Marine heatwave temperatures enhance larval performance but are meditated by paternal thermal history and inter-individual differences in the purple sea urchin, Strongylocentrotus purpuratus

Marine heatwave (MHW) events, characterized by periods of anomalous temperatures, are an increasingly prevalent threat to coastal marine ecosystems. Given the seasonal phenology of MHWs, the full extent of their biological consequences may depend on how these thermal stress events align with an organism's reproductive cycle. In organisms with more complex life cycles (e.g., many marine invertebrate species) the alignment of adult and larval environments may be an important factor determining offspring success, setting the stage for MHW events to influence reproduction and development in situ. Here, the influence of MHW-like temperatures on the early development of the California purple sea urchin, Strongylocentrotus purpuratus, were explored within the context of paternal thermal history. Based on temperature data collected during MHW events seen in Southern California from 2014-2020, adult urchins were acclimated to either MHW or non-MHW temperatures for 28 days before their sperm was used to produce embryos that were subsequently raised under varying thermal conditions. Once offspring reached an early larval stage, the impact of paternal and offspring environments were assessed on two aspects of offspring performance: larval size and thermal tolerance. Exposure to elevated temperatures during early development resulted in larger, more thermally tolerant larvae, with further influences of paternal identity and thermal history, respectively. The alignment of paternal and offspring exposure to MHW temperatures had additional positive benefits on larval thermal tolerance, but this tolerance significantly decreased when their thermal experience mismatched. As the highest recorded temperatures within past MHW events have occurred during the gametogenesis of many kelp forest benthic marine invertebrate species, such as the purple sea urchin, such parental mediated impacts may represent important drivers of future recruitment and population composition for these species.

Associations between DNA methylation and gene regulation depend on chromatin accessibility during transgenerational plasticity

BACKGROUND

Epigenetic processes are proposed to be a mechanism regulating gene expression during phenotypic plasticity. However, environmentally induced changes in DNA methylation exhibit little-to-no association with differential gene expression in metazoans at a transcriptome-wide level. It remains unexplored whether associations between environmentally induced differential methylation and expression are contingent upon other epigenomic processes such as chromatin accessibility. We quantified methylation and gene expression in larvae of the purple sea urchin Strongylocentrotus purpuratus exposed to different ecologically relevant conditions during gametogenesis (maternal conditioning) and modeled changes in gene expression and splicing resulting from maternal conditioning as functions of differential methylation, incorporating covariates for genomic features and chromatin accessibility. We detected significant interactions between differential methylation, chromatin accessibility, and genic feature type associated with differential expression and splicing.

RESULTS

Differential gene body methylation had significantly stronger effects on expression among genes with poorly accessible transcriptional start sites while baseline transcript abundance influenced the direction of this effect. Transcriptional responses to maternal conditioning were 4-13 × more likely when accounting for interactions between methylation and chromatin accessibility, demonstrating that the relationship between differential methylation and gene regulation is partially explained by chromatin state.

CONCLUSIONS

DNA methylation likely possesses multiple associations with gene regulation during transgenerational plasticity in S. purpuratus and potentially other metazoans, but its effects are dependent on chromatin accessibility and underlying genic features.

Genetic variation underlies plastic responses to global change drivers in the purple sea urchin, Strongylocentrotus purpuratus

Phenotypic plasticity and adaptive evolution enable population persistence in response to global change. However, there are few experiments that test how these processes interact within and across generations, especially in marine species with broad distributions experiencing spatially and temporally variable temperature and pCO2. We employed a quantitative genetics experiment with the purple sea urchin, Strongylocentrotus purpuratus, to decompose family-level variation in transgenerational and developmental plastic responses to ecologically relevant temperature and pCO2. Adults were conditioned to controlled non-upwelling (high temperature, low pCO2) or upwelling (low temperature, high pCO2) conditions. Embryos were reared in either the same conditions as their parents or the crossed environment, and morphological aspects of larval body size were quantified. We find evidence of family-level phenotypic plasticity in response to different developmental environments. Among developmental environments, there was substantial additive genetic variance for one body size metric when larvae developed under upwelling conditions, although this differed based on parental environment. Furthermore, cross-environment correlations indicate significant variance for genotype-by-environment interactive effects. Therefore, genetic variation for plasticity is evident in early stages of S. purpuratus, emphasizing the importance of adaptive evolution and phenotypic plasticity in organismal responses to global change.

Gene expression patterns of red sea urchins (Mesocentrotus franciscanus) exposed to different combinations of temperature and pCO2 during early development

BACKGROUND

The red sea urchin Mesocentrotus franciscanus is an ecologically important kelp forest herbivore and an economically valuable wild fishery species. To examine how M. franciscanus responds to its environment on a molecular level, differences in gene expression patterns were observed in embryos raised under combinations of two temperatures (13 °C or 17 °C) and two pCO2 levels (475 μatm or 1050 μatm). These combinations mimic various present-day conditions measured during and between upwelling events in the highly dynamic California Current System with the exception of the 17 °C and 1050 μatm combination, which does not currently occur. However, as ocean warming and acidification continues, warmer temperatures and higher pCO2 conditions are expected to increase in frequency and to occur simultaneously. The transcriptomic responses of the embryos were assessed at two developmental stages (gastrula and prism) in light of previously described plasticity in body size and thermotolerance under these temperature and pCO2 treatments.

RESULTS

Although transcriptomic patterns primarily varied by developmental stage, there were pronounced differences in gene expression as a result of the treatment conditions. Temperature and pCO2 treatments led to the differential expression of genes related to the cellular stress response, transmembrane transport, metabolic processes, and the regulation of gene expression. At each developmental stage, temperature contributed significantly to the observed variance in gene expression, which was also correlated to the phenotypic attributes of the embryos. On the other hand, the transcriptomic response to pCO2 was relatively muted, particularly at the prism stage.

CONCLUSIONS

M. franciscanus exhibited transcriptomic plasticity under different temperatures, indicating their capacity for a molecular-level response that may facilitate red sea urchins facing ocean warming as climate change continues. In contrast, the lack of a robust transcriptomic response, in combination with observations of decreased body size, under elevated pCO2 levels suggest that this species may be negatively affected by ocean acidification. High present-day pCO2 conditions that occur due to coastal upwelling may already be influencing populations of M. franciscanus.

