Vulnerability of the calcifying larval stage of the Antarctic sea urchin Sterechinus neumayeri to near‐future ocean acidification and warming

Stenothermal polar benthic marine invertebrates are highly sensitive to environmental perturbations but little is known about potential synergistic effects of concurrent ocean warming and acidification on development of their embryos and larvae. We examined the effects of these stressors on development to the calcifying larval stage in the Antarctic sea urchin Sterechinus neumayeri in embryos reared in present and future (2100+) ocean conditions from fertilization. Embryos were reared in 2 temperature (ambient: ?1.0 °C, + 2 °C : 1.0 °C) and 3 pH (ambient: pH 8.0, ?0.2–0.4 pH units: 7.8,7.6) levels. Principle coordinates analysis on five larval metrics showed a significant effect of temperature and pH on the pattern of growth. Within each temperature, larvae were separated by pH treatment, a pattern primarily influenced by larval arm and body length. Growth was accelerated by temperature with a 20–28% increase in postoral (PO) length at +2 °C across all pH levels. Growth was strongly depressed by reduced pH with a 8–19% decrease in PO length at pH 7.6–7.8 at both temperatures. The boost in growth caused by warming resulted in larvae that were larger than would be observed if acidification was examined in the absence of warming. However, there was no significant interaction between these stressors. The increase in left‐right asymmetry and altered body allometry indicated that decreased pH disrupted developmental patterning and acted as a teratogen (agent causing developmental malformation). Decreased developmental success with just a 2 °C warming indicates that development in S. neumayeri is particularly sensitive to increased temperature. Increased temperature also altered larval allometry. Altered body shape impairs swimming and feeding in echinoplutei. In the absence of adaptation, it appears that the larval phase may be a bottleneck for survivorship of S. neumayeri in a changing ocean in a location where poleward migration to escape inhospitable conditions is not possible.     

Larvae of the coral eating crown‐of‐thorns starfish,Acanthaster planci in a warmer‐high CO2 ocean

Outbreaks of crown‐of‐thorns starfish (COTS), Acanthaster planci, contribute to major declines of coral reef ecosystems throughout the Indo‐Pacific. As the oceans warm and decrease in pH due to increased anthropogenic CO₂ production_, coral reefs are also susceptible to bleaching, disease and reduced calcification. The impacts of ocean acidification and warming may be exacerbated by COTS predation, but it is not known how this major predator will fare in a changing ocean. Because larval success is a key driver of population outbreaks, we investigated the sensitivities of larval A. planci to increased temperature (2–4 °C above ambient) and acidification (0.3–0.5 pH units below ambient) in flow‐through cross‐factorial experiments (3 temperature × 3 pH/pCO₂ levels). There was no effect of increased temperature or acidification on fertilization or very early development. Larvae reared in the optimal temperature (28 °C) were the largest across all pH treatments. Development to advanced larva was negatively affected by the high temperature treatment (30 °C) and by both experimental pH levels (pH 7.6, 7.8). Thus, planktonic life stages of A. planci may be negatively impacted by near‐future global change. Increased temperature and reduced pH had an additive negative effect on reducing larval size. The 30 °C treatment exceeded larval tolerance regardless of pH. As 30 °C sea surface temperatures may become the norm in low latitude tropical regions, poleward migration of A. planci may be expected as they follow optimal isotherms. In the absence of acclimation or adaptation, declines in low latitude populations may occur. Poleward migration will be facilitated by strong western boundary currents, with possible negative flow‐on effects on high latitude coral reefs. The contrasting responses of the larvae of A. planci and those of its coral prey to ocean acidification and warming are considered in context with potential future change in tropical reef ecosystems.     

Combined effects of two ocean change stressors, warming and acidification, on fertilization and early development of the Antarctic echinoid Sterechinus neumayeri

The effects of concurrent ocean warming and acidification on Antarctic marine benthos warrant investigation as little is known about potential synergies between these climate change stressors. We examined the interactive effects of warming and acidification on fertilization and embryonic development of the ecologically important sea urchin Sterechinus neumayeri reared from fertilization in elevated temperature (+1.5°C and 3°C) and decreased pH (?0.3 and ?0.5 pH units) treatments. Fertilization using gametes from multiple males and females, to represent populations of spawners, was resilient to acidification at ambient temperature (0°C). At elevated temperatures, there was a negative interactive effect of temperature and pH on percentage of fertilization (11% reduction at 3°C). For cleavage stage embryos, there was a significant, but small reduction (6%) in the percentage of normal embryos at pH 7.5. For blastulae, a 10–11% decrease in normal development occurred in the +3°C treatments across all pH levels. Our results highlight the importance of considering the impacts of both temperature and pH in assessing the life history response of S. neumayeri in a changing polar ocean. While fertilization and development to the blastula stage were robust to levels of temperature and pH change predicted over coming decades, deleterious interactive effects were evident between these stressors at levels projected to occur by 2100 and beyond.     

