Posts Tagged 'molecular biology'

The dynamics of rapid adaptation to ocean acidification in the Mediterranean mussel

Global climate change has intensified the need to assess if, and how, natural populations adapt to abrupt shifts in their environment. The tempo of adaptation in natural systems has been the subject of theoretical and empirical investigation for decades. Recent evidence from genome-wide sequencing approaches has indicated that evolution may proceed at a pace previously deemed theoretically impossible. Such studies, however, have largely observed these processes in the context of model systems, and the extent to which these patterns will hold in ecologically-relevant species subject to the dramatic environmental perturbations associated with global change is unclear. Accordingly, this thesis investigates the capacity for, and mechanisms by which, the Mediterranean mussel, Mytilus galloprovincialis, may rapidly adapt to expected declines in global seawater pH. Reductions in seawater pH constitute a global change stressor impacting marine species globally, with anticipated impacts altering the structure and services of numerous ecological communities. Due to its experimental tractability, as well as its ecological and economic importance, M. galloprovincialis has become a model-species for exploring the physiological and morphological impacts of low pH seawater. Yet, the extent to which evolution may offset observed phenotypic consequences is unknown. To address this knowledge gap the present thesis explores the following: (i) the processes shaping and maintaining variation in low pH tolerance across the species’ native range; (ii) the extent to which the standing variation within natural populations of M. galloprovincialis can facilitate the magnitude of evolution necessary for persistence under global change conditions; and (iii) the molecular basis of low pH adaptation in marine bivalves and beyond. My results elucidate how contemporary gradients in pH variability shape distinct patterns of low pH plasticity across natural populations. Furthermore, my findings demonstrate that the standing variation within natural populations is sufficient for rapid adaptation to even extreme reductions in seawater pH. Lastly, I provide mechanistic links between the molecular mechanisms influenced by shifts in the external seawater pH environment and fitness-related abnormalities observed in M. galloprovincialis, a finding that likely explains observed low pH sensitivity across a broad range of marine metazoans. This thesis thus lends to our conceptual understanding regarding the dynamics of rapid adaptation in natural populations, while explicitly informing the management of an ecologically and economically important marine species as global change progresses.

Continue reading ‘The dynamics of rapid adaptation to ocean acidification in the Mediterranean mussel’

Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity

Ambient conditions shape microbiome responses to both short- and long-duration environment changes through processes including physiological acclimation, compositional shifts, and evolution. Thus, we predict that microbial communities inhabiting locations with larger diel, episodic, and annual variability in temperature and pH should be less sensitive to shifts in these climate-change factors. To test this hypothesis, we compared responses of surface ocean microbes from more variable (nearshore) and more constant (offshore) sites to short-term factorial warming (+3 °C) and/or acidification (pH −0.3). In all cases, warming alone significantly altered microbial community composition, while acidification had a minor influence. Compared with nearshore microbes, warmed offshore microbiomes exhibited larger changes in community composition, phylotype abundances, respiration rates, and metatranscriptomes, suggesting increased sensitivity of microbes from the less-variable environment. Moreover, while warming increased respiration rates, offshore metatranscriptomes yielded evidence of thermal stress responses in protein synthesis, heat shock proteins, and regulation. Future oceans with warmer waters may enhance overall metabolic and biogeochemical rates, but they will host altered microbial communities, especially in relatively thermally stable regions of the oceans.

Continue reading ‘Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity’

Temperature elevation and acidification damage microstructure of abalone via expression change of crystal induction genes


• Thermal and acidification stress destroy the microstructure of abalone shells.

• Expression pattern change of direct crystal induction genes interfered the microstructure of shell under stress.

• Thermal stress changed the shell microstructure via Expression pattern change of direct crystal induction genes.