Combined stress of ocean acidification and warming influence survival and drives differential gene expression patterns in the Antarctic pteropod, Limacina helicina antarctica

The ecologically important thecosome pteropods in the Limacina spp. complex have recently been the focus of studies examining the impacts global change factors - e.g., ocean acidification (OA) and ocean warming (OW) - on their performance and physiology. This focus is driven by conservation concerns where the health of pteropod populations is threatened by the high susceptibility of their shells to dissolution in low aragonite saturation states associated with OA and how coupling of these stressors may push pteropods past the limits of physiological plasticity. In this manipulation experiment, we describe changes in the transcriptome of the Antarctic pteropod, Limacina helicina antarctica, to these combined stressors. The conditions used in the laboratory treatments met or exceeded those projected for the Southern Ocean by the year 2100. We made two general observations regarding the outcome of the data: (1) Temperature was more influential than pH in terms of changing patterns of gene expression, and (2) these Antarctic pteropods appeared to have a significant degree of transcriptomic plasticity to respond to acute abiotic stress in the laboratory. In general, differential gene expression was observed amongst the treatments; here, for example, transcripts associated with maintaining protein structure and cell proliferation were up-regulated. To disentangle the effects of OA and OW, we used a weighted gene co-expression network analysis to explore patterns of change in the transcriptome. This approach identified gene networks associated with OW that were enriched for transcripts proposed to be involved in increasing membrane fluidity at warmer temperatures. Together these data provide evidence that L.h.antarctica has a limited capacity to acclimate to the combined conditions of OA and OW used in this study. This reduced scope of acclimation argues for continued study of how adaptation to polar aquatic environments may limit the plasticity of present-day populations in responding to future environmental change.

Ocean acidification promotes broad transcriptomic responses in marine metazoans: a literature survey

For nearly a decade, the metazoan-focused research community has explored the impacts of ocean acidification (OA) on marine animals, noting that changes in ocean chemistry can impact calcification, metabolism, acid-base regulation, stress response and behavior in organisms that hold high ecological and economic value. Because OA interacts with several key physiological processes in marine organisms, transcriptomics has become a widely-used method to characterize whole organism responses on a molecular level as well as inform mechanisms that explain changes in phenotypes observed in response to OA. In the past decade, there has been a notable rise in studies that examine transcriptomic responses to OA in marine metazoans, and here we attempt to summarize key findings across these studies. We find that organisms vary dramatically in their transcriptomic responses to pH although common patterns are often observed, including shifts in acid-base ion regulation, metabolic processes, calcification and stress response mechanisms. We also see a rise in transcriptomic studies examining organismal response to OA in a multi-stressor context, often reporting synergistic effects of OA and temperature. In addition, there is an increase in studies that use transcriptomics to examine the evolutionary potential of organisms to adapt to OA conditions in the future through population and transgenerational experiments. Overall, the literature reveals complex organismal responses to OA, in which some organisms will face more dramatic consequences than others. This will have wide-reaching impacts on ocean communities and ecosystems as a whole.

Transcriptional profiles of early stage red sea urchins (Mesocentrotus franciscanus) reveal differential regulation of gene expression across development

The red sea urchin, Mesocentrotus franciscanus, is an ecologically important kelp forest species that also serves as a valuable fisheries resource. In this study, we have assembled and annotated a developmental transcriptome for M. franciscanus that represents eggs and six stages of early development (8- to 16-cell, morula, hatched blastula, early gastrula, prism and early pluteus). Characterization of the transcriptome revealed distinct patterns of gene expression that corresponded to major developmental and morphological processes. In addition, the period during which maternally-controlled transcription was terminated and the zygotic genome was activated, the maternal-to-zygotic transition (MZT), was found to begin during early cleavage and persist through the hatched blastula stage, an observation that is similar to the timing of the MZT in other sea urchin species. The presented developmental transcriptome will serve as a useful resource for investigating, in both an ecological and fisheries context, how the early developmental stages of this species respond to environmental stressors.

Seasonal transcriptomes of the Antarctic pteropod, Limacina helicina antarctica

High latitude seas will be among the first marine systems to be impacted by ocean acidification (OA). Previous research studying the effects of OA on the pteropod, Limacina helicina antarctica, has led this species to be identified as a sentinel organism for OA in polar oceans. Here, we present gene expression data on L. h. antarctica, collected in situ during the seasonal transition from early spring to early summer. Our findings suggest that after over-wintering under seasonal sea ice, pteropods progress toward full maturity in the early summer when food becomes increasingly available. This progression is highlighted by a dramatic shift in gene expression that supports the development of cytoskeletal structures, membrane ion transportation, and metabolically important enzymes associated with glycolysis. In addition, we observed signs of defense of genomic integrity and maturation as evidenced by an up-regulation of genes involved in DNA replication, DNA repair, and gametogenesis. These data contribute to a broader understanding of the life-cycle dynamics for L. h. antarctica and provide key insights into the transcriptomic signals of pteropod maturation and growth during this key seasonal transition.

Lipid consumption in coral larvae differs among sites: a consideration of environmental history in a global ocean change scenario

The success of early life-history stages is an environmentally sensitive bottleneck for many marine invertebrates. Responses of larvae to environmental stress may vary due to differences in maternal investment of energy stores and acclimatization/adaptation of a population to local environmental conditions. In this study, we compared two populations from sites with different environmental regimes (Moorea and Taiwan). We assessed the responses of Pocillopora damicornis larvae to two future co-occurring environmental stressors: elevated temperature and ocean acidification. Larvae from Taiwan were more sensitive to temperature, producing fewer energy-storage lipids under high temperature. In general, planulae in Moorea and Taiwan responded similarly to pCO₂ Additionally, corals in the study sites with different environments produced larvae with different initial traits, which may have shaped the different physiological responses observed. Notably, under ambient conditions, planulae in Taiwan increased their stores of wax ester and triacylglycerol in general over the first 24 h of their dispersal, whereas planulae from Moorea consumed energy-storage lipids in all cases. Comparisons of physiological responses of P. damicornis larvae to conditions of ocean acidification and warming between sites across the species' biogeographic range illuminates the variety of physiological responses maintained within P. damicornis, which may enhance the overall persistence of this species in the light of global climate change.

