(Table S1) Boron isotope and trace element data and reconstructed carbonate system parameters, ODP Holes 122-761B and 154-926A

The middle Miocene Climatic Optimum (17-15 Ma; MCO) is a period of global warmth and relatively high CO2 and is thought to be associated with a significant retreat of the Antarctic Ice Sheet (AIS). We present here a new planktic foraminiferal d11B record from 16.6 to 11.8 Ma from two deep ocean sites currently in equilibrium with the atmosphere with respect to CO2. These new data demonstrate that the evolution of global climate during the middle Miocene (as reflected by changes in the cyrosphere) was well correlated to variations in the concentration of atmospheric CO2. What is more, within our sampling resolution (~1 sample per 300 kyr) there is no evidence of hysteresis in the response of ice volume to CO2 forcing during the middle Miocene, contrary to what is understood about the Antarctic Ice Sheet from ice sheet modelling studies. In agreement with previous data, we show that absolute levels of CO2 during the MCO were relatively modest (350-400 ppm) and levels either side of the MCO are similar or lower than the pre-industrial (200-260 ppm). These new data imply the presence of either a very dynamic AIS at relatively low CO2 during the middle Miocene or the advance and retreat of significant northern hemisphere ice. Recent drilling on the Antarctic margin and shore based studies indicate significant retreat and advance beyond the modern limits of the AIS did occur during the middle Miocene, but the complete loss of the AIS was unlikely. Consequently, it seems that ice volume and climate variations during the middle Miocene probably involved a more dynamic AIS than the modern but also some component of land-based ice in the northern hemisphere.

Carbonate system during the May 2013 MedSeA cruise

Most global ocean models are based on the assumption of a "steady state" ocean. Here, we investigate the validation of this hypothesis for the anthropized Mediterranean Sea. In order to do so, we calculated the mixing coefficients of the water masses detected in this sea via an optimum multiparameter analysis referred to as the MIX approach, using data from the BOUM (2008) and MedSeA (2013) cruises. The comparison of the mixing coefficients of each water mass, between 2008 and 2013, indicates that some of their proportions have significantly changed. Surface water mass proportions did not change significantly (Delta0.05-0.1), while intermediate and deep water mass mixing coefficients of both Eastern and Western basins were significantly modified (~Delata 0.35). This study clearly shows that the Mediterranean seawater is not in a "steady state".

Seawater carbonate chemistry and photosynthetic response of Emiliania huxleyi (CS-369) to UV radiation and elevated temperature duirng experiments, 2011

Changes in calcification of coccolithophores may affect their photosynthetic responses to both, ultraviolet radiation (UVR, 280-400 nm) and temperature. We operated semi-continuous cultures of Emiliania huxleyi (strain CS-369) at reduced (0.1 mM, LCa) and ambient (10 mM, HCa) Ca2+ concentrations and, after 148 generations, we exposed cells to six radiation treatments (>280, >295, >305, >320, >350 and >395 nm by using Schott filters) and two temperatures (20 and 25 °C) to examine photosynthesis and calcification responses. Overall, our study demonstrated that: (1) decreased calcification resulted in a down regulation of photoprotective mechanisms (i.e., as estimated via non-photochemical quenching, NPQ), pigments contents and photosynthetic carbon fixation; (2) calcification (C) and photosynthesis (P) (as well as their ratio) have different responses related to UVR with cells grown under the high Ca2+ concentration being more resistant to UVR than those grown under the low Ca2+ level; (3) elevated temperature increased photosynthesis and calcification of E. huxleyi grown at high Ca2+concentrations whereas decreased both processes in low Ca2+ grown cells. Therefore, a decrease in calcification rates in E. huxleyi is expected to decrease photosynthesis rates, resulting in a negative feedback that further reduces calcification.