Ocean warming and acidification caused by global climate change interferes with the shell growth of mollusks. In abalone Haliotis discus hannai, the microstructural changes in the shell under stress are unclear, and the effect of thermal stress on biomineralization is unknown. The lack of gene information has also hampered the study of abalone biomineralization mechanisms. In this study, the microstructure of reconstructed shell in H. discus hannai was observed to determine the effects of thermal and acidification stress on shell growth. Three nacre protein genes, Hdh-AP7, Hdh-AP24, and Hdh-perlustrin, were characterized, and their expression pattern during shell repair was measured under thermal and acidification stress and compared with those of two known biomineralization-related genes, Hdh-AP-1 and Hdh-defensin. The stress resulted in aragonite plates with corroded or irregular microstructures. The gene expression of two nacre proteins (Hdh-AP7 and Hdh-AP24), which directly induce crystal formation, were more sensitive to thermal stress than to acidification, but the expression of the regulatory nacre protein (Hdh-perlustrin) and the two known genes (Hdh-AP-1 and Hdh-defensin), which are also related to immunity, showed an interlinked, complex pattern change. We concluded that high temperature and acidification damages the shell microstructure by disturbing the expression pattern of biomineralization-related genes.

Continue reading ‘Temperature elevation and acidification damage microstructure of abalone via expression change of crystal induction genes’

Physiological and molecular responses to ocean acidification among strains of a model diatom

Differential responses of diatoms, an important group of marine primary producers to ocean acidification, have been well documented. However, studies so far are based on limited representative strains from key species. Investigation of strain level responses will help us better understand the contrasting discrepancy in diatom responses to ocean acidification. Here, we selected four strains of the model diatom Phaeodactylum tricornutum isolated from different regions of the global ocean, representing all genotypes based on internal transcribed spacer 2 sequences, and investigated strain‐specific responses to ocean acidification. In response to ocean acidification, changes in carbon metabolism varied among strains, although no significant effects of ocean acidification on growth rates or pigments were observed in any strains. The expression of genes encoding plasma membrane bicarbonate transporters was downregulated in strain Pt4, reflecting a potential decrease in active urn:x-wiley:00243590:media:lno11565:lno11565-math-0001 uptake, which was not observed in the other strains. Reduction of CO2 concentrating mechanism efficiency was also indicated by the regulated expression of genes encoding carbonic anhydrases that catalyze the interconversion of urn:x wiley:00243590:media:lno11565:lno11565-math-0002 and CO2 in the pyrenoids and pyrenoid‐penetrating thylakoid, which exhibited different patterns among the strains. Under ocean acidification conditions, C4‐like metabolism appeared to redistribute carbon flux to gluconeogenesis in strain Pt1, and lipid synthesis in strains Pt8 and Pt11, rather than participating in net photosynthetic carbon fixation. These variations were incompletely correlated with phylogenetic relationship in different strains, implying that the habitat‐adapted imprints of the different strains could also be responsible for their differential responses to ocean acidification.

Continue reading ‘Physiological and molecular responses to ocean acidification among strains of a model diatom’

Effects of multiple drivers of ocean global change on the physiology and functional gene expression of the coccolithophore Emiliania huxleyi

Ongoing ocean global change due to anthropogenic activities is causing multiple chemical and physical seawater properties to change simultaneously, which may affect the physiology of marine phytoplankton. The coccolithophore Emiliania huxleyi is a model species often employed in the study of the marine carbon cycle. The effect of ocean acidification (OA) on coccolithophore calcification has been extensively studied; however, physiological responses to multiple environmental drivers are still largely unknown. Here we examined two‐way and multiple driver effects of OA and other key environmental drivers—nitrate, phosphate, irradiance, and temperature—on the growth, photosynthetic, and calcification rates, and the elemental composition of E. huxleyi. In addition, changes in functional gene expression were examined to understand the molecular mechanisms underpinning the physiological responses. The single driver manipulation experiments suggest decreased nitrate supply being the most important driver regulating E. huxleyi physiology, by significantly reducing the growth, photosynthetic, and calcification rates. In addition, the interaction of OA and decreased nitrate supply (projected for year 2100) had more negative synergistic effects on E. huxleyi physiology than all other two‐way factorial manipulations, suggesting a linkage between the single dominant driver (nitrate) effects and interactive effects with other drivers. Simultaneous manipulation of all five environmental drivers to the conditions of the projected year 2100 had the largest negative effects on most of the physiological metrics. Furthermore, functional genes associated with inorganic carbon acquisition (RubisCO, AEL1, and δCA) and calcification (CAX3, AEL1, PATP, and NhaA2) were most downregulated by the multiple driver manipulation, revealing linkages between responses of functional gene expression and associated physiological metrics. These findings together indicate that for more holistic projections of coccolithophore responses to future ocean global change, it is necessary to understand the relative importance of environmental drivers both individually (i.e., mechanistic understanding) and interactively (i.e., cumulative effect) on coccolithophore physiology.