Additive effects of pCO2 and temperature on respiration rates of the Antarctic pteropod Limacina helicina antarctica

The Antarctic pteropod, Limacina helicina antarctica, is a dominant member of the zooplankton in the Ross Sea and supports the vast diversity of marine megafauna that designates this region as an internationally protected area. Here, we observed the response of respiration rate to abiotic stressors associated with global change-environmentally relevant temperature treatments (-0.8°C, 4°C) and pH treatments reflecting current-day and future modeled extremes (8.2, 7.95 and 7.7 pH at -0.8°C; 8.11, 7.95 and 7.7 pH at 4°C). Sampling repeatedly over a 14-day period in laboratory experiments and using microplate respirometry techniques, we found that the metabolic rate of juvenile pteropods increased in response to low-pH exposure (pH 7.7) at -0.8°C, a near-ambient temperature. Similarly, metabolic rate increased when pteropods were exposed simultaneously to multiple stressors: lowered pH conditions (pH 7.7) and a high temperature (4°C). Overall, the results showed that pCO₂ and temperature interact additively to affect metabolic rates in pteropods. Furthermore, we found that L. h. antarctica can tolerate acute exposure to temperatures far beyond its maximal habitat temperature. Overall, L. h. antarctica appears to be susceptible to pH and temperature stress, two abiotic stressors which are expected to be especially deleterious for ectothermic marine metazoans in polar seas.

Gene expression profiling during the embryo-to-larva transition in the giant red sea urchin Mesocentrotus franciscanus

In echinoderms, major morphological transitions during early development are attributed to different genetic interactions and changes in global expression patterns that shape the regulatory program for the specification of embryonic territories. In order more thoroughly to understand these biological and molecular processes, we examined the transcriptome structure and expression profiles during the embryo‐to‐larva transition of a keystone species, the giant red sea urchin Mesocentrotus franciscanus. Using a de novo assembly approach, we obtained 176,885 transcripts from which 60,439 (34%) had significant alignments to known proteins. From these transcripts, ~80% were functionally annotated allowing the identification of ~2,600 functional, structural, and regulatory genes involved in developmental process. Analysis of expression profiles between gastrula and pluteus stages of M. franciscanus revealed 791 differentially expressed genes with 251 GO overrepresented terms. For gastrula, up‐regulated GO terms were mainly linked to cell differentiation and signal transduction involved in cell cycle checkpoints. In the pluteus stage, major GO terms were associated with phosphoprotein phosphatase activity, muscle contraction, and olfactory behavior, among others. Our evolutionary comparative analysis revealed that several of these genes and functional pathways are highly conserved among echinoids, holothuroids, and ophiuroids.

Transcriptomic responses to seawater acidification among sea urchin populations inhabiting a natural pH mosaic

Increasing awareness of spatial and temporal variation in ocean pH suggests some marine populations may be adapted to local pH regimes and will therefore respond differently to present-day pH variation and to long-term ocean acidification. In the Northeast Pacific Ocean, differences in the strength of coastal upwelling cause latitudinal variation in prevailing pH regimes that are hypothesized to promote local adaptation and unequal pH tolerance among resident populations. In this study, responses to experimental seawater acidification were compared among embryos and larvae from six populations of purple sea urchins (Strongylocentrotus purpuratus) inhabiting areas that differ in their frequency of low pH exposure and that prior research suggests are locally adapted to seawater pH. Transcriptomic analyses demonstrate urchin populations most frequently exposed to low pH seawater responded to experimental acidification by expressing genes within major ATP-producing pathways at greater levels than populations encountering low pH less often. Multiple genes within the tricarboxylic acid cycle, electron transport chain and fatty acid beta oxidation pathways were upregulated in urchin populations experiencing low pH conditions most frequently. These same metabolic pathways were significantly over-represented among genes both expressed in a population-specific manner and putatively under selection to enhance low pH tolerance. Collectively, these data suggest natural selection is acting on metabolic gene networks to redirect ATP toward maintaining acid-base homeostasis and enhance tolerance of seawater acidification. As a trade-off, marine populations more tolerant of low pH may have less energy to put towards other aspects of fitness and to respond to additional ocean change.

Sensitivity of sea urchin fertilization to pH varies across a natural pH mosaic

In the coastal ocean, temporal fluctuations in pH vary dramatically across biogeographic ranges. How such spatial differences in pH variability regimes might shape ocean acidification resistance in marine species remains unknown. We assessed the pH sensitivity of the sea urchin Strongylocentrotus purpuratus in the context of ocean pH variability. Using unique male-female pairs, originating from three sites with similar mean pH but different variability and frequency of low pH (pHT ≤ 7.8) exposures, fertilization was tested across a range of pH (pHT 7.61-8.03) and sperm concentrations. High fertilization success was maintained at low pH via a slight right shift in the fertilization function across sperm concentration. This pH effect differed by site. Urchins from the site with the narrowest pH variability regime exhibited the greatest pH sensitivity. At this site, mechanistic fertilization dynamics models support a decrease in sperm-egg interaction rate with decreasing pH. The site differences in pH sensitivity build upon recent evidence of local pH adaptation in S. purpuratus and highlight the need to incorporate environmental variability in the study of global change biology.

Long-term, high frequency in situ measurements of intertidal mussel bed temperatures using biomimetic sensors

At a proximal level, the physiological impacts of global climate change on ectothermic organisms are manifest as changes in body temperatures. Especially for plants and animals exposed to direct solar radiation, body temperatures can be substantially different from air temperatures. We deployed biomimetic sensors that approximate the thermal characteristics of intertidal mussels at 71 sites worldwide, from 1998-present. Loggers recorded temperatures at 10–30 min intervals nearly continuously at multiple intertidal elevations. Comparisons against direct measurements of mussel tissue temperature indicated errors of ~2.0–2.5 °C, during daily fluctuations that often exceeded 15°–20 °C. Geographic patterns in thermal stress based on biomimetic logger measurements were generally far more complex than anticipated based only on ‘habitat-level’ measurements of air or sea surface temperature. This unique data set provides an opportunity to link physiological measurements with spatially- and temporally-explicit field observations of body temperature.

