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Epigenetic modifications based on DNA methylation can rapidly improve the potential of corals to adapt to environmental pressures by increasing their phenotypic plasticity, a factor important for scleractinian corals to adapt to future global warming. However, the extent to which corals develop similar adaptive mechanisms and their specific adaptation processes remain unclear. Here, to reveal the regulatory mechanism by which DNA methylation improves thermal tolerance in Pocillopora damicornis under fluctuating environments, we analyzed genome-wide DNA methylation signatures in P. damicornis and compared the differences in the methylation and transcriptional responses of P. damicornis from fluctuating and stable environments using whole-genome bisulfite sequencing and nanopore-based RNA sequencingtranscriptome sequencing. We discovered low methylation levels in P. damicornis (average methylation 4.14%), with CpG accounting for 74.88%, CHH for 13.27%, and CHG for 11.85% of this methylation. However, methylation levels did not change between coral samples from the fluctuating and stable environments. The varied methylation levels in different regions of the gene revealed that the overall methylation level of the gene body was relatively high and showed a bimodal methylation pattern. Methylation occurs primarily in exons rather than introns within the gene body In P. damicornis , there was only a weak correlation between methylation and transcriptional changes at the individual gene level, and the methylation and gene expression levels generally exhibited a bell-shaped relationship, which we speculate may be due to the specificity of cnidarian species. Correlation analysis between methylation levels and the transcriptome revealed that the highest proportion of the top 20 enriched KEGG pathways was related to immunity. Additionally, P. damicornis collected from a high-temperature pool had a lower metabolic rate than those collected from a low-temperature pool. We hypothesize that the dynamic balance of energy–expenditure costs between immunity and metabolism is an important strategy for increasing P. damicornis tolerance. The fluctuating environment of high-temperature pools may increase the heat tolerance in corals by increasing their immunity and thus lowering their metabolism. • Scleractinian corals are more tolerant in fluctuating reef-dwelling environments. • Low methylation levels in P. damicornis. • Thermal acclimation increase tolerance in corals by increasing coral immunity and thus lowering their metabolism. • Dynamic balance of energy–expenditure costs between immunity and metabolism is an important strategy. [ABSTRACT FROM AUTHOR]

Coral bleaching heat stress products provide real-time and rapid coral bleaching alerts for coral reefs globally. However, geographical variations in the alert accuracy of multi-source coral bleaching heat stress products exist. Taking the coral reefs in the South China Sea (SCS) as the study area, we evaluated and improved the coral bleaching alert capabilities of two coral bleaching heat stress products: Coral Reef Watch (CRW) and Coral Reef Temperature Anomaly Database (CoRTAD). Using in situ coral bleaching survey data and evaluation indicators, the optimized thresholds of degree heating weeks (DHWs) for coral bleaching alerts were determined. The results in the SCS indicated that, first, CRW was better than CoRTAD for coral bleaching event alerts. However, both products underestimated coral bleaching events using the common DHW thresholds of 4°C-weeks and 8°C-weeks. Second, the DHW optimized threshold for CRW was 3.32°C-weeks for coral bleaching event alerts and 4.52°C-weeks for severe coral bleaching event alerts. For CoRTAD products, the DHW optimized threshold was 2.36°C-weeks for coral bleaching event alerts and 4.14°C-weeks for severe coral bleaching event alerts. This study proposed a method to evaluate and optimize the alert capability of multi-source coral bleaching heat stress products, which can provide more accurate basic data for coral reef ecosystem health assessment and contribute to global coral reef ecosystem protection and restoration. • A method to evaluate and optimize the alert capability of coral bleaching heat stress products in the SCS. • Optimized DHW thresholds for coral bleaching alerts were 3.32°C-weeks for CRW and 2.36°C-weeks for CoRTAD. • Optimized DHW thresholds for coral severe bleaching alerts were 4.52°C-weeks for CRW and 4.14°C-weeks for CoRTAD. • CRW was better than CoRTAD for coral bleaching event alerts in the SCS. [ABSTRACT FROM AUTHOR]

Most studies on coral bleaching alerts use common Degree Heating Week (DHW) thresholds; however, these may underestimate historical patterns of heat stress for coral reef ecosystems. Taking an optimized DHW threshold for coral bleaching alerts for Coral Reef Watch (CRW) and Coral Reef Temperature Anomaly Database (CoRTAD) products, we analyzed the precise spatial and temporal pattern of heat stress on China's coral reefs from 2010 to 2021 in the South China Sea (SCS) and the Beibu Gulf (BG). We compared acute heat stress using common and optimized thresholds. Results indicated that the ocean warming rate in 2010–2021 was approximately 0.43 ± 0.22 °C/10a, showing a significant increase in the northern SCS and the BG. More severe bleaching events were predicted by the optimized thresholds and the high-frequency areas were mainly in the northern SCS. The number and intensity of years with severe heat stress anomalies was in the order 2020 > 2014 > 2010 > 2015. Heat stress duration was the longest in the Xisha Islands among offshore archipelagos, and longest in 2020–2021 in Weizhou Island in BG in the relative high-latitude inshore reefs. These abnormal events were mainly caused by El Niño, but La Niña was also involved in 2020. • The most intense severe heat stress anomaly years were 2010 > 2014>2020 > 2015. • The anomaly duration of offshore islands was Xisha > Dongsha > Zhongsha > Nansha Islands. • High-latitude reefs were predicted not to be future thermal refuges for SCS reefs. • The optimized DHW threshold more accurately predicted spatiotemporal heat stress. [ABSTRACT FROM AUTHOR]