Seawater carbonate chemistry and accumulation of radiotracers in squid, Loligo vulgaris during experiments, 2011

The anthropogenic release of carbon dioxide (CO2) into the atmosphere leads to an increase in the CO2 partial pressure (pCO2) in the ocean, which may reach 950 ?atm by the end of the 21st century. The resulting hypercapnia (high pCO2) and decreasing pH ("ocean acidification") are expected to have appreciable effects on water-breathing organisms, especially on their early-life stages. For organisms like squid that lay their eggs in coastal areas where the embryo and then paralarva are also exposed to metal contamination, there is a need for information on how ocean acidification may influence trace element bioaccumulation during their development. In this study, we investigated the effects of enhanced levels of pCO2 (380, 850 and 1500 ?atm corresponding to pHT of 8.1, 7.85 and 7.60) on the accumulation of dissolved 110mAg, 109Cd, 57Co, 203Hg, 54Mn and 65Zn radiotracers in the whole egg strand and in the different compartments of the egg of Loligo vulgaris during the embryonic development and also in hatchlings during their first days of paralarval life. Retention properties of the eggshell for 110mAg, 203Hg and 65Zn were affected by the pCO2 treatments. In the embryo, increasing seawater pCO2 enhanced the uptake of both 110mAg and 65Zn while 203Hg showed a minimum concentration factor (CF) at the intermediate pCO2. 65Zn incorporation in statoliths also increased with increasing pCO2. Conversely, uptake of 109Cd and 54Mn in the embryo decreased as a function of increasing pCO2. Only the accumulation of 57Co in embryos was not affected by increasing pCO2. In paralarvae, the CF of 110mAg increased with increasing pCO2, whereas the 57Co CF was reduced at the highest pCO2 and 203Hg showed a maximal uptake rate at the intermediate pCO2. 54Mn and 65Zn accumulation in paralarvae were not significantly modified by hypercapnic conditions. Our results suggest a combined effect of pH on the adsorption and protective properties of the eggshell and of hypercapnia on the metabolism of embryo and paralarvae, both causing changes to the accumulation of metals in the tissues of L. vulgaris.

In-situ seawater pH and temperature during and fitness traits of a calcifying polychaete after a reciprocal transplant experiment in June-July near Ischia, italy

Ocean acidification (OA) is likely to exert selective pressure on natural populations. Our ability to predict which marine species will adapt to OA, and what underlies this adaptive potential, are of high conservation and resource management priority. Using a naturally low pH vent site in the Mediterranean Sea (Castello Aragonese, Ischia) mirroring projected future OA conditions, we carried out a reciprocal transplant experiment to investigate the relative importance of phenotypic plasticity and local adaptation in two populations of the sessile, calcifying polychaete /Simplaria /sp. (Annelida, Serpulidae, Spirorbinae): one residing in low pH and the other from a nearby ambient (i.e. high) pH site. We measured a suite of fitness related traits (i.e. survival, reproductive output, maturation, population growth) and tube growth rates in laboratory-bred F2 generation individuals from both populations reciprocally transplanted back into both ambient and low pH /in situ/ habitats. Both populations showed lower expression in all traits, but increased tube growth rates, when exposed to low pH compared to high pH conditions, regardless of their site of origin suggesting that local adaptation to low pH conditions has not occurred. We also found comparable levels of plasticity in the two populations investigated, suggesting no influence of long-term exposure to low pH on the ability of populations to adjust their phenotype. Despite high variation in trait values among sites and the relatively extreme conditions at sites close to the vents (pH < 7.36), response trends were consistent across traits. Hence, our data suggest that, for /Simplaria /and possibly other calcifiers, neither local adaptations nor sufficient phenotypic plasticity levels appear to suffice in order to compensate for the negative impacts of OA on long-term survival. Our work also underlines the utility of field experiments in natural environments subjected to high level of /p/CO_2 for elucidating the potential for adaptation to future scenarios of OA.