Physiological plasticity and local adaptation to elevated pCO2 in calcareous algae: an ontogenetic and geographic approach

To project how ocean acidification will impact biological communities in the future, it is critical to understand the potential for local adaptation and the physiological plasticity of marine organisms throughout their entire life cycle, as some stages may be more vulnerable than others. Coralline algae are ecosystem engineers that play significant functional roles in oceans worldwide and are considered vulnerable to ocean acidification. Using different stages of coralline algae, we tested the hypothesis that populations living in environments with higher environmental variability and exposed to higher levels of pCO ₂ would be less affected by high pCO ₂ than populations from a more stable environment experiencing lower levels of pCO ₂. Our results show that spores are less sensitive to elevated pCO ₂ than adults. Spore growth and mortality were not affected by pCO ₂ level; however, elevated pCO ₂ negatively impacted the physiology and growth rates of adults, with stronger effects in populations that experienced both lower levels of pCO ₂ and lower variability in carbonate chemistry, suggesting local adaptation. Differences in physiological plasticity and the potential for adaptation could have important implications for the ecological and evolutionary responses of coralline algae to future environmental changes.

Interacting environmental mosaics drive geographic variation in mussel performance and predation vulnerability

Although theory suggests geographic variation in species' performance is determined by multiple niche parameters, little consideration has been given to the spatial structure of interacting stressors that may shape local and regional vulnerability to global change. Here, we use spatially explicit mosaics of carbonate chemistry, food availability and temperature spanning 1280 km of coastline to test whether persistent, overlapping environmental mosaics mediate the growth and predation vulnerability of a critical foundation species, the mussel Mytilus californianus. We find growth was highest and predation vulnerability was lowest in dynamic environments with frequent exposure to low pH seawater and consistent food. In contrast, growth was lowest and predation vulnerability highest when exposure to low pH seawater was decoupled from high food availability, or in exceptionally warm locations. These results illustrate how interactions among multiple drivers can cause unexpected, yet persistent geographic mosaics of species performance, interactions and vulnerability to environmental change.

Interacting environmental mosaics drive geographic variation in mussel performance and predation vulnerability

Although theory suggests geographic variation in species' performance is determined by multiple niche parameters, little consideration has been given to the spatial structure of interacting stressors that may shape local and regional vulnerability to global change. Here, we use spatially explicit mosaics of carbonate chemistry, food availability and temperature spanning 1280 km of coastline to test whether persistent, overlapping environmental mosaics mediate the growth and predation vulnerability of a critical foundation species, the mussel Mytilus californianus. We find growth was highest and predation vulnerability was lowest in dynamic environments with frequent exposure to low pH seawater and consistent food. In contrast, growth was lowest and predation vulnerability highest when exposure to low pH seawater was decoupled from high food availability, or in exceptionally warm locations. These results illustrate how interactions among multiple drivers can cause unexpected, yet persistent geographic mosaics of species performance, interactions and vulnerability to environmental change.

The effect of temperature adaptation on the ubiquitin-proteasome pathway in notothenioid fishes

There is an accumulating body of evidence suggesting that the sub-zero Antarctic marine environment places physiological constraints on protein homeostasis. Levels of ubiquitin (Ub)-conjugated proteins, 20S proteasome activity and mRNA expression of many proteins involved in both the ubiquitin (Ub) tagging of damaged proteins as well as the different complexes of the 26S proteasome were measured to examine whether there is thermal compensation of the Ub-proteasome pathway in Antarctic fishes to better understand the efficiency of the protein degradation machinery in polar species. Both Antarctic (Trematomus bernacchii, Pagothenia borchgrevinki) and non-Antarctic (Notothenia angustata, Bovichtus variegatus) notothenioids were included in this study to investigate the mechanisms of cold adaptation of this pathway in polar species. Overall, there were significant differences in the levels of Ub-conjugated proteins between the Antarctic notothenioids and B. variegatus, with N. angustata possessing levels very similar to the Antarctic fishes. Proteasome activity in the gills of Antarctic fishes demonstrated a high degree of temperature compensation such that activity levels were similar to activities measured in their temperate relatives at ecologically relevant temperatures. A similar level of thermal compensation of proteasome activity was not present in the liver of two Antarctic fishes. Higher gill proteasome activity is likely due in part to higher cellular levels of proteins involved in the Ub-proteasome pathway, as evidenced by high mRNA expression of relevant genes. Reduced activity of the Ub-proteasome pathway does not appear to be the mechanism responsible for elevated levels of denatured proteins in Antarctic fishes, at least in the gills.

Assessing the components of adaptive capacity to improve conservation and management efforts under global change

Natural-resource managers and other conservation practitioners are under unprecedented pressure to categorize and quantify the vulnerability of natural systems based on assessment of the exposure, sensitivity, and adaptive capacity of species to climate change. Despite the urgent need for these assessments, neither the theoretical basis of adaptive capacity nor the practical issues underlying its quantification has been articulated in a manner that is directly applicable to natural-resource management. Both are critical for researchers, managers, and other conservation practitioners to develop reliable strategies for assessing adaptive capacity. Drawing from principles of classical and contemporary research and examples from terrestrial, marine, plant, and animal systems, we examined broadly the theory behind the concept of adaptive capacity. We then considered how interdisciplinary, trait- and triage-based approaches encompassing the oft-overlooked interactions among components of adaptive capacity can be used to identify species and populations likely to have higher (or lower) adaptive capacity. We identified the challenges and value of such endeavors and argue for a concerted interdisciplinary research approach that combines ecology, ecological genetics, and eco-physiology to reflect the interacting components of adaptive capacity. We aimed to provide a basis for constructive discussion between natural-resource managers and researchers, discussions urgently needed to identify research directions that will deliver answers to real-world questions facing resource managers, other conservation practitioners, and policy makers. Directing research to both seek general patterns and identify ways to facilitate adaptive capacity of key species and populations within species, will enable conservation ecologists and resource managers to maximize returns on research and management investment and arrive at novel and dynamic management and policy decisions.