Experimental influence of pH on the early life-stages of sea urchins I: different rates of introduction give rise to different responses

Many early life-stage response studies to ocean acidification utilize gametes/offspring obtained from ambient-sourced parents, which are then directly introduced to experimentally altered seawater pH. This approach may produce a stress response potentially impacting development and survival. Hence, this study determined whether this approach is suitable by subjecting embryos/larvae to different rates of introduction to lowered seawater pH to assess larval success under acute and staggered experimental pH scenarios. Embryos and 4-armed larvae of the sea urchin Psammechinus miliaris were introduced to pH conditions, widely used in ocean acidification studies, from ambient conditions utilizing 380, 470, 560, 700 and 840?ppm CO₂ changed at incremental steps at two rates: fast (every 3rd hour) or slow (every 48th hour). Direct transfers from ambient to low seawater pH gave rise to dramatic negative impacts (smaller size and low survival), but slower rates of introductions gave rise to lesser negative responses (low survival). There was no treatment effect on settled juveniles. Fast introductions utilized in many studies are likely not ideal approaches when assessing pre-settlement larval developmental responses. Therefore, careful consideration of the pattern of response is needed when studies report the responses of offspring, derived from ambient conditions, introduced directly to forecasted ocean acidification conditions.     

Quantitative analysis of oyster larval proteome provides new insights into the effects of multiple climate change stressors

The metamorphosis of planktonic larvae of the Pacific oyster (Crassostrea gigas) underpins their complex life‐history strategy by switching on the molecular machinery required for sessile life and building calcite shells. Metamorphosis becomes a survival bottleneck, which will be pressured by different anthropogenically induced climate change‐related variables. Therefore, it is important to understand how metamorphosing larvae interact with emerging climate change stressors. To predict how larvae might be affected in a future ocean, we examined changes in the proteome of metamorphosing larvae under multiple stressors: decreased pH (pH 7.4), increased temperature (30 °C), and reduced salinity (15 psu). Quantitative protein expression profiling using iTRAQ‐LC‐MS/MS identified more than 1300 proteins. Decreased pH had a negative effect on metamorphosis by down‐regulating several proteins involved in energy production, metabolism, and protein synthesis. However, warming switched on these down‐regulated pathways at pH 7.4. Under multiple stressors, cell signaling, energy production, growth, and developmental pathways were up‐regulated, although metamorphosis was still reduced. Despite the lack of lethal effects, significant physiological responses to both individual and interacting climate change related stressors were observed at proteome level. The metamorphosing larvae of the C. gigas population in the Yellow Sea appear to have adequate phenotypic plasticity at the proteome level to survive in future coastal oceans, but with developmental and physiological costs.     

Effects of ocean acidification on the early life history of a tropical marine fish

Little is known about how fishes and other non-calcifying marine organisms will respond to the increased levels of dissolved CO₂ and reduced sea water pH that are predicted to occur over the coming century. We reared eggs and larvae of the orange clownfish, Amphiprion percula, in sea water simulating a range of ocean acidification scenarios for the next 50–100 years (current day, 550, 750 and 1030 ppm atmospheric CO₂). CO₂ acidification had no detectable effect on embryonic duration, egg survival and size at hatching. In contrast, CO₂ acidification tended to increase the growth rate of larvae. By the time of settlement (11 days post-hatching), larvae from some parental pairs were 15 to 18 per cent longer and 47 to 52 per cent heavier in acidified water compared with controls. Larvae from other parents were unaffected by CO₂ acidification. Elevated CO₂ and reduced pH had no effect on the maximum swimming speed of settlement-stage larvae. There was, however, a weak positive relationship between length and swimming speed. Large size is usually considered to be advantageous for larvae and newly settled juveniles. Consequently, these results suggest that levels of ocean acidification likely to be experienced in the near future might not, in isolation, significantly disadvantage the growth and performance of larvae from benthic-spawning marine fishes.     

