The oceans are becoming warmer and more acidic as a result of rising atmospheric pCO2. Transcriptome plasticity may facilitate marine organisms’ acclimation to thermal and acidification stress by tailoring gene expression to mitigate the impacts of these stressors. Here, we produce the first transcriptome of the abundant, ubiquitous, and resilient Caribbean reef-building coral Siderastrea siderea, and investigate this corals’ transcriptomic response to 95 days of thermal (T = 25, 28, 32°C) and CO2-induced acidification (324, 477, 604, 2553 µatm) stress. The S. siderea transcriptome was assembled using RNAseq and then Weighted Gene Correlation Network Analysis was employed to obtain systems-level insights into the coral’s stress response. Exposure of the coral to both elevated temperature and acidification elicited strong but divergent transcriptomic responses. Gene Ontology analysis suggests that long-term thermal stress disrupts homeostasis by increasing transcription of protein-coding genes associated with protein catabolism and suppressing transcription of genes involved in responding to environmental stimuli. Both next century (604 µatm) and extreme-high (2553 µatm) pCO2 stress increased transcription of genes associated with respiration, highlighting the potentially greater energetic requirements of maintaining calcification under high-pCO2 conditions. Under extreme-high-pCO2, increased transcription of H+-transporter genes was observed, consistent with the proposed role of proton transport in facilitating coral calcification under elevated pCO2. These results suggest that 95 days of exposure to 32°C seawater elicits a more adverse transcriptomic response (i.e., broad scale reductions in gene expression) than exposure to extreme-high acidification (2553 µatm; i.e., increased expression of genes associated with ion transport) within S. siderea—with the response to extreme warming suggesting cellular shutdown and the response to extreme acidification indicating capacity for acclimation. These results are consistent with the observation that rates of net calcification for the investigated corals were more negatively affected by the prescribed thermal stress than by the prescribed acidification stress. This study demonstrates how transcriptome plasticity may promote coral acclimation to these global change stressors, but that there are limits to the efficacy of this plasticity.

The combination of thermal stress and ocean acidification (OA) can more negatively affect coral calcification than an individual stressors, but the mechanism behind this interaction is unknown. We used two independent methods (microelectrode and boron geochemistry) to measure calcifying fluid pH (pH_cf) and carbonate chemistry of the corals Pocillopora damicornis and Stylophora pistillata grown under various temperature and pCO₂ conditions. Although these approaches demonstrate that they record pH_cf over different time scales, they reveal that both species can cope with OA under optimal temperatures (28°C) by elevating pH_cf and aragonite saturation state (Ω_cf) in support of calcification. At 31°C, neither species elevated these parameters as they did at 28°C and, likewise, could not maintain substantially positive calcification rates under any pH treatment. These results reveal a previously uncharacterized influence of temperature on coral pH_cf regulation—the apparent mechanism behind the negative interaction between thermal stress and OA on coral calcification.

Trophic cascades and climate change are together reshaping an iconic kelp forest ecosystem after the loss of sea otters.

The response of marine-calcifying organisms to ocean acidification (OA) is highly variable, although the mechanisms behind this variability are not well understood. Here, we use the boron isotopic composition (δ¹¹B) of biogenic calcium carbonate to investigate the extent to which organisms’ ability to regulate pH at their site of calcification (pH_CF) determines their calcification responses to OA. We report comparative δ¹¹B analyses of 10 species with divergent calcification responses (positive, parabolic, threshold, and negative) to OA. Although the pH_CF is closely coupled to calcification responses only in 3 of the 10 species, all 10 species elevate pH_CF above pH_sw under elevated pCO₂. This result suggests that these species may expend additional energy regulating pH_CF under future OA. This strategy of elevating pH_CF above pH_sw appears to be a polyphyletic, if not universal, response to OA among marine calcifiers—although not always the principal factor governing a species’ response to OA.

Ocean acidification will potentially inhibit calcification by marine organisms; however, the response of the most prolific ocean calcifiers, coccolithophores, to this perturbation remains under characterized. Here we report novel chemical constraints on the response of the widespread coccolithophore speciesOchrosphaera neapolitana(O. neapolitana) to changing-CO₂conditions. We cultured this algae under threepCO₂-controlled seawater pH conditions (8.05, 8.22, and 8.33). Boron isotopes within the algae’s extracellular calcite plates show that this species maintains a constant pH at the calcification site, regardless of CO₂-induced changes in pH of the surrounding seawater. Carbon and oxygen isotopes in the algae’s calcite plates and carbon isotopes in the algae’s organic matter suggest thatO. neapolitanautilize carbon from a single internal dissolved inorganic carbon (DIC) pool for both calcification and photosynthesis, and that a greater proportion of dissolved CO₂relative to HCO₃⁻enters the internal DIC pool under acidified conditions. These two observations may explain howO. neapolitanacontinues calcifying and photosynthesizing at a constant rate under different atmospheric-pCO₂conditions.