Ocean acidification research in the 'post-genomic' era: Roadmaps from the purple sea urchin Strongylocentrotus purpuratus

Advances in nucleic acid sequencing technology are removing obstacles that historically prevented use of genomics within ocean change biology. As one of the first marine calcifiers to have its genome sequenced, purple sea urchins (Strongylocentrotus purpuratus) have been the subject of early research exploring genomic responses to ocean acidification, work that points to future experiments and illustrates the value of expanding genomic resources to other marine organisms in this new 'post-genomic' era. This review presents case studies of S. purpuratus demonstrating the ability of genomic experiments to address major knowledge gaps within ocean acidification. Ocean acidification research has focused largely on species vulnerability, and studies exploring mechanistic bases of tolerance toward low pH seawater are comparatively few. Transcriptomic responses to high pCO₂ seawater in a population of urchins already encountering low pH conditions have cast light on traits required for success in future oceans. Secondly, there is relatively little information on whether marine organisms possess the capacity to adapt to oceans progressively decreasing in pH. Genomics offers powerful methods to investigate evolutionary responses to ocean acidification and recent work in S. purpuratus has identified genes under selection in acidified seawater. Finally, relatively few ocean acidification experiments investigate how shifts in seawater pH combine with other environmental factors to influence organism performance. In S. purpuratus, transcriptomics has provided insight into physiological responses of urchins exposed simultaneously to warmer and more acidic seawater. Collectively, these data support that similar breakthroughs will occur as genomic resources are developed for other marine species.

Abiotic versus biotic drivers of ocean pH variation under fast sea ice in McMurdo Sound, Antarctica

Ocean acidification is expected to have a major effect on the marine carbonate system over the next century, particularly in high latitude seas. Less appreciated is natural environmental variation within these systems, particularly in terms of pH, and how this natural variation may inform laboratory experiments. In this study, we deployed sensor-equipped moorings at 20 m depths at three locations in McMurdo Sound, comprising deep (bottom depth>200 m: Hut Point Peninsula) and shallow environments (bottom depth ∼25 m: Cape Evans and New Harbor). Our sensors recorded high-frequency variation in pH (Hut Point and Cape Evans only), tide (Cape Evans and New Harbor), and water mass properties (temperature and salinity) during spring and early summer 2011. These collective observations showed that (1) pH differed spatially both in terms of mean pH (Cape Evans: 8.009±0.015; Hut Point: 8.020±0.007) and range of pH (Cape Evans: 0.090; Hut Point: 0.036), and (2) pH was not related to the mixing of two water masses, suggesting that the observed pH variation is likely not driven by this abiotic process. Given the large daily fluctuation in pH at Cape Evans, we developed a simple mechanistic model to explore the potential for biotic processes – in this case algal photosynthesis – to increase pH by fixing carbon from the water column. For this model, we incorporated published photosynthetic parameters for the three dominant algal functional groups found at Cape Evans (benthic fleshy red macroalgae, crustose coralline algae, and sea ice algal communities) to estimate oxygen produced/carbon fixed from the water column underneath fast sea ice and the resulting pH change. These results suggest that biotic processes may be a primary driver of pH variation observed under fast sea ice at Cape Evans and potentially at other shallow sites in McMurdo Sound.

Ocean acidification and fertilization in the antarctic sea urchin Sterechinus neumayeri: the importance of polyspermy

Ocean acidification (OA), the reduction of the seawater pH as a result of increasing levels of atmospheric CO2, is an important climate change stressor in the Southern Ocean and Antarctic. We examined the impact of OA on fertilization success in the Antarctic sea urchin Sterechinus neumayeri using pH treatment conditions reflective of the current and near-future "pH seascape" for this species: current (control: pH 8.052, 384.1 μatm of pCO2), a high CO2 treatment approximating the 0.2-0.3 unit decrease in pH predicted for 2100 (high CO2: pH 7.830, 666.0 μatm of pCO2), and an intermediate medium CO2 (pH 7.967, 473.4 μatm of pCO2). Using a fertilization kinetics approach and mixed-effect models, we observed significant variation in the OA response between individual male/female pairs (N = 7) and a significant population-level increase (70-100%) in tb (time for a complete block to polyspermy) at medium and high CO2, a mechanism that potentially explains the higher levels of abnormal development seen in OA conditions. However, two pairs showed higher fertilization success with CO2 treatment and a nonsignificant effect. Future studies should focus on the mechanisms and levels of interindividual variability in OA response, so that we can consider the potential for selection and adaptation of organisms to a future ocean.

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.

Temperature and CO(2) additively regulate physiology, morphology and genomic responses of larval sea urchins, Strongylocentrotus purpuratus

Ocean warming and ocean acidification, both consequences of anthropogenic production of CO2, will combine to influence the physiological performance of many species in the marine environment. In this study, we used an integrative approach to forecast the impact of future ocean conditions on larval purple sea urchins (Strongylocentrotus purpuratus) from the northeast Pacific Ocean. In laboratory experiments that simulated ocean warming and ocean acidification, we examined larval development, skeletal growth, metabolism and patterns of gene expression using an orthogonal comparison of two temperature (13°C and 18°C) and pCO2 (400 and 1100 μatm) conditions. Simultaneous exposure to increased temperature and pCO2 significantly reduced larval metabolism and triggered a widespread downregulation of histone encoding genes. pCO2 but not temperature impaired skeletal growth and reduced the expression of a major spicule matrix protein, suggesting that skeletal growth will not be further inhibited by ocean warming. Importantly, shifts in skeletal growth were not associated with developmental delay. Collectively, our results indicate that global change variables will have additive effects that exceed thresholds for optimized physiological performance in this keystone marine species.

Transcriptomic responses to ocean acidification in larval sea urchins from a naturally variable pH environment

Some marine ecosystems already experience natural declines in pH approximating those predicted with future anthropogenic ocean acidification (OA), the decline in seawater pH caused by the absorption of atmospheric CO2 . The molecular mechanisms that allow organisms to inhabit these low pH environments, particularly those building calcium carbonate skeletons, are unknown. Also uncertain is whether an enhanced capacity to cope with present day pH variation will confer resistance to future OA. To address these issues, we monitored natural pH dynamics within an intertidal habitat in the Northeast Pacific, demonstrating that upwelling exposes resident species to pH regimes not predicted to occur elsewhere until 2100. Next, we cultured the progeny of adult purple sea urchins (Strongylocentrotus purpuratus) collected from this region in CO2 -acidified seawater representing present day and near future ocean scenarios and monitored gene expression using transcriptomics. We hypothesized that persistent exposure to upwelling during evolutionary history will have selected for increased pH tolerance in this population and that their transcriptomic response to low pH seawater would provide insight into mechanisms underlying pH tolerance in a calcifying species. Resulting expression patterns revealed two important trends. Firstly, S. purpuratus larvae may alter the bioavailability of calcium and adjust skeletogenic pathways to sustain calcification in a low pH ocean. Secondly, larvae use different strategies for coping with different magnitudes of pH stress: initiating a robust transcriptional response to present day pH regimes but a muted response to near future conditions. Thus, an enhanced capacity to cope with present day pH variation may not translate into success in future oceans.