Continue reading ‘Effects of multiple drivers of ocean global change on the physiology and functional gene expression of the coccolithophore Emiliania huxleyi’

Warming, but not acidification, restructures epibacterial communities of the Baltic macroalga Fucus vesiculosus with seasonal variability

Due to ocean acidification and global warming, surface seawater of the western Baltic Sea is expected to reach an average of ∼1100 μatm pCO2 and an increase of ∼5°C by the year 2100. In four consecutive experiments (spanning 10–11 weeks each) in all seasons within 1 year, the abiotic factors temperature (+5°C above in situ) and pCO2 (adjusted to ∼1100 μatm) were tested for their single and combined effects on epibacterial communities of the brown macroalga Fucus vesiculosus and on bacteria present in the surrounding seawater. The experiments were set up in three biological replicates using the Kiel Outdoor Benthocosm facility (Kiel, Germany). Phylogenetic analyses of the respective microbiota were performed by bacterial 16S (V1-V2) rDNA Illumina MiSeq amplicon sequencing after 0, 4, 8, and 10/11 weeks per season. The results demonstrate (I) that the bacterial community composition varied in time and (II) that relationships between operational taxonomic units (OTUs) within an OTU association network were mainly governed by the habitat. (III) Neither single pCO2 nor pCO2:Temperature interaction effects were statistically significant. However, significant impact of ocean warming was detected varying among seasons. (IV) An indicator OTU (iOTU) analysis identified several iOTUs that were strongly influenced by temperature in spring, summer, and winter. In the warming treatments of these three seasons, we observed decreasing numbers of bacteria that are commonly associated with a healthy marine microbial community and—particularly during spring and summer—an increase in potentially pathogenic and bacteria related to intensified microfouling. This might lead to severe consequences for the F. vesiculosus holobiont finally affecting the marine ecosystem.

Continue reading ‘Warming, but not acidification, restructures epibacterial communities of the Baltic macroalga Fucus vesiculosus with seasonal variability’

Season specific influence of projected ocean changes on the response to cadmium of stress-related genes in Mytilus galloprovincialis


• Seasonal effects of Cd, warming and acidification on mussels target genes were assessed.

• mt-20 showed higher responsiveness to Cd exposure in digestive gland than in gills.

• hsp70 was sensitive to acidification in summer in digestive gland and in winter in gills.

• Cu/Zn-sod, gst-pi and cat showed tissue- and season-specific responses.

•Differences between tissues and seasons of investigation were demonstrated to occur.


Anthropogenic inputs of carbon dioxide in the atmosphere are driving ocean warming and acidification. The potential threat represented by these changes for marine species could be amplified in coastal areas, characterized by higher levels of pollutants. In addition, temperate organisms may exhibit a different seasonal tolerance to stressors influenced by fluctuations of environmental and physiological factors. In this study, Mediterranean mussels Mytilus galloprovincialis collected both in summer and winter were exposed to combinations of two temperatures (SST, seasonal surface temperature and SST+5 °C) and two levels of pH (8.20 and 7.40) in clean or cadmium contaminated seawater (20 μg/L Cd). mRNA levels of genes related to metal-induced stress response were investigated, including metallothionein mt-20, heat-shock protein hsp70, superoxide dismutase Cu/Zn-sod, catalase cat, glutathione peroxidase gpx1 and glutathione S-transferase gst-pi. To further elucidate if tissues with different physiological roles could exhibit different responsiveness, such analyses were carried out in digestive gland and in gills of exposed mussels. mt-20 mRNA increase after Cd-exposure was higher in the digestive gland than in the gills, with few modulations by temperature or pH only in the latter. Acidification, alone or in combination with other stressors, increased hsp70 mRNA, with seasonal- and tissue-specificities (higher in summer and in digestive gland). Among antioxidants, gpx1 mRNA was affected by Cd in both tissues and seasons, with further modulations due to pH and temperature variation tissue- and season-specific; in winter the combination of Cd, warming and acidification affected Cu/Zn-sod both in digestive gland and gills and cat only in gills, while weak seasonal variations were observed for gst-pi transcripts only in digestive gland. The overall results highlighted the importance of considering seasonality and responsiveness of different tissues to predict the effects of sudden changes in environmental parameters on responsiveness to and toxicity of chemicals in marine coastal organisms.

