Climate-induced changes in temperature are a major threat to coral reef ecosystems, and extensive research has highlighted several key areas for investigation [53,205], with marine heatwaves, solar radiation, heat tolerance, and thermal thresholds representing the most promising areas for future research. Marine heat waves have become increasingly prevalent and intense as a result of climate change. These extreme events, characterized by prolonged periods of elevated water temperatures, significantly impact coral reef ecosystems. For instance, the mass global coral bleaching event of 2016–2017 was the most extensive and long lasting on record, as documented by Eakin et al. [206]. The event, which was associated with the El Niño Southern Oscillation (ENSO), had varying impacts on coral reefs worldwide [207], with some regions experiencing more severe bleaching than others, as reported by Kim et al. [208].

Corals are thermophilic, but their thermal tolerance is narrowly defined [169,209]. For instance, the rate of calcification increases with temperature up to a threshold level, beyond which it declines [210,211,212]. Tropical corals live close to their upper thermal limits and are, therefore, highly sensitive to periods of elevated sea surface temperatures and ocean warming [187,213]. Coral reefs in the Persian Gulf have been observed to have the highest upper-temperature thresholds of approximately 35–36 °C [214]. However, it has also been noted that these corals remain highly vulnerable to thermal stress when temperatures surpass their local maximum summer temperatures [215]. The escalating frequency and gravity of thermally induced mass bleaching events have sparked worldwide attention to the elevated temperature impacts on corals [28]. As a result, research endeavors have focused on establishing maximum thermal tolerance thresholds and variations in diverse coral species and regions and exploring potential coral refugia to brace for future ocean warming [216].

Corals rely on their symbiotic relationship with unicellular algae of the genus Symbiodinium for photosynthesis, and over 90% of their energy budget is needed for essential functions, such as calcification, tissue growth, and reproduction [212]. This critical association is threatened when corals experience thermal stress, such as elevated sea surface temperatures (SST), resulting in coral bleaching, where the algal endosymbionts are expelled. The resulting impairment and expulsion of the algal symbionts are linked to reactive oxygen species (ROS) generation from the host, the algal symbiont, or both, triggering a host immune response [217].

Protracted coral bleaching can lead to extensive coral mortality, severely affecting the ecosystem and associated reef fauna. Based on the timeline cocitation analysis, it was evident that the Red Sea (Cluster #3) and Great Barrier Reef (GBR) (cluster #8) are major research hotspots in terms of geographic regions. Although the Persian Gulf is a hot sea that supports coral reef ecosystems, the Red Sea harbors corals with greater thermal stress tolerance, with some coral genotypes capable of surviving temperatures over 5 °C above their summer maxima [216,218]. Corals in the southern end of the Red Sea are more heat resistant, surviving prolonged high temperatures, while the northern Red Sea benefits from heat-resistant genotypes that have migrated from the south [219]. The importance of broad latitudinal temperature gradients in promoting adaptation to high temperatures and exchanging heat-resistant genotypes across latitudes for genetic rescue in coral reefs is exemplified in the evolutionary history of coral reefs in the northern Red Sea [9,216]. On the other hand, the GBR, known as the world’s largest coral ecosystem, was severely impacted by the 2015–2016 climate change-amplified strong El Niño event that triggered the warmest temperatures on record. This resulted in a massive bleaching event affecting nearly 90% of reefs along the northern region, leading to a loss of approximately 30% of live coral cover in the following six months [28,220,221]. Research has increasingly linked climate change to a rise in coral diseases. Bruno et al. [222] used a high-resolution satellite dataset to investigate the relationship between temperature anomalies and coral disease on a large spatial scale of 1500 km in Australia’s Great Barrier Reef. Their findings showed a significant positive correlation between warm temperature anomalies and the incidence of the white syndrome, an emergent disease in Pacific reef-building corals. In a similar vein, Tignat-Perrier et al. [223] noted a decline in populations of two gorgonian species (Paramuricea clavata and Eunicella cavolini) found in the Mediterranean Sea due to the fact of microbial diseases during thermal stress events. These studies illustrate the growing concern that climate change is contributing to the increased incidence and severity of coral diseases, which could ultimately lead to a decline in the health of marine ecosystems.