Growth attenuation with developmental schedule progression in embryos and early larvae of Sterechinus neumayeri raised under elevated CO2

The Southern Ocean, a region that will be an ocean acidification hotspot in the near future, is home to a uniquely adapted fauna that includes a diversity of lightly-calcified invertebrates. We exposed the larvae of the echinoid Sterechinus neumayeri to environmental levels of CO(2) in McMurdo Sound (control: 410 µatm, Ω = 1.35) and mildly elevated pCO(2) levels, both near the level of the aragonite saturation horizon (510 µatm pCO(2), Ω = 1.12), and to under-saturating conditions (730 µatm, Ω = 0.82). Early embryological development was normal under these conditions with the exception of the hatching process, which was slightly delayed. Appearance of the initial calcium carbonate (CaCO(3)) spicule nuclei among the primary mesenchyme cells of the gastrulae was synchronous between control and elevated pCO(2) treatments. However, by prism (7 days after the initial appearance of the spicule nucleus), elongating arm rod spicules were already significantly shorter in the highest CO(2) treatment. Unfed larvae in the 730 µatm pCO(2) treatment remained significantly smaller than unfed control larvae at days 15-30, and larvae in the 510 µatm treatment were significantly smaller at day 20. At day 30, the arm lengths were more differentiated between 730 µatm and control CO(2) treatments than were body lengths as components of total length. Arm length is the most plastic morphological aspect of the echinopluteus, and appears to exhibit the greatest response to high pCO(2)/low pH/low carbonate, even in the absence of food. Thus, while the effects of elevated pCO(2) representative of near future climate scenarios are proportionally minor on these early developmental stages, the longer term effects on these long-lived invertebrates is still unknown.

Development under elevated pCO2 conditions does not affect lipid utilization and protein content in early life-history stages of the purple sea urchin, Strongylocentrotus purpuratus

Ocean acidification (OA) is expected to have a major impact on marine species, particularly during early life-history stages. These effects appear to be species-specific and may include reduced survival, altered morphology, and depressed metabolism. However, less information is available regarding the bioenergetics of development under elevated CO(2) conditions. We examined the biochemical and morphological responses of Strongylocentrotus purpuratus during early development under ecologically relevant levels of pCO(2) (365, 1030, and 1450 μatm) that may occur during intense upwelling events. The principal findings of this study were (1) lipid utilization rates and protein content in S. purpuratus did not vary with pCO(2); (2) larval growth was reduced at elevated pCO(2) despite similar rates of energy utilization; and (3) relationships between egg phospholipid content and larval length were found under control but not high pCO(2) conditions. These results suggest that this species may either prioritize endogenous energy toward development and physiological function at the expense of growth, or that reduced larval length may be strictly due to higher costs of growth under OA conditions. This study highlights the need to further expand our knowledge of the physiological mechanisms involved in OA response in order to better understand how present populations may respond to global environmental change.

Early developmental gene regulation in Strongylocentrotus purpuratus embryos in response to elevated CO₂ seawater conditions

Ocean acidification, or the increased uptake of CO(2) by the ocean due to elevated atmospheric CO(2) concentrations, may variably impact marine early life history stages, as they may be especially susceptible to changes in ocean chemistry. Investigating the regulatory mechanisms of early development in an environmental context, or ecological development, will contribute to increased understanding of potential organismal responses to such rapid, large-scale environmental changes. We examined transcript-level responses to elevated seawater CO(2) during gastrulation and the initiation of spiculogenesis, two crucial developmental processes in the purple sea urchin, Strongylocentrotus purpuratus. Embryos were reared at the current, accepted oceanic CO(2) concentration of 380 microatmospheres (μatm), and at the elevated levels of 1000 and 1350 μatm, simulating predictions for oceans and upwelling regions, respectively. The seven genes of interest comprised a subset of pathways in the primary mesenchyme cell gene regulatory network (PMC GRN) shown to be necessary for the regulation and execution of gastrulation and spiculogenesis. Of the seven genes, qPCR analysis indicated that elevated CO(2) concentrations only had a significant but subtle effect on two genes, one important for early embryo patterning, Wnt8, and the other an integral component in spiculogenesis and biomineralization, SM30b. Protein levels of another spicule matrix component, SM50, demonstrated significant variable responses to elevated CO(2). These data link the regulation of crucial early developmental processes with the environment that these embryos would be developing within, situating the study of organismal responses to ocean acidification in a developmental context.

Patterns of Hsp gene expression in ectothermic marine organisms on small to large biogeographic scales

The goal of my research program is to employ biochemical and molecular techniques to gain ecological insight into the role of temperature in setting species' distribution patterns in the marine environment. Our central focus is the study of the environmental regulation of gene expression, where we are particularly interested in a set of inducible molecular chaperones, the heat-shock proteins (Hsps), and how the expression of these genes varies with the thermal history of organisms in natural populations. The primary study organisms are intertidal invertebrates and marine fish that experience dramatic changes in body temperature on varying temporal and spatial scales. In this review, I present studies that address the variable expression of Hsps, how these genes are differentially regulated in ectothermic animals in response to ecologically relevant temperature conditions, and how such plasticity in gene expression contributes to physiological plasticity in the environment.

