons can react with photosynthetic pigments and molecular oxygen to produce atomic highly reactive oxygen. All the above-mentioned ROS spread to the host tissues triggering innate immunity, via the transcription factor NF-kB, leading to apoptosis [52]. Activation of NF-κB also induces iNOS expression, increasing the levels of nitric oxide, which reacts with superoxide ion to form peroxynitrite (ONOO-). This anion is highly reactive and damages the mitochondrial membrane, which releases pro-apoptotic molecules, such as AIF, promoting apoptosis (Figure 3) [96].
Another hypothesis to explain the molecular events that lead to bleaching proposes disruption to the carbon-concentrating mechanisms of the coral host. According to this hypothesis, bleaching is initiated by the inability of the coral to efficiently supply its symbionts with CO 2 , mainly in periods of high solar radiation, when the algal CO 2 demand is very high. The lack of CO 2 needed for "dark reactions" reduces consumption of ATP and NADPH, blocking electron transport components. Sustained concentration of light excitation energy into the over-reduced electron transport chain triggers photoinhibition, damage to the photosynthetic components (mainly PSII), and ROS generation [97]. Excessive ROS production stimulates antioxidant defenses in the cnidarians and their symbionts, and it is also related to the exit of photosynthetic algae [98]. Moreover, bleaching can be caused by damage to "dark reactions" in the absence of thermal stress [99].
On the other hand, proteomic approaches have been applied to assess the effect of post-translational environmental stress on marine organisms [29. A recent study carried out on Acropora palmata showed that bleaching induced a differential protein expression response in this cnidarian. Thirty-eight key proteins were differentially expressed, primarily transcription factors involved in heat stress/UV responses, immunity, apoptosis, biomineralization, the cytoskeletal organization, and endo-exophagocytosis [24].
It is evident that up to now, the studies of climate-related stress on coral reefs have indicated that bleaching does not result from a single process, but rather from a complex interaction of environmental and genetic factors, operating at several levels within the reef-forming holobionts [99,102,103], which highlights the need for further detailed investigations directed toward a better understanding of the mechanisms underlying bleaching.

Mechanisms by which cnidarians face bleaching
Coral bleaching events have increased in frequency and intensity. Actually, some studies project that if this trend continues, tropical coral reefs might disappear this century [104,105].
Mass coral bleaching and mortality events that have been registered worldwide over the past three decades have raised serious concerns about the future of coral reef ecosystems [77,106]. Ecological extinction of corals reefs in some regions has been predicted to occur within the next 20-50 years, if reef-forming cnidarians are unable to adapt sufficiently rapidly to keep pace with global warming [107].
The ability to recover from a bleaching event has been associated with the energy reserves and heterotrophic feeding capacity of the cnidarian host [16,108,109]. Symbiodinium can provide up to 100% of a healthy coral's daily fixed carbon requirements; however, following bleaching, recovering corals may heavily rely on alternate sources of fixed carbon, which is acquired via catabolism of energy reserves and/or by increased heterotrophy [16,110,111].
Some evidences suggest that cnidarians are able to deal with thermal stress, through a series of adaptive processes (e.g., acclimatization, genetic adaptation, and symbiont shuffling), which may help reduce the harmful consequences and mortality provoked by bleaching [112,113].
Acclimatization or acclimation is a type of phenotypic plasticity in which organisms, such as corals and their symbionts, can optimize their physiological performance in response to environmental changes [114]. The capacity for acclimation and adaptation of cnidarians and Symbiodinium clades is currently poorly known. Differentially expressed genes in Acropora hyacinthus, under physiological and stress conditions, suggested that the acclimatization that occurs less than 2 years after exposure to thermal stress is the same as that might have been expected from natural selection over many generations. Incorporating these adaptive capacities to ecosystem models will likely reduce the predictions of the disappearance of coral reef ecosystems [115].