In the past, studies on the impact of climate change on coral reefs primarily centered on the thermal tolerance of corals and the consequences of massive, abrupt coral loss on organisms associated with reefs [224]. However, research has recently shifted towards investigating the distinct and synergistic effects of ocean warming and ocean acidification resulting from increased atmospheric CO₂ levels. The timeline co-citation analysis reveals that these emerging research fields are highly significant with recent citation bursts, as evidenced by their identification as Cluster #2 (Ocean acidification) and Cluster #10 (Elevated CO₂), respectively.

The escalation of atmospheric carbon dioxide (CO₂) concentrations has resulted in ocean acidification, which is among the foremost threats to coral reef ecosystems. Forecasts for 2100 anticipate a rise in CO₂ concentrations to between 540 and 970 ppm, leading to a global decrease in seawater pH by 0.14 to 0.35 units [31,68,116,225]. As demonstrated by Fabricius et al. [68], ecological traits of coral reefs will gradually transform as seawater pH decreases to 7.8, and a decline below this level (at 750 ppm pCO₂) would be catastrophic for these ecosystems. Ocean acidification reduces the availability of carbonate ions that corals require to form their calcium carbonate skeletons, ultimately leading to a decrease in coral calcification rates [33]. Ocean acidification has also been shown to decrease the ability of coral larvae to settle and survive [226] and increase their susceptibility to disease [227]. Research has shown that even modest increases in ocean acidity can impact the physiological processes of corals. For example, exposure to high levels of CO₂ reduces coral growth and calcification rates [68,226]. In addition to the direct effects on coral physiology, ocean acidification can have cascading impacts on the entire coral reef ecosystem. For instance, reduced calcification by corals can reduce the complexity of the coral reef structure, potentially leading to the loss of important habitats for fish and other marine organisms [228]. Furthermore, ocean acidification can impact the symbiotic relationship between corals and their algal symbionts, potentially leading to a decline in the productivity of the reef ecosystem as a whole [229]. The combination of ocean warming and acidification is particularly concerning, as they act synergistically to exacerbate the negative impacts on coral reef ecosystems [22]. With continuing increases in atmospheric CO₂ levels, the effects of ocean acidification on coral reefs are expected to become even more pronounced, highlighting the need for urgent action to reduce greenhouse gas emissions and protect these valuable and vulnerable ecosystems.

The rate of atmospheric CO₂ increase continues to accelerate, with emission scenarios predicting CO₂ concentrations of 540–970 ppm and a decline in seawater pH by 0.14–0.35 units globally for 2100 [68,225]. Fabricius et al. [68] demonstrated that many ecological properties in coral reefs will gradually change as pH declines to 7.8 and that it would be catastrophic for coral reefs if seawater pH dropped below 7.8 (at 750 ppm pCO₂).

Coral resistance and resilience are scientific constructs that pertain to the capacity of coral reefs to withstand and recuperate from various stressors. Coral resistance is defined as the ability of corals to endure or tolerate perturbations and stressors, such as variations in water temperature, ocean acidification, pollution, and physical injury. Corals that possess a greater resistance to these stressors exhibit a greater ability to sustain their structure and function despite disturbances and are less prone to suffering from coral bleaching, disease, or mortality [229,230]. A myriad of studies has reported on the bleaching thresholds of corals inhabiting the Persian Gulf, despite conditions at least 2 °C higher than other coral reef ecosystems worldwide [231]. Additionally, corals from the Indo-Pacific and Caribbean regions have been found to maintain calcification rates even in low aragonite saturation states, present in naturally acidified locales [68,232]. The eastern Pacific region of Palau has revealed the thriving of reefs in waters with natural acidification, resulting from biological processes and reef system circulation patterns [232,233]. However, it is noteworthy that coral communities in Palau’s relatively acidic reef zones developed over thousands of years, fostering an inherent resistance that differs from coral communities in regions affected by higher anthropogenic interventions.