Patterns of variation in levels of hsp70 in natural rocky shore populations from microscales to mesoscales

An important step in connecting the organismal response to thermal stress to patterns of community structure is determining at what scale discernable levels of variation are manifested. The temperature signal to which organisms may potentially respond varies at many spatial scales including microhabitat, tidal height, site and latitude. A number of studies have taken physiological assessment of the heat shock response (HSR) into the intertidal both as a tool for examining the HSR in nature and for examining the utility of HSR molecules as population or community level indicators. Most commonly, immunodetection of the total pool of the Hsp70 family of isoforms is used. Here we present data on levels of Hsp70 in intertidal organisms from microhabitat to the mesoscale. Our data and previously published work show that Hsp70 levels vary at all scales examined, similar to other physical and biological variables of interest. This demonstrates both the potential utility of Hsp70 detection as a molecular tool for field biologists and to the care that must be taken in assessing scale of variation when looking for potential bioindicator molecules.

Defining the limits of physiological plasticity: how gene expression can assess and predict the consequences of ocean change

Anthropogenic stressors, such as climate change, are driving fundamental shifts in the abiotic characteristics of marine ecosystems. As the environmental aspects of our world's oceans deviate from evolved norms, of major concern is whether extant marine species possess the capacity to cope with such rapid change. In what many scientists consider the post-genomic era, tools that exploit the availability of DNA sequence information are being increasingly recognized as relevant to questions surrounding ocean change and marine conservation. In this review, we highlight the application of high-throughput gene-expression profiling, primarily transcriptomics, to the field of marine conservation physiology. Through the use of case studies, we illustrate how gene expression can be used to standardize metrics of sub-lethal stress, track organism condition in natural environments and bypass phylogenetic barriers that hinder the application of other physiological techniques to conservation. When coupled with fine-scale monitoring of environmental variables, gene-expression profiling provides a powerful approach to conservation capable of informing diverse issues related to ocean change, from coral bleaching to the spread of invasive species. Integrating novel approaches capable of improving existing conservation strategies, including gene-expression profiling, will be critical to ensuring the ecological and economic health of the global ocean.

High-frequency dynamics of ocean pH: a multi-ecosystem comparison

The effect of Ocean Acidification (OA) on marine biota is quasi-predictable at best. While perturbation studies, in the form of incubations under elevated pCO₂, reveal sensitivities and responses of individual species, one missing link in the OA story results from a chronic lack of pH data specific to a given species' natural habitat. Here, we present a compilation of continuous, high-resolution time series of upper ocean pH, collected using autonomous sensors, over a variety of ecosystems ranging from polar to tropical, open-ocean to coastal, kelp forest to coral reef. These observations reveal a continuum of month-long pH variability with standard deviations from 0.004 to 0.277 and ranges spanning 0.024 to 1.430 pH units. The nature of the observed variability was also highly site-dependent, with characteristic diel, semi-diurnal, and stochastic patterns of varying amplitudes. These biome-specific pH signatures disclose current levels of exposure to both high and low dissolved CO₂, often demonstrating that resident organisms are already experiencing pH regimes that are not predicted until 2100. Our data provide a first step toward crystallizing the biophysical link between environmental history of pH exposure and physiological resilience of marine organisms to fluctuations in seawater CO₂. Knowledge of this spatial and temporal variation in seawater chemistry allows us to improve the design of OA experiments: we can test organisms with a priori expectations of their tolerance guardrails, based on their natural range of exposure. Such hypothesis-testing will provide a deeper understanding of the effects of OA. Both intuitively simple to understand and powerfully informative, these and similar comparative time series can help guide management efforts to identify areas of marine habitat that can serve as refugia to acidification as well as areas that are particularly vulnerable to future ocean change.

Transcriptome profiles link environmental variation and physiological response of Mytilus californianus between Pacific tides

SUMMARY: The marine intertidal zone is characterized by large variation in temperature, pH, dissolved oxygen and the supply of nutrients and food on seasonal and daily time scales. These oceanic fluctuations drive of ecological processes such as recruitment, competition and consumer-prey interactions largely via physiological mehcanisms. Thus, to understand coastal ecosystem dynamics and responses to climate change, it is crucial to understand these mechanisms.Here we utilize transcriptome analysis of the physiological response of the mussel Mytilus californianus at different spatial scales to gain insight into these mechanisms. We used mussels inhabiting different vertical locations within Strawberry Hill on Cape Perpetua, OR and Boiler Bay on Cape Foulweather, OR to study inter- and intra-site variation of gene expression.The results highlight two distinct gene expression signatures related to the cycling of metabolic activity and perturbations to cellular homeostasis. Intermediate spatial scales show a strong influence of oceanographic differences in food and stress environments between sites separated by ~65 km.Together, these new insights into environmental control of gene expression may allow understanding of important physiological drivers within and across populations.

The Effect of Ocean Acidification on Calcifying Organisms in Marine Ecosystems: An Organism-to-Ecosystem Perspective

Ocean acidification (OA), a consequence of anthropogenic carbon dioxide emissions, poses a serious threat to marine organisms in tropical, open-ocean, coastal, deep-sea, and high-latitude sea ecosystems. The diversity of taxonomic groups that precipitate calcium carbonate from seawater are at particularly high risk. Here we review the rapidly expanding literature concerning the biological and ecological impacts of OA on calcification, using a cross-scale, process-oriented approach. In comparison to calcification, we find that areas such as fertilization, early life-history stages, and interaction with synergistic stressors are understudied. Although understanding the long-term consequences of OA are critical, available studies are largely short-term experiments that do not allow for tests of long-term acclimatization or adaptation. Future research on the phenotypic plasticity of contemporary organisms and interpretations of performance in the context of current environmental heterogeneity of pCO2 will greatly aid in our understanding of how organisms will respond to OA in the future.

Thermal tolerance of Strongylocentrotus purpuratus early life history stages: mortality, stress-induced gene expression and biogeographic patterns

In this study, we examined the differential thermal tolerance of Strongylocentrotus purpuratus early life history stages by comparing high temperature-induced mortality and the relative levels of the stress-induced gene, hsp70, between S. purpuratus embryos and larvae from adults collected throughout the species range. There was no significant difference between gastrulae and 4-arm plutei mortality from all sites examined. Furthermore, there was little variability in temperature tolerance across the biogeographic range as southern gastrulae and 4-arm plutei exhibited similar tolerances to northern individuals. Relative levels of hsp70 mRNA expression did not differ overall between the two developmental stages at each site. Across sites, all gastrulae and 4-arm plutei exhibited maximum hsp70 expression at approximately 25°C; however, the range of hsp70 expression was narrower in southern individuals, suggesting they are living closer to their upper thermal limit than northern individuals.