Effects of Ocean Acidification on Juvenile Red King Crab (Paralithodes camtschaticus) and Tanner Crab (Chionoecetes bairdi) Growth,Condition, Calcification,and Survival

Ocean acidification, a decrease in the pH in marine waters associated with rising atmospheric CO₂ levels, is a serious threat to marine ecosystems. In this paper, we determine the effects of long-term exposure to near-future levels of ocean acidification on the growth, condition, calcification, and survival of juvenile red king crabs, Paralithodes camtschaticus, and Tanner crabs, Chionoecetes bairdi. Juveniles were reared in individual containers for nearly 200 days in flowing control (pH 8.0), pH 7.8, and pH 7.5 seawater at ambient temperatures (range 4.4–11.9 °C). In both species, survival decreased with pH, with 100% mortality of red king crabs occurring after 95 days in pH 7.5 water. Though the morphology of neither species was affected by acidification, both species grew slower in acidified water. At the end of the experiment, calcium concentration was measured in each crab and the dry mass and condition index of each crab were determined. Ocean acidification did not affect the calcium content of red king crab but did decrease the condition index, while it had the opposite effect on Tanner crabs, decreasing calcium content but leaving the condition index unchanged. This suggests that red king crab may be able to maintain calcification rates, but at a high energetic cost. The decrease in survival and growth of each species is likely to have a serious negative effect on their populations in the absence of evolutionary adaptation or acclimatization over the coming decades.     

Regulation of gene expression is associated with tolerance of the Arctic copepod Calanus glacialis to CO2‐acidified sea water

Ocean acidification is the increase in seawater pCO₂ due to the uptake of atmospheric anthropogenic CO₂, with the largest changes predicted to occur in the Arctic seas. For some marine organisms, this change in pCO₂, and associated decrease in pH, represents a climate change‐related stressor. In this study, we investigated the gene expression patterns of nauplii of the Arctic copepod Calanus glacialis cultured at low pH levels. We have previously shown that organismal‐level performance (development, growth, respiration) of C. glacialis nauplii is unaffected by low pH. Here, we investigated the molecular‐level response to lowered pH in order to elucidate the physiological processes involved in this tolerance. Nauplii from wild‐caught C. glacialis were cultured at four pH levels (8.05, 7.9, 7.7, 7.5). At stage N6, mRNA was extracted and sequenced using RNA‐seq. The physiological functionality of the proteins identified was categorized using Gene Ontology and KEGG pathways. We found that the expression of 151 contigs varied significantly with pH on a continuous scale (93% downregulated with decreasing pH). Gene set enrichment analysis revealed that, of the processes downregulated, many were components of the universal cellular stress response, including DNA repair, redox regulation, protein folding, and proteolysis. Sodium:proton antiporters were among the processes significantly upregulated, indicating that these ion pumps were involved in maintaining cellular pH homeostasis. C. glacialis significantly alters its gene expression at low pH, although they maintain normal larval development. Understanding what confers tolerance to some species will support our ability to predict the effects of future ocean acidification on marine organisms.     

Calcification, growth and mortality of juvenile clams Ruditapes decussatus under increased pCO2 and reduced pH: Variable responses to ocean acidification at local scales?

We investigated the effects of ocean acidification on juvenile clams Ruditapes decussatus (average shell length 10.24 mm) in a controlled CO₂ perturbation experiment. The carbonate chemistry of seawater was manipulated by diffusing pure CO₂, to attain two reduced pH levels (by −0.4 and −0.7 pH units), which were compared to unmanipulated seawater. After 75 days we found no differences among pH treatments in terms of net calcification, size or weight of the clams. The naturally elevated total alkalinity of local seawater probably contributed to buffer the effects of increased pCO₂ and reduced pH. Marine organisms may, therefore, show diverse responses to ocean acidification at local scales, particularly in coastal, estuarine and transitional waters, where the physical-chemical characteristics of seawater are most variable. Mortality was significantly reduced in the acidified treatments. This trend was probably related to the occurrence of spontaneous spawning events in the control and intermediate acidification treatments. Spawning, which was unexpected due to the small size of the clams, was not observed for the pH −0.7 treatment, suggesting that the increased survival under acidified conditions may have been associated with a delay in the reproductive cycle of the clams. Future research about the impacts of ocean acidification on marine biodiversity should be extended to other types of biological and ecological processes, apart from biological calcification.     