Some studies have determined the existence of coral species that have survived high temperatures, indicating that they have higher thermal tolerance thresholds than others. Resistant species belong to the genera Cyphastrea, Goniopora, Galaxea, and Pavona, whereas species of the genera Stylophora, Pocillopora, and Acropora are more vulnerable to thermal stress [59]. In the case of Symbiodinium algae, some clades have been recognized as being more resistant than others. A study carried out on the major reef-building species in the Caribbean showed that Symbiodinium algae of the clade D display a significant thermal tolerance [116]. This was confirmed in a further study on Orbicella faveolata that demonstrated that under nonstressful conditions, thermally sensitive Symbiodinium of the clades B17 and C7 are prevalent, whereas after a bleaching event, clades D1 and A3 proliferated and repopulated cnidarian tissues previously evacuated by clades B17 and C7 [117].
Various mechanisms have been proposed to explain adaptive capacity of cnidarian species to face heat and radiation stress [7]. One of them involves photoprotection provided by pigments within the host tissues. Evidences supporting this proposal were obtained from a study of the coral Montipora monasteriata, which was selected since it occurs in multiple color morphs (tan, blue, brown, green, and red). That study demonstrated that two of the non-fluorescent host pigments (CP-420 and CP-580) are up-regulated in response to elevated irradiance. This behavior appeared to favor retention of antennal chlorophyll by endosymbionts and therefore, photosynthetic capacity. It was found that up-regulated host pigments can facilitate the establishment of new or restructured dinoflagellate chloroplasts by modifying the internal light field. Particularly, high concentrations of CP-420 provided photoprotection for Symbiodinium by intercepting photons destined for photochemical quenching by dinoflagellate algae [118].
Another adaptive process entails non-photochemical quenching (NPQ) that dissipates excess light as heat. Reef corals produce fluorescent pigments belonging to a family related to green fluorescent proteins, which through the absorption, scattering, and dissipation of high-energy solar radiation by fluorescence reduce photoinhibition and the severity of bleaching [113]. Some of these sunscreen compounds are mycosporine-like amino acids, such as shinorine. This pigment showed no detectable fluorescence when excited at a frequency of 312-348 nm, which corresponds to the band of its mean-maximum absorption. Furthermore, electron paramagnetic resonance spectroscopy (EPR) revealed that purified shinorine (50 μM) produced no detectable radicals when irradiated with 305-700 nm. The lack of free radical formation by UV irradiation and the lack of fluorescence are consistent with the high efficiency dissipation of thermally absorbed UV energy [113,119].
A well-known biochemical adaptation to thermal stress is the heat-shock response (HSR), which comprises the induced expression of a conserved set of molecular chaperones, known as heat-shock proteins. These molecules are critical for protein homeostasis, defense mechanisms, the refolding of denatured proteins, and the breakdown and replacement of nonreplaceable proteins [120].
An additional adaptive response implies increased expression of enzymes that sequester oxygen radicals. The use of recent molecular techniques has improved our understanding of the magnitude of the transcriptional response of corals to various stressors, including high temperatures. An analysis carried out on Acropora millepora indicated that thermally stressed samples experienced a significant overexpression of four genes associated to cnidarian oxidative stress responses (HSP70, MnSOD, ferritin, and Zn 2+ -metalloprotease) [121].
A caspase-mediated apoptotic cascade, caused by reactive oxygen species mainly generated by the algal symbionts, is a well-known factor that triggers bleaching and death of the host cnidarian. It has been shown that under high temperatures, some corals are able to naturally suppress caspase activity and significantly reduce caspase concentration as a mechanism to avoid colony death from apoptosis. It has been hypothesized that variability in response to thermal stress is determined by a four-element, combinatorial genetic matrix intrinsic to the specific symbiotic association [109].
On the other hand, symbiont shuffling and/or switching are considered other important mechanisms for explaining the way coral reef communities can counter environmental stress conditions. In some cases, the distribution of certain clades of Symbiodinium can substantially change after bleaching, via shuffling (a shift in symbiont dominance) or by symbiont switching (algae are acquired from exogenous sources). A case study was performed on Stylophora pistillata that belonged to a coral reef that had suffered bleaching in March 2006. The objective of the study was to determine the percentages of different Symbiodinium clades populating the host after bleaching, and after the coral recovered from the event. Samples were collected in November 2006 and July 2007, and the results indicated the initial presence of clades C79, C78, C8/a, and C35/a, the last two in greater proportion. However, once the coral recovered from bleaching and repopulated, the proportions of C79, C35/a, and C78 decreased, while the population of C8/a increased considerably. Furthermore, other more resistant Symbiodinium clades appeared [122].