Continue reading ‘Season specific influence of projected ocean changes on the response to cadmium of stress-related genes in Mytilus galloprovincialis’

The role of aspartic acid in reducing coral calcification under ocean acidification conditions

Biomolecules play key roles in regulating the precipitation of CaCO3 biominerals but their response to ocean acidification is poorly understood. We analysed the skeletal intracrystalline amino acids of massive, tropical Porites spp. corals cultured over different seawater pCO2. We find that concentrations of total amino acids, aspartic acid/asparagine (Asx), glutamic acid/glutamine and alanine are positively correlated with seawater pCO2 and inversely correlated with seawater pH. Almost all variance in calcification rates between corals can be explained by changes in the skeletal total amino acid, Asx, serine and alanine concentrations combined with the calcification media pH (a likely indicator of the dissolved inorganic carbon available to support calcification). We show that aspartic acid inhibits aragonite precipitation from seawater in vitro, at the pH, saturation state and approximate aspartic acid concentrations inferred to occur at the coral calcification site. Reducing seawater saturation state and increasing [aspartic acid], as occurs in some corals at high pCO2, both serve to increase the degree of inhibition, indicating that biomolecules may contribute to reduced coral calcification rates under ocean acidification.

Continue reading ‘The role of aspartic acid in reducing coral calcification under ocean acidification conditions’

Fluctuating seawater pCO2/pH induces opposing interactions with copper toxicity for two intertidal invertebrates


• Fluctuating pCO2/pH doubled copper-induced antioxidant activity and DNA damage in mussels.

• In contrast, fluctuating conditions mitigated some of the effects of copper for ragworms.

• These effects were associated with the differing acid-base physiology of the two species.

• Physiology was as important as changing copper chemistry in determining overall toxicity.


Global ocean pCO2 is increasing as a result of anthropogenic CO2 emissions, driving a decline in seawater pH. However, coastal waters already undergo fluctuations in pCO2/pH conditions over far shorter timescales, with values regularly exceeding those predicted for the open ocean by the year 2100. The speciation of copper, and therefore its potential toxicity, is affected by changing seawater pH, yet little is known concerning how present-day natural fluctuations in seawater pH affect copper toxicity to marine biota. Here, we test the hypothesis that a fluctuating seawater pCO2/pH regime will alter the responses of the mussel Mytilus edulis and the ragworm Alitta virens to sub-lethal copper, compared to a static seawater pCO2/pH scenario. Mussels and worms were exposed to 0.1 and 0.25 μM copper respectively, concentrations determined to produce comparable toxicity responses in these species, for two weeks under a fluctuating 12-hour pCO2/pH cycle (pH 8.14–7.53, pCO2 445–1747 μatm) or a static pH 8.14 (pCO2 432 μatm) treatment. Mussels underwent a haemolymph acidosis of 0.1–0.2 pH units in the fluctuating treatments, alongside two-fold increases in the superoxide dismutase activity and DNA damage induced by copper, compared to those induced by copper under static pH conditions. Conversely, ragworms experienced an alkalosis of 0.3 pH units under fluctuating pH/pCO2, driven by a two-fold increase in coelomic fluid bicarbonate. This mitigated the copper-induced oxidative stress to slightly reduce both antioxidant activity and DNA damage, relative to the static pH + copper treatment. These opposing responses suggest that differences in species acid-base physiology were more important in determining toxicity responses than the pH-induced speciation change. With variability in seawater chemistry predicted to increase as climate change progresses, understanding how fluctuating conditions interact with the toxicity of pH-sensitive contaminants will become more crucial in predicting their risk to coastal biota.

