Posts