Effects of seawater acidification on a coral reef meiofauna community

Despite the increasing risk that ocean acidification will modify benthic communities, great uncertainty remains about how this impact will affect the lower trophic levels, such as members of the meiofauna. A mesocosm experiment was conducted to investigate the effects of water acidification on a phytal meiofauna community from a coral reef. Community samples collected from the coral reef subtidal zone (Recife de Fora Municipal Marine Park, Porto Seguro, Bahia, Brazil), using artificial substrate units, were exposed to a control pH (ambient seawater) and to three levels of seawater acidification (pH reductions of 0.3, 0.6, and 0.9 units below ambient) and collected after 15 and 30 d. After 30 d of exposure, major changes in the structure of the meiofauna community were observed in response to reduced pH. The major meiofauna groups showed divergent responses to acidification. Harpacticoida and Polychaeta densities did not show significant differences due to pH. Nematoda, Ostracoda, Turbellaria, and Tardigrada exhibited their highest densities in low-pH treatments (especially at the pH reduction of 0.6 units, pH 7.5), while harpacticoid nauplii were strongly negatively affected by low pH. This community-based mesocosm study supports previous suggestions that ocean acidification induces important changes in the structure of marine benthic communities. Considering the importance of meiofauna in the food web of coral reef ecosystems, the results presented here demonstrate that the trophic functioning of coral reefs is seriously threatened by ocean acidification.     

Experimental influence of pH on the early life-stages of sea urchins II: increasing parental exposure times gives rise to different responses

Many studies into the responses of early life-stages to ocean acidification utilise offspring obtained from parents reared under present-day conditions. Their offspring are directly introduced to altered-pH conditions. This study determined whether this approach is suitable by pre-exposing parent sea urchins (Psammechinus miliaris) to altered seawater pH (~1000?μatm) for several durations, spawning them and rearing their offspring to settlement. Parents acclimated when exposed to low seawater pH for extended periods (>42?d). Longer adult pre-exposures reduced larval survival and less competent offspring were removed from populations earlier than in controls. Control offspring were larger during earlier development stages (2–7?d), but smaller during later development stages (14?+?d) than offspring reared under low pH conditions. Juvenile settlement levels were similar across all treatments. After 17?d, offspring sourced from parents pre-exposed to low pH for 42 and 70?d were larger than those pre-exposed for 28?d and ambient sourced offspring directly transferred to low pH. These different responses show that the use of ambient derived offspring utilised in many studies is likely not an ideal approach when assessing larval development responses via morphometric measurements and survivorship prior to settlement. This study also suggests that calcifying organisms have capacities to acclimate and possibly adapt towards conditions beyond natural rates of ocean acidification.     

Signals of resilience to ocean change: high thermal tolerance of early stage Antarctic sea urchins (Sterechinus neumayeri) reared under present-day and future pCO2 and temperature

We tested the hypothesis that development of the Antarctic urchin Sterechinus neumayeri under future ocean conditions of warming and acidification would incur physiological costs, reducing the tolerance of a secondary stressor. The aim of this study is twofold: (1) quantify current austral spring temperature and pH near sea urchin habitat at Cape Evans in McMurdo Sound, Antarctica and (2) spawn S. neumayeri in the laboratory and raise early developmental stages (EDSs) under ambient (?0.7 °C; 400 µatm pCO₂) and future (+2.6 °C; 650 and 1,000 µatm pCO₂) ocean conditions and expose four EDSs (blastula, gastrula, prism, and 4-arm echinopluteus) to a one hour acute heat stress and assess survivorship. Results of field data from 2011 to 2012 show extremely stable inter-annual pH conditions ranging from 7.99 to 8.08, suggesting that future ocean acidification will drastically alter the pH-seascape for S. neumayeri. In the laboratory, S. neumayeri EDSs appear to be tolerant of temperatures and pCO₂ levels above their current habitat conditions. EDSs survived acute heat exposures >20 °C above habitat temperatures of ?1.9 °C. No pCO₂ effect was observed for EDSs reared at ?0.7 °C. When reared at +2.6 °C, small but significant pCO₂ effects were observed at the blastula and prism stage, suggesting that multiple stressors are more detrimental than single stressors. While surprisingly tolerant overall, blastulae were the most sensitive stage to ocean warming and acidification. We conclude that S. neumayeri may be unexpectedly physiologically tolerant of future ocean conditions.     

