Effects of multiple climate change stressors on gene expression in blue rockfish (Sebastes mystinus)


  • Marine fishes will be exposed to multiple stressors under climate change.
  • Hypoxia and high pCO2 are both expected to cause shifts in energy metabolism.
  • No signs of energetic shifts were observed at transcriptomic or enzymatic levels.
  • Multiple stressor transcriptomes are not predictable based on responses to single stressors.
  • Blue rockfish may be relatively tolerant to intensified upwelling conditions.


Global climate change is predicted to increase the co-occurrence of high pCO2 and hypoxia in upwelling zones worldwide. Yet, few studies have examined the effects of these stressors on economically and ecologically important fishes. Here, we investigated short-term responses of juvenile blue rockfish (Sebastes mystinus) to independent and combined high pCO2 and hypoxia at the molecular level, using changes in gene expression and metabolic enzymatic activity to investigate potential shifts in energy metabolism. Fish were experimentally exposed to conditions associated with intensified upwelling under climate change: high pCO2 (1200 μatm, pH~7.6), hypoxia (4.0 mg O2/L), and a combined high pCO2/hypoxia treatment for 12 h, 24 h or two weeks. Muscle transcriptome profiles varied significantly among the three treatments, with limited overlap among genes responsive to both the single and combined stressors. Under elevated pCO2, blue rockfish increased expression of genes encoding proteins involved in the electron transport chain and muscle contraction. Under hypoxia, blue rockfish up-regulated genes involved in oxygen and ion transport and down-regulated transcriptional machinery. Under combined high pCO2 and hypoxia, blue rockfish induced a unique set of ionoregulatory and hypoxia-responsive genes not expressed under the single stressors. Thus, high pCO2 and hypoxia exposure appears to induce a non-additive transcriptomic response that cannot be predicted from single stressor exposures alone, further highlighting the need for multiple stressor studies at the molecular level. Overall, lack of a major shift in cellular energetics indicates that blue rockfish may be relatively resistant to intensified upwelling conditions in the short term.

Continue reading ‘Effects of multiple climate change stressors on gene expression in blue rockfish (Sebastes mystinus)’

Purification and characterization of thymol blue for spectrophotometric pH measurements in rivers, estuaries, and oceans


  • Thymol blue (TB) was purified using flash chromatography.
  • TB is useful for pH measurements above the range of meta-cresol purple (mCP).
  • Paired pH measurements directly link the equilibrium characteristics of TB and mCP.


Thymol blue (TB) is one of a suite of indicator dyes appropriate for spectrophotometric determinations of the pH of aqueous solutions. For measurements of seawater pH, meta-cresol purple (mCP) is most often used, but TB is especially well suited for measurements in surface or shallow waters where the pH may exceed the optimal indicating range of mCP (e.g., due to photosynthesis). This work presents flash chromatography procedures for purifying commercially available TB and describes physical–chemical characteristics of the purified dye, thus enabling the acquisition of spectrophotometric pH measurements over a wide range of practical salinities (SP) and temperatures (T). The essential TB characteristics for 0 ≤ SP ≤ 40 and 278.15 ≤ T ≤ 308.15 K are described by:





e1 = −0.00132 + 0.00001600T

e4 = −0.005042 + 0.0002094T + 0.01916SP0.5/T

where pHT is pH determined on the total hydrogen ion concentration scale; R is the ratio of TB absorbances (A) at 435 and 596 nm (596A/435A); K2T is the equilibrium constant for the second TB dissociation step on the total scale; and e1, e2, and e4 are TB molar absorptivity ratios. This characterization was developed in a manner that ensures consistency with the primary TRIS buffer standards used in previously published characterizations of mCP. With this characterization, TB joins mCP as a sulfonephthalein indicator that has been characterized over the ranges of salinity and temperature required to make high-quality pH measurements in rivers, estuaries, and the open ocean. The full characterization of purified TB reported here extends the upper range of pHT that can be accessed with precise spectrophotometric measurements by approximately 0.50 pH units.

Continue reading ‘Purification and characterization of thymol blue for spectrophotometric pH measurements in rivers, estuaries, and oceans’

Changes in the metabolic potential of the sponge microbiome under ocean acidification

Anthropogenic CO2 emissions are causing ocean acidification, which can affect the physiology of marine organisms. Here we assess the possible effects of ocean acidification on the metabolic potential of sponge symbionts, inferred by metagenomic analyses of the microbiomes of two sponge species sampled at a shallow volcanic CO2 seep and a nearby control reef. When comparing microbial functions between the seep and control sites, the microbiome of the sponge Stylissa flabelliformis (which is more abundant at the control site) exhibits at the seep reduced potential for uptake of exogenous carbohydrates and amino acids, and for degradation of host-derived creatine, creatinine and taurine. The microbiome of Coelocarteria singaporensis (which is more abundant at the seep) exhibits reduced potential for carbohydrate import at the seep, but greater capacity for archaeal carbon fixation via the 3-hydroxypropionate/4-hydroxybutyrate pathway, as well as archaeal and bacterial urea production and ammonia assimilation from arginine and creatine catabolism. Together these metabolic features might contribute to enhanced tolerance of the sponge symbionts, and possibly their host, to ocean acidification.