Continue reading ‘Fluctuating seawater pCO2/pH induces opposing interactions with copper toxicity for two intertidal invertebrates’

Physiological and ecotoxicological interactions of copper and ocean acidification in the polychaete worms Hediste diversicolor and Alitta virens

For coastal aquatic habitats the change in seawater pH occurring as a result of ocean acidification has the potential to alter the speciation and toxicity of the many contaminants that remain in high concentrations in coastal systems. Of particular concern are metals, such as copper, whose speciation is pH sensitive within the OA range. A meta-analysis of studies to date investigating OA-contaminant interactions using marine invertebrates reveals that 72% of the 44 studies conducted have indeed focused on metals such as copper, with only a few studies looking at polycyclic aromatic hydrocarbons (PAH) and pharmaceuticals. No clear trends in the pH-effect size on contaminant toxicity for either species or contaminant group were present however, suggesting species specific physiological responses may influence this interaction as well as contaminant chemistry. A relatively understudied group were the polychaetes, a key functional group for many coastal sediments. Sediments act as a sink for contaminants where they can accumulate to high concentrations. Hence there is high potential for polychaetes to experience elevated metal exposures under reduced seawater pH as OA progresses. To address this knowledge gap, the responses of two common coastal polychaete, Alitta virens and Hediste diversicolor, were studied under three different experimental scenarios (both water-borne and sediment based) focusing on the physiological and toxicological responses under combined exposures to ocean acidification and copper. Water-borne exposures of Alitta virens to 0.25 μM copper under ambient seawater (pH 8.10) showed a significant increase in DNA damage, along with a rise in both SOD activity and lipid peroxidation. However, when exposed to copper under OA conditions (pH 7.70) there was no further increase in DNA damage and a significant decrease in SOD activity was observed alongside a fall in lipid peroxidation suggesting that OA looks to buffer the toxicity responses to this species. This is in contrast to previous studies using mussels and sea urchins, where copper toxicity responses were significantly higher when exposed under OA conditions. To assess whether local adaptations to high levels of copper contamination influences this OA-copper interaction, a population comparison using a metal resistance population of the harbour ragworm, Hediste diversicolor and a nearby non-resistant population was then conducted. Exposures were run using copper concentrations that elicit comparable toxicity responses, using 0.50 uM copper for the resistant population, compared to 0.25 uM for the non-resistant population, reflecting the two-fold differences in LC50 values for these population. These experiments reveal a significant increase by 19.70% in metabolic rate effect size (the combined stressor when compared to the control) in the resistant population compared to a decrease by 24.02% the non-resistant population, along with differences in ammonia excretion rate and the O:N ratio, thus revealing an energetic cost of this genetic resistance when faced with the combined stressors of OA and copper. These data are in line with the emerging energy limited tolerance to stressors’ hypothesis which states that tolerance to stress can be energy limited, with bioenergetics playing a central role in the tolerance to environmental stress. Finally, a more environmentally realistic exposure scenario was conducted using Alitta virens to test the influence of sediment and tidal cycles on worm acid-base and oxidative stress responses. Field measurements of sediment pH revealed that the pHNBS range over a tidal cycle varies from 6.97 to 7.87, indicating that polychaetes are already experiencing pH’s lower than the predictions for near future open oceans. In aquarium exposures, with overlying water of pHNBS 8.10, sediment pHNBS remained within the range of 7.45 to 7.31, when the overlying water was manipulated to OA conditions (pHNBS 7.70) sediment pHNBS was within the same range as the ambient treatment. The lack of change in sediment pH, despite a 0.40 unit drop in seawater pH, removed any comparative differences in physiological and toxicity end points in the worms between treatments. Tidal emersion induced a slight reduction in sediment pH, with a significant copper effect on sediment pH causing a further decrease in pH levels. Interestingly emersion resulted in a significant OA-copper interaction for coelomic fluid bicarbonate, which increased over the emersion period, however, there was no emersion driven acidosis within coelomic fluid. Overall this work further points to contaminant-OA interactions being species specific driven, in part driven by animal physiology. It also highlights the importance of environmentally relevant exposures with sediment dwelling organisms experiencing lower pH levels than the overlying seawater which could potentially affect metal speciation and could lead to OA-contaminant interactions occurring very differently in this environment. These are important considerations for ecotoxicology studies in the face of global ocean changes.

Continue reading ‘Physiological and ecotoxicological interactions of copper and ocean acidification in the polychaete worms Hediste diversicolor and Alitta virens’

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Ocean acidification in the IPCC AR5 WG II

OUP book