Seawater carbonate chemistry, growth rate and PIC and POC production during experiments with Emiliania huxleyi (B92/11), 2011

The coccolithophore Emiliania huxleyi was cultured under a broad range of carbonate chemistry conditions to distinguish the effects of individual carbonate system parameters on growth, primary production, and calcification. In the first experiment, alkalinity was kept constant and the fugacity of CO2(fCO2) varied from 2 to 600 Pa (1Pa ~ 10 µatm). In the second experiment, pH was kept constant (pHfree = 8) with fCO2 varying from 4 to 370 Pa. Results of the constant-alkalinity approach revealed physiological optima for growth, calcification, and organic carbon production at fCO2 values of ~20Pa, ~40 Pa, and ~80 Pa, respectively. Comparing this with the constant-pH approach showed that growth and organic carbon production increased similarly from low to intermediate CO2 levels but started to diverge towards higher CO2 levels. In the high CO2 range, growth rates and organic carbon production decreased steadily with declining pH at constant alkalinity while remaining consistently higher at constant pH. This suggests that growth and organic carbon production rates are directly related to CO2 at low (sub-saturating) concentrations, whereas towards higher CO2 levels they are adversely affected by the associated decrease in pH. A pH dependence at high fCO2 is also indicated for calcification rates, while the key carbonate system parameter determining calcification at low fCO2 remains unclear. These results imply that key metabolic processes in coccolithophores have their optima at different carbonate chemistry conditions and are influenced by different parameters of the carbonate system at both sides of the optimum.

Seawater carbonate chemistry and diatom Phaeodactylum tricornutum (CCMA 106) biological processes during experiments, 2010

CO2/pH perturbation experiments were carried out under two different pCO2 levels (39.3 and 101.3 Pa) to evaluate effects of CO2-induced ocean acidification on the marine diatom Phaeodactylum tricornutum. After acclimation (>20 generations) to ambient and elevated CO2 conditions (with corresponding pH values of 8.15 and 7.80, respectively), growth and photosynthetic carbon fixation rates of high CO2 grown cells were enhanced by 5% and 12%, respectively, and dark respiration stimulated by 34% compared to cells grown at ambient CO2. The half saturation constant (Km) for carbon fixation (dissolved inorganic carbon, DIC) increased by 20% under the low pH and high CO2 condition, reflecting a decreased affinity for HCO3- or/and CO2 and down-regulated carbon concentrating mechanism (CCM). In the high CO2 grown cells, the electron transport rate from photosystem II (PSII) was photoinhibited to a greater extent at high levels of photosynthetically active radiation, while non-photochemical quenching was reduced compared to low CO2 grown cells. This was probably due to the down-regulation of CCM, which serves as a sink for excessive energy. The balance between these positive and negative effects on diatom productivity will be a key factor in determining the net effect of rising atmospheric CO2 on ocean primary production.

Seawater acidification affects the physiological energetics and spawning capacity of the Manila clam Ruditapes philippinarum during gonadal maturation

Ocean acidification is predicted to have widespread implications for marine bivalve mollusks. While our understanding of its impact on their physiological and behavioral responses is increasing, little is known about their reproductive responses under future scenarios of anthropogenic climate change. In this study, we examined the physiological energetics of the Manila clam Ruditapes philippinarum exposed to CO2-induced seawater acidification during gonadal maturation. Three recirculating systems filled with 600 L of seawater were manipulated to three pH levels (8.0, 7.7, and 7.4) corresponding to control and projected pH levels for 2100 and 2300. In each system, temperature was gradually increased ca. 0.3 °C per day from 10 to 20 °C for 30 days and maintained at 20 °C for the following 40 days. Irrespective of seawater pH levels, clearance rate (CR), respiration rate (RR), ammonia excretion rate (ER), and scope for growth (SFG) increased after a 30-day stepwise warming protocol. When seawater pH was reduced, CR, ratio of oxygen to nitrogen, and SFG significantly decreased concurrently, whereas ammonia ER increased. RR was virtually unaffected under acidified conditions. Neither temperature nor acidification showed a significant effect on food absorption efficiency. Our findings indicate that energy is allocated away from reproduction under reduced seawater pH, potentially resulting in an impaired or suppressed reproductive function. This interpretation is based on the fact that spawning was induced in only 56% of the clams grown at pH 7.4. Seawater acidification can therefore potentially impair the physiological energetics and spawning capacity of R. philippinarum.