Coral resilience, in contrast, refers to the ability of coral reefs to recover from disturbances and stressors. Corals that exhibit higher resilience can reproduce, regenerate, and rebuild their structural complexity after experiencing bleaching [234]. These mechanisms are attributable to genetic diversity within coral populations and their symbiotic association with Symbiodinium algae, which are critical to their health and survival [235,236]. Genetic adaptation in corals is mediated through various factors, including the activation of heat-shock proteins, oxidoreductase enzymes, and microsporine-like amino acids. The coral surface micro-layer that absorbs UV radiation has also been identified as a significant mechanism for adaptation [180,237,238]. In-depth research on corals that thrive in the warm waters of the Persian Gulf has demonstrated their capacity for resilience, attributable to metabolic trade-offs, unique physiological characteristics, and specific genetic signatures, including a heat-specialist algal endosymbiont, Symbiodinium thermophilum [236,239]. S. thermophilum can thrive in high-temperature and high-salinity environments, allowing the coral to develop a temperature-stress-resistant phenotype [239].

Symbiodinium, a diverse group of dinoflagellates, is classified into nine clades (A–I) based on their phylogenetic characteristics [240]. Among these clades, Symbiodinium clade D has garnered attention for its exceptional thermal resilience ability, despite its relatively low representation (less than 10%) in the endosymbiotic community of coral hosts [241]. Various coral species, including fast-growing branching types, such as Acropora, Stylophora, and Pocillopora, as well as slow-growing massive, encrusting, and solitary corals, have been associated with Symbiodinium clade D [242]. The prevalence of clade D Symbiodinium in corals from the Persian Gulf has been linked to their higher thermal tolerance, particularly in comparison to corals associated with clade C, which is the dominant lineage in corals from the Great Barrier Reef and other Pacific coral reef ecosystems [243], and clade B in corals from the Atlantic [244]. These findings highlight the significance of Symbiodinium diversity in understanding the thermal resilience of coral reefs and the potential mechanisms underlying their adaptation to changing environmental conditions.

McCulloch et al. [234] explored the ability of coral species to withstand the adverse impacts of ocean acidification and global warming on coral reefs. Their study revealed that some coral species (i.e., Stylophora pistillata and Porites spp.) exhibit the capacity to increase pH levels within their calcifying fluid, crucial for the deposition of calcium carbonate and maintenance of the coral structure, even in the face of declining seawater pH levels. The study demonstrated the significance of acid-base regulation mechanisms for corals’ resilience to the effects of ocean acidification, allowing them to maintain or increase their calcification rates despite rising ocean acidification. Moreover, the study indicated that corals could acclimate to extended acidification, which enables them to maintain or increase their calcification rates by upregulating their internal pH levels, thus providing insight into potential strategies for mitigating the effects of climate change on coral reefs. A similar adaptation resilience strategy against ocean acidification was observed in cold-water scleractinian corals (i.e., Caryophyllia smithii, Desmophyllum dianthus, Enallopsammia rostrata, Lophelia pertusa, and Madrepora oculate) [245].

Oceanographic processes, such as upwelling and tidal currents, also play a significant role in helping corals avoid bleaching. In areas where upwelling events mix deeper, cooler water with shallow warmer water, thermal stress is reduced [246,247]; for example, in northern Galapagos during the 2015/16 ENSO [248] and Nanwan Bay, southern Taiwan, during summer [249]. Similarly, a coral reef’s ability to resist bleaching is bolstered by the elimination of potentially damaging oxygen radicals due to the swift water flow associated with tidal currents [230,250,251].