It is worth mentioning that studies directed toward understanding the causes and effects of bleaching, as well as the tolerance mechanisms that counteract this phenomenon have focused on Anthozoa species, showing that bleaching affects various processes that are essential to the survival of cnidarians. However, an integrative analysis is still needed to understand the molecular mechanisms underlying the different responses (adaptation or death) of cnidarians to coral bleaching.

Consequences of bleaching in coral reefs ecology
Undoubtedly, the bleaching phenomenon has seriously affected corals reefs. Although it has been observed that some reef-building cnidarians that suffer the loss of their symbiotic algae can, in some cases, survive and recover [90], bleaching can also lead to massive death [79,104,123], inflicting an enormous damage to the ecological balance of entire reef communities.
Coral reef monitoring programs exist in all regions of the world, recording reef features such as coral cover, fish biomass, and macroalgal cover, among others. However, at present the way of interpreting coral reef monitoring data has not been globally standardized, which hampers decision making directed toward protecting and rehabilitating coral reefs [124].
Several aspects regarding coral resistance and resilience are still unclear. For example, it is uncertain which Symbiodinium clades remain fairly viable following a stressful event and if they are able to significantly contribute to the recovery of bleached corals [30]. In this regard, some researchers reported that a majority of the expelled symbionts remained healthy, whereas others claimed that the survival of Symbiodinium did not last; some Symbiodinium cells, released into the water column after a thermal stress, had a drastically reduced photosynthetic activity after 5 days, suggesting that their survival could be compromised. Therefore, their contribution to the free-living stocks may be limited [125].
At present, coral resilience ability is the object of various research projects, since it has been widely documented that many corals that apparently recover from a bleaching event display a decrease in growth rate and calcification [114,126], and are more susceptible to disease [127,128], which is not surprising, since their supply of energy available for fundamental processes is diminished.
Gene expression biomarkers are emerging as powerful diagnosis tools for identifying and characterizing coral stress. Among the most plausible candidates are genes related to expression of heat-shock proteins, immune and oxidative stress responses, some metabolic processes, and structural genes. Other genes, such as hsp16, Cacna1, MnSOD, SLC26, and Nf-kB, are showing excellent potential as reliable indicators of thermal stress in corals [107].
The impact on the reduction of the biodiversity of corals has not been fully envisaged. However, it is predicted that if reef-forming cnidarians do not evolve rapidly toward thermal tolerance, they will no longer dominate the reefs in the coming years [129,130]. A possible scenario, according to some ecology specialists, is that if global warming continues at the present rate, a phase shift in coral reefs to an alternate state dominated by a different kind of organisms might occur [131,132]. This alternate state might represent a substantial degradation of the coral reefs. Furthermore, degraded states can also be resilient to change, which complicates their possible reversal [11,105].

Concluding remarks
Mass coral bleaching and mortality events that have been registered worldwide over the past three decades have raised serious concerns about the future of coral reef ecosystems. In fact, ecological extinction of corals reefs in some regions has been predicted to occur within the next 20-50 years, if reef-forming cnidarians are unable to adapt sufficiently rapidly to keep pace with global warming [104,117,133].
It is clear that the survival of coral reefs strongly depends on the functionality of the symbiosis between cnidarians and Symbiodinium algae, and up to now, we are just beginning to understand the molecular and cellular mechanisms underlying this relationship. Omics approaches have enabled a better comprehension about the way cnidarian-algal symbiosis functions and how holobiont physiology is modified by bleaching. Studies of the effects of global warming and coral bleaching have indicated that this event is the result of a complex interaction of environmental and genetic factors. Investigations of coral bleaching have also provided important insight into the mechanisms responsible for coral resistance to thermal stress.
It is evident that the key to understanding the future of coral reefs requires an insightful comprehension of the molecular and physiological mechanisms that promote thermal tolerance in the cnidarians and their symbionts, and to identify the genetic characteristics responsible for the variety of responses that occur in a coral bleaching event. Therefore, it is very important to continue studies in this regard to better understand cnidarian-Symbiodinium symbiosis, causes and effects of bleaching, the survival mechanisms of hosts and symbionts, as well as their ecological importance. Surely, the results derived from these studies will be useful to design strategies and policies to restore coral reefs and to promote their conservation.