The Early Life History of the Clam Macoma balthica in a High CO(2) World

This study investigated the effects of experimentally manipulated seawater carbonate chemistry on several early life history processes of the Baltic tellin (Macoma balthica), a widely distributed bivalve that plays a critical role in the functioning of many coastal habitats. We demonstrate that ocean acidification significantly depresses fertilization, embryogenesis, larval development and survival during the pelagic phase. Fertilization and the formation of a D-shaped shell during embryogenesis were severely diminished: successful fertilization was reduced by 11% at a 0.6 pH unit decrease from present (pH 8.1) conditions, while hatching success was depressed by 34 and 87%, respectively at a 0.3 and 0.6 pH unit decrease. Under acidified conditions, larvae were still able to develop a shell during the post-embryonic phase, but higher larval mortality rates indicate that fewer larvae may metamorphose and settle in an acidified ocean. The cumulative impact of decreasing seawater pH on fertilization, embryogenesis and survival to the benthic stage is estimated to reduce the number of competent settlers by 38% for a 0.3 pH unit decrease, and by 89% for a 0.6 pH unit decrease from present conditions. Additionally, slower growth rates and a delayed metamorphosis at a smaller size were indicative for larvae developed under acidified conditions. This may further decline the recruit population size due to a longer subjection to perturbations, such as predation, during the pelagic phase. In general, early life history processes were most severely compromised at ～pH 7.5, which corresponds to seawater undersaturated with respect to aragonite. Since recent models predict a comparable decrease in pH in coastal waters in the near future, this study indicates that future populations of Macoma balthica are likely to decline as a consequence of ongoing ocean acidification.     

Impact of Ocean Warming and Ocean Acidification on Larval Development and Calcification in the Sea Urchin Tripneustes gratilla

Background

As the oceans simultaneously warm, acidify and increase in P _CO2, prospects for marine biota are of concern. Calcifying species may find it difficult to produce their skeleton because ocean acidification decreases calcium carbonate saturation and accompanying hypercapnia suppresses metabolism. However, this may be buffered by enhanced growth and metabolism due to warming.

Methodology/Principal Findings

We examined the interactive effects of near-future ocean warming and increased acidification/P _CO2 on larval development in the tropical sea urchin Tripneustes gratilla. Larvae were reared in multifactorial experiments in flow-through conditions in all combinations of three temperature and three pH/P _CO2 treatments. Experiments were placed in the setting of projected near future conditions for SE Australia, a global change hot spot. Increased acidity/P _CO2 and decreased carbonate mineral saturation significantly reduced larval growth resulting in decreased skeletal length. Increased temperature (+3°C) stimulated growth, producing significantly bigger larvae across all pH/P _CO2 treatments up to a thermal threshold (+6°C). Increased acidity (-0.3-0.5 pH units) and hypercapnia significantly reduced larval calcification. A +3°C warming diminished the negative effects of acidification and hypercapnia on larval growth.

Conclusions and Significance

This study of the effects of ocean warming and CO₂ driven acidification on development and calcification of marine invertebrate larvae reared in experimental conditions from the outset of development (fertilization) shows the positive and negative effects of these stressors. In simultaneous exposure to stressors the dwarfing effects of acidification were dominant. Reduction in size of sea urchin larvae in a high P _CO2 ocean would likely impair their performance with negative consequent effects for benthic adult populations.     

Unshelled abalone and corrupted urchins: development of marine calcifiers in a changing ocean

The most fragile skeletons produced by benthic marine calcifiers are those that larvae and juveniles make to support their bodies. Ocean warming, acidification, decreased carbonate saturation and their interactive effects are likely to impair skeletogenesis. Failure to produce skeleton in a changing ocean has negative implications for a diversity of marine species. We examined the interactive effects of warming and acidification on an abalone (Haliotis coccoradiata) and a sea urchin (Heliocidaris erythrogramma) reared from fertilization in temperature and pH/pCO(2) treatments in a climatically and regionally relevant setting. Exposure of ectodermal (abalone) and mesodermal (echinoid) calcifying systems to warming (+2°C to 4°C) and acidification (pH 7.6-7.8) resulted in unshelled larvae and abnormal juveniles. Haliotis development was most sensitive with no interaction between stressors. For Heliocidaris, the percentage of normal juveniles decreased in response to both stressors, although a +2°C warming diminished the negative effect of low pH. The number of spines produced decreased with increasing acidification/pCO(2), and the interactive effect between stressors indicated that a +2°C warming reduced the negative effects of low pH. At +4°C, the developmental thermal tolerance was breached. Our results show that projected near-future climate change will have deleterious effects on development with differences in vulnerability in the two species.     