Continue reading ‘Changes in the metabolic potential of the sponge microbiome under ocean acidification’

Co-culture in marine farms: macroalgae can act as chemical refuge for shell-forming molluscs under an ocean acidification scenario

With ongoing climate change, aquaculture faces environmental challenges similar to those of natural ecosystems. These include increasing stress for calcifying species, e.g. macroalgae and shellfish. In this context, ocean acidification (OA) has the potential to affect important socioeconomic activities, including shellfish aquaculture, due to changes in the seawater carbonate system. However, coastal environments are characterised by strong diurnal pH fluctuations associated with the metabolic activity of macroalgae; that is, photosynthesis and respiration. This suggests that calcifying organisms that inhabit these ecosystems are adapted to this fluctuating pH environment. Macrophyte-dominated environments may have the potential to act as an OA buffering system in the form of a photosynthetic footprint, by reducing excess of CO2 and increasing the seawater pH and Ωarg. This can support calcification and other threatened physiological processes of calcifying organisms under a reduced pH environment. Because this footprint is supportive beyond the macroalgal canopy spatial area, this chemical refuge mechanism can be applied to support shellfish aquaculture, e.g. mussels. However, this approach should be tested in commercial shellfish farms to determine critical aspects of implementation. This includes critical factors such as target species and productivity rates. The degree of OA buffering capacity caused by the metabolic activity of macroalgae might depend on community structure and hydrodynamic conditions, creating site-specific responses. This concept might aid the development of future adaptive strategies, supporting marine ecological planning for the mussel aquaculture industry in Chile.

Continue reading ‘Co-culture in marine farms: macroalgae can act as chemical refuge for shell-forming molluscs under an ocean acidification scenario’

Variation in the effects of ocean acidification on shell growth and strength in two intertidal gastropods

Many marine organisms rely on calcified hard parts to resist predation, and ocean acidification (OA) affects calcification negatively. However, calcification-related consequences may manifest in variable and/or cryptic ways across species. For example, shell strength is a primary defense for resisting shell-crushing predation, yet the consequences of OA on such biomechanical properties cannot be assessed visually. We exposed 2 species of intertidal gastropods common to the west coast of North America (the black turban snail Tegula funebralis and the striped dogwhelk Nucella ostrina) to OA (pH decreased by ~0.5 units) and predation cues for 6 mo, then measured both shell growth and strength. Shell growth in T. funebralis was significantly depressed under OA and in the presence of predation cues (declines of 83 and 63%, respectively). Shells produced by OA-exposed T. funebralis were also 50% weaker. In contrast, shell growth of N. ostrina was unaffected by OA, yet its shells were still 10% weaker. These findings highlight the potential for both different and easily overlooked responses of organisms to seawater acidification. Moreover, such results raise the possibility of ensuing shifts in consumption rates and rankings of prey items by shell-crushing predators, leading to shifts in the balance of species interactions in temperate shoreline communities.

Continue reading ‘Variation in the effects of ocean acidification on shell growth and strength in two intertidal gastropods’

Job opportunity: Ocean acidification senior scientist


The Environmental Assessment Program (EAP) within the Department of Ecology is looking to fill an Ocean Acidification Senior Scientist (Natural Resource Scientist 4) position. This position will be located at our Headquarters Building in Lacey, WA.

The Ocean Acidification Senior Scientist position serves as the designated technical expert in the agency on ocean acidification science.

Continue reading ‘Job opportunity: Ocean acidification senior scientist’

Ocean acidification reduces net calcification and wound healing in the tropical crustose coralline alga, Porolithon onkodes (Corallinales, Rhodophyta)


  • Wounding did not affect net calcification or tissue mortality in Porolithon onkodes.
  • In contrast, elevated pCO2 reduced net calcification and living tissue.
  • Elevated pCO2 also reduced tissue regeneration within wounds.
  • Reduced wound healing under elevated pCO2 could affect the ecology of coralline algae.


Reef dwelling algae employ a variety of physical and chemical defenses against herbivory, and the response to wounding is extremely important in algal communities. Wound healing mechanisms in crustose coralline algae (CCA) are related to skeletal growth and net calcification rate. Ocean acidification (OA) is known to affect rates of net calcification in a number of calcifying organisms, including CCA. Reduced rates of net calcification in CCA are likely to alter wound healing, and thus affect the consequences of herbivore-CCA interactions on coral reefs. The response of the tropical CCA Porolithon onkodes to OA and artificial wounding was quantified in a 51-day laboratory experiment. Eight artificially wounded (cut to a mean depth of 182 μm) and eight non-wounded samples of P. onkodes were randomly placed into each of four treatments (n = 64 samples total). Each treatment was maintained at a different pCO2 level representative of either ambient conditions or end-of-the-century, predicted conditions (IPCC, 2014); 429.31 ± 20.84 (ambient), 636.54 ± 27.29 (RCP4.5), 827.33 ± 38.51 (RCP6.0), and 1179.39 ± 88.85 μatm (RCP8.5; mean ± standard error). Elevated pCO2 significantly reduced rates of net calcification in both wounded and non-wounded samples of P. onkodes (slopes = −6.4 × 10−4 and −5.5 × 10−4 mg cm−2 d−1 per μatm pCO2, respectively over 51 days). There also was a significant reduction in the rate of vertical regeneration of thallus tissue within the wounds as pCO2 increased (slope = −1.5 × 10−3 μm d−1 per μatm pCO2 over 51 days). This study provides evidence that elevated pCO2 could reduce the ability of this important alga to recover from wounding. Because wounding by herbivores plays an important role in determining CCA community structure, we propose reduced wound healing as a mechanism by which OA might affect the structure and functional roles of CCA communities on coral reefs.

Continue reading ‘Ocean acidification reduces net calcification and wound healing in the tropical crustose coralline alga, Porolithon onkodes (Corallinales, Rhodophyta)’

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Ocean acidification in the IPCC AR5 WG II

OUP book