Living in the now: physiological mechanisms to tolerate a rapidly changing environment

Rising atmospheric carbon dioxide has resulted in scientific projections of changes in global temperatures, climate in general, and surface seawater chemistry. Although the consequences to ecosystems and communities of metazoans are only beginning to be revealed, a key to forecasting expected changes in animal communities is an understanding of species' vulnerability to a changing environment. For example, environmental stressors may affect a particular species by driving that organism outside a tolerance window, by altering the costs of metabolic processes under the new conditions, or by changing patterns of development and reproduction. Implicit in all these examples is the foundational understanding of physiological mechanisms and how a particular environmental driver (e.g., temperature and ocean acidification) will be transduced through the animal to alter tolerances and performance. In this review, we highlight examples of mechanisms, focusing on those underlying physiological plasticity, that operate in contemporary organisms as a means to consider physiological responses that are available to organisms in the future.

Physiological tolerances across latitudes: thermal sensitivity of larval marine snails (Nucella spp.)

A critical step in understanding how temperature will affect biodiversity in coastal ecosystems is to gain insight into how the tolerances, and ultimately survival, of early life history stages will influence the distribution and abundance of adults. We assessed the thermal tolerance of encapsulated veliger-stage larvae of a common dogwhelk, Nucella ostrina, that occur in the rocky intertidal zone on the west coast of North America. Results showed that veligers collected from northern latitudes in Washington State were less tolerant of heat stress than those from central sites in California. For all sites, we found there to be a subtle difference between the temperatures at which veligers first began to die compared to when veligers reached 100% mortality. On a biogeographic scale, the LT₅₀ temperatures, a measure of larval sensitivity, for N. ostrina veligers displayed a strong latitudinal trend. These findings provide a conservative measurement of the upper thermal limits of encapsulated veligers while illustrating how these early life history stages could be physiologically compromised under future climate warming scenarios.

Transcriptomic response of sea urchin larvae Strongylocentrotus purpuratus to CO2-driven seawater acidification

Ocean acidification from the uptake of anthropogenic CO2 is expected to have deleterious consequences for many calcifying marine animals. Forecasting the vulnerability of these marine organisms to climate change is linked to an understanding of whether species possess the physiological capacity to compensate for the potentially adverse effects of ocean acidification. We carried out a microarray-based transcriptomic analysis of the physiological response of larvae of a calcifying marine invertebrate, the purple sea urchin, Strongylocentrotus purpuratus, to CO2-driven seawater acidification. In lab-based cultures, larvae were raised under conditions approximating current ocean pH conditions (pH 8.01) and at projected, more acidic pH conditions (pH 7.96 and 7.88) in seawater aerated with CO2 gas. Targeting expression of ∼1000 genes involved in several biological processes, this study captured changes in gene expression patterns that characterize the transcriptomic response to CO2-driven seawater acidification of developing sea urchin larvae. In response to both elevated CO2 scenarios, larvae underwent broad scale decreases in gene expression in four major cellular processes:biomineralization, cellular stress response, metabolism and apoptosis. This study underscores that physiological processes beyond calcification are impacted greatly, suggesting that overall physiological capacity and not just a singular focus on biomineralization processes is essential for forecasting the impact of future CO2 conditions on marine organisms. Conducted on targeted and vulnerable species, genomics-based studies, such as the one highlighted here, have the potential to identify potential `weak links' in physiological function that may ultimately determine an organism's capacity to tolerate future ocean conditions.

Is cold the new hot? Elevated ubiquitin-conjugated protein levels in tissues of Antarctic fish as evidence for cold-denaturation of proteins in vivo

Levels of ubiquitin (Ub)-conjugated proteins, as an index of misfolded or damaged proteins, were measured in notothenioid fishes, with both Antarctic (Trematomus bernacchii, T. pennellii, Pagothenia borchgrevinki) and non-Antarctic (Notothenia angustata, Bovichtus variegatus) distributions, as well as non-notothenioid fish from the Antarctic (Lycodichthys dearborni, Family Zoarcidae) and New Zealand (Bellapiscis medius, Family Tripterygiidae), in an effort to better understand the effect that inhabiting a sub-zero environment has on maintaining the integrity of the cellular protein pool. Overall, levels of Ub-conjugated proteins in cold-adapted Antarctic fishes were significantly higher than New Zealand fishes in gill, liver, heart and spleen tissues suggesting that life at sub-zero temperatures impacts protein homeostasis. The highest tissue levels of ubiquitinated proteins were found in the spleen of all fish. Ub conjugate levels in the New Zealand N. angustata, more closely resembled levels measured in other Antarctic fishes than levels measured in other New Zealand species, likely reflecting their recent shared ancestry with Antarctic notothenioids.

Marine macrophysiology: Studying physiological variation across large spatial scales in marine systems

A new approach toward understanding marine ecosystems has emerged through the integration of ecological physiology and macroecology. This multidisciplinary approach, titled here marine macrophysiology, facilitates unique insight into the foundation of macro-scale ecological patterns, such as biogeographic distributions, via examination of functional attributes of marine organisms across large spatial scales. For example, these broad-scale physiological inquiries confer the ability to directly assess the abundant-center hypothesis (aka Brown's principle) which proposes that species have decreased performance toward their range edges. By extension, the marine macrophysiological perspective also stands to clarify our understanding of more complex macro-scale phenomena such as biological invasions, the design of marine protected areas, and species' responses to global climate change. In this article, we review recent marine macrophysiology research and offer insights into future directions for this emerging field.

Genomics-fueled approaches to current challenges in marine ecology

As a result of recent advances in genomic technology, a 'tool set' is emerging that can be used by marine ecologists to gain new perspectives on central questions in the field. Techniques such as gene expression profiling using DNA microarrays, when placed in an ecological context, stand to advance greatly our understanding of how organisms respond to abiotic and biotic stresses. Here, we target areas in which adding genomics to ecological and physiological investigations will significantly advance our understanding of crucial issues ranging from the general biological effects of environmental temperature changes on individuals and communities to the interactions between symbionts in coral bleaching. At a time when both short- and long-term perturbations of marine ecosystems are increasing in severity, this kind of integrative approach could generate new and exciting hypotheses about the functioning of marine organisms and communities.