Natural variation and the capacity to adapt to ocean acidification in the keystone sea urchin Strongylocentrotus purpuratus

A rapidly growing body of literature documents the potential negative effects of CO₂‐driven ocean acidification (OA) on marine organisms. However, nearly all this work has focused on the effects of future conditions on modern populations, neglecting the role of adaptation. Rapid evolution can alter demographic responses to environmental change, ultimately affecting the likelihood of population persistence, but the capacity for adaptation will differ among populations and species. Here, we measure the capacity of the ecologically important purple sea urchin Strongylocentrotus purpuratus to adapt to OA, using a breeding experiment to estimate additive genetic variance for larval size (an important component of fitness) under future high‐pCO₂/low‐pH conditions. Although larvae reared under future conditions were smaller than those reared under present‐day conditions, we show that there is also abundant genetic variation for body size under elevated pCO₂, indicating that this trait can evolve. The observed heritability of size was 0.40 ± 0.32 (95% CI) under low pCO₂, and 0.50 ± 0.30 under high‐pCO₂ conditions. Accounting for the observed genetic variation in models of future larval size and demographic rates substantially alters projections of performance for this species in the future ocean. Importantly, our model shows that after incorporating the effects of adaptation, the OA‐driven decrease in population growth rate is up to 50% smaller, than that predicted by the ‘no‐adaptation’ scenario. Adults used in the experiment were collected from two sites on the coast of the Northeast Pacific that are characterized by different pH regimes, as measured by autonomous sensors. Comparing results between sites, we also found subtle differences in larval size under high‐pCO₂ rearing conditions, consistent with local adaptation to carbonate chemistry in the field. These results suggest that spatially varying selection may help to maintain genetic variation necessary for adaptation to future OA.     

Effects of seawater acidification on Diopatra neapolitana (Polychaete,Onuphidae): Biochemical and regenerative capacity responses

Changes in atmospheric CO₂ concentrations and, consequently, ocean acidification, together with changes in seawater chemistry, are likely to have a large impact on marine ecosystems. Much of the current research concerning the consequences of ocean acidification has been limited to organisms dependent on the availability of carbonate ions in seawater, especially bivalves. Nevertheless, many marine organisms do not rely on calcium carbonate structures, such as most of the polychaete species that might also be affected by seawater acidification. However the effects of ocean acidification on these organisms are almost unknown. Thus, in the present study, the effects of pH decrease were studied in the polychaete Diopatra neapolitana, using tissue regenerative capacity and biochemical alterations as biomarkers. The results obtained revealed that individuals exposed for 28 days to low pH levels (7.5, 7.3, 7.1) exhibited lower capacity to regenerate their body, in comparison to control organisms (pH 7.8). This study also evidenced that seawater acidification induced oxidative stress in D. neapolitana, with individuals under lower pH levels showing higher LPO, lower GSH/GSSG values and higher enzymatic activity (CAT, SOD and GSTs). Additionally, organisms exposed to low pH presented significantly lower glycogen and protein content. Thus, the present work revealed the effects of pH on the polychaete species D. neapolitana, both at physiological and biochemical levels. Furthermore, our results validate the use of D. neapolitana as a test organism in laboratory-based bioassays, and also as an adequate bioindicator species to pH decrease in the environment. Finally, the regenerative capacity appears to be a promising endpoint to evaluate the effects of pH on D. neapolitana.     

Divergent responses of Atlantic cod to ocean acidification and food limitation

In order to understand the effect of global change on marine fishes, it is imperative to quantify the effects on fundamental parameters such as survival and growth. Larval survival and recruitment of the Atlantic cod (Gadus morhua) were found to be heavily impaired by end‐of‐century levels of ocean acidification. Here, we analysed larval growth among 35–36 days old surviving larvae, along with organ development and ossification of the skeleton. We combined CO₂ treatments (ambient: 503 µatm, elevated: 1,179 µatm) with food availability in order to evaluate the effect of energy limitation in addition to the ocean acidification stressor. As expected, larval size (as a proxy for growth) and skeletogenesis were positively affected by high food availability. We found significant interactions between acidification and food availability. Larvae fed ad libitum showed little difference in growth and skeletogenesis due to the CO₂ treatment. Larvae under energy limitation were significantly larger and had further developed skeletal structures in the elevated CO₂ treatment compared to the ambient CO₂ treatment. However, the elevated CO₂ group revealed impairments in critically important organs, such as the liver, and had comparatively smaller functional gills indicating a mismatch between size and function. It is therefore likely that individual larvae that had survived acidification treatments will suffer from impairments later during ontogeny. Our study highlights important allocation trade‐off between growth and organ development, which is critically important to interpret acidification effects on early life stages of fish.