Seawater carbonate chemistry and biological processes during experiments with early life stages of the blue mussel Mytilus edulis, 2010

Several experiments have shown a decrease of growth and calcification of organisms at decreased pH levels. There is a growing interest to focus on early life stages that are believed to be more sensitive to environmental disturbances such as hypercapnia. Here, we present experimental data, acquired in a commercial hatchery, demonstrating that the growth of planktonic mussel (Mytilus edulis) larvae is significantly affected by a decrease of pH to a level expected for the end of the century. Even though there was no significant effect of a 0.25-0.34 pH unit decrease on hatching and mortality rates during the first 2 days of development nor during the following 13-day period prior to settlement, final shells were respectively 4.5±1.3 and 6.0±2.3% smaller at pHNBS~7.8 (pCO2~1100-1200 µatm) than at a control pHNBS of ~8.1 (pCO2~460-640 µatm). Moreover, a decrease of 12.0±5.4% of shell thickness was observed after 15d of development. More severe impacts were found with a decrease of ~0.5 pHNBS unit during the first 2 days of development which could be attributed to a decrease of calcification due to a slight undersaturation of seawater with respect to aragonite. Indeed, important effects on both hatching and D-veliger shell growth were found. Hatching rates were 24±4% lower while D-veliger shells were 12.7±0.9% smaller at pHNBS~7.6 (pCO2~1900 µatm) than at a control pHNBS of ~8.1 (pCO2~540 µatm). Although these results show that blue mussel larvae are still able to develop a shell in seawater undersaturated with respect to aragonite, the observed decreases of hatching rates and shell growth could lead to a significant decrease of the settlement success. As the environmental conditions considered in this study do not necessarily reflect the natural conditions experienced by this species at the time of spawning, future studies will need to consider the whole larval cycle (from fertilization to settlement) under environmentally relevant conditions in order to investigate the potential ecological and economical losses of a decrease of this species fitness in the field.

Seawater carbonate chemistry and particulate organic particles during a semicontinuous batch culture experiment with Trichodesmium IMS101, 2007

Diazotrophic (N2-fixing) cyanobacteria provide the biological source of new nitrogen for large parts of the ocean. However, little is known about their sensitivity to global change. Here we show that the single most important nitrogen fixer in today's ocean, Trichodesmium, is strongly affected by changes in CO2 concentrations. Cell division rate doubled with rising CO2 (glacial to projected year 2100 levels) prompting lower carbon, nitrogen and phosphorus cellular contents, and reduced cell dimensions. N2 fixation rates per unit of phosphorus utilization as well as C:P and N:P ratios more than doubled at high CO2, with no change in C:N ratios. This could enhance the productivity of N-limited oligotrophic oceans, drive some of these areas into P limitation, and increase biological carbon sequestration in the ocean. The observed CO2 sensitivity of Trichodesmium could thereby provide a strong negative feedback to atmospheric CO2 increase.

Impact of atmospheric pCO2, seawater temperature, and calcification rate on the delta 18O and delta 13C composition of echinoid calcite (Echinometra viridis)

The tropical echinoid Echinometra viridis was reared in controlled laboratory experiments at temperatures of approximately 20°C and 30°C to mimic winter and summer temperatures and at carbon dioxide (CO2) partial pressures of approximately 487 ppm-v and 805 ppm-v to simulate current and predicted-end-of-century levels. Spine material produced during the experimental period and dissolved inorganic carbon (DIC) of the corresponding culture solutions were then analyzed for stable oxygen (delta 18Oe, delta 18ODIC) and carbon (The tropical echinoid Echinometra viridis was reared in controlled laboratory experiments at temperatures of approximately 20°C and 30°C to mimic winter and summer temperatures and at carbon dioxide (CO2) partial pressures of approximately 487 ppm-v and 805 ppm-v to simulate current and predicted-end-of-century levels. Spine material produced during the experimental period and dissolved inorganic carbon (DIC) of the corresponding culture solutions were then analyzed for stable oxygen (delta18Oe, delta18ODIC) and carbon (delta13Ce, delta13CDIC) isotopic composition. Fractionation of oxygen stable isotopes between the echinoid spines and DIC of their corresponding culture solutions (delta18O = delta18Oe - delta18ODIC) was significantly inversely correlated with seawater temperature but not significantly correlated with atmospheric pCO2. Fractionation of carbon stable isotopes between the echinoid spines and DIC of their corresponding culture solutions (Delta delta13C = delta13Ce - delta13CDIC) was significantly positively correlated with pCO2 and significantly inversely correlated with temperature, with pCO2 functioning as the primary factor and temperature moderating the pCO2-delta13C relationship. Echinoid calcification rate was significantly inversely correlated with both delta18O and delta13C, both within treatments (i.e., pCO2 and temperature fixed) and across treatments (i.e., with effects of pCO2 and temperature controlled for through ANOVA). Therefore, calcification rate and potentially the rate of co-occurring dissolution appear to be important drivers of the kinetic isotope effects observed in the echinoid spines. Study results suggest that echinoid delta18O monitors seawater temperature, but not atmospheric pCO2, and that echinoid delta13C monitors atmospheric pCO2, with temperature moderating this relationship. These findings, coupled with echinoids' long and generally high-quality fossil record, supports prior assertions that fossil echinoid delta18O is a viable archive of paleo-seawater temperature throughout Phanerozoic time, and that delta13C merits further investigation as a potential proxy of paleo-atmospheric pCO2. However, the apparent impact of calcification rate on echinoid delta18O and delta13C suggests that paleoceanographic reconstructions derived from these proxies in fossil echinoids could be improved by incorporating the effects of growth rate.13Ce, delta13CDIC) isotopic composition. Fractionation of oxygen stable isotopes between the echinoid spines and DIC of their corresponding culture solutions (delta18O = delta18Oe - delta18ODIC) was significantly inversely correlated with seawater temperature but not significantly correlated with atmospheric pCO2. Fractionation of carbon stable isotopes between the echinoid spines and DIC of their corresponding culture solutions (delta13C = delta13Ce - delta13CDIC) was significantly positively correlated with pCO2 and significantly inversely correlated with temperature, with pCO2 functioning as the primary factor and temperature moderating the pCO2-delta13C relationship. Echinoid calcification rate was significantly inversely correlated with both delta18O and delta13C, both within treatments (i.e., pCO2 and temperature fixed) and across treatments (i.e., with effects of pCO2 and temperature controlled for through ANOVA). Therefore, calcification rate and potentially the rate of co-occurring dissolution appear to be important drivers of the kinetic isotope effects observed in the echinoid spines. Study results suggest that echinoid delta18O monitors seawater temperature, but not atmospheric pCO2, and that echinoid delta13C monitors atmospheric pCO2, with temperature moderating this relationship. These findings, coupled with echinoids' long and generally high-quality fossil record, supports prior assertions that fossil echinoid delta18O is a viable archive of paleo-seawater temperature throughout Phanerozoic time, and that delta13C merits further investigation as a potential proxy of paleo-atmospheric pCO2. However, the apparent impact of calcification rate on echinoid delta18O and delta13C suggests that paleoceanographic reconstructions derived from these proxies in fossil echinoids could be improved by incorporating the effects of growth rate.

Maintained larval growth in mussel larvae exposed to acidified undersaturated seawater

Ocean acidification (OA) is known to affect bivalve early life-stages. We tested responses of blue mussel larvae to a wide range of pH in order to identify their tolerance threshold. Our results confirmed that decreasing seawater pH and decreasing saturation state increases larval mortality rate and the percentage of abnormally developing larvae. Virtually no larvae reared at average pHT 7.16 were able to feed or reach the D-shell stage and their development appeared to be arrested at the trochophore stage. However larvae were capable of reaching the D-shell stage under milder acidification (pHT=7.35, 7.6, 7.85) including in under-saturated seawater with omega Aragonite as low as 0.54±0.01 (mean±s. e. m.), with a tipping point for normal development identified at pHT 7.765. Additionally growth rate of normally developing larvae was not affected by lower pHT despite potential increased energy costs associated with compensatory calcification in response to increased shell dissolution. Overall, our results on OA impacts on mussel larvae suggest an average pHT of 7.16 is beyond their physiological tolerance threshold and indicate a shift in energy allocation towards growth in some individuals revealing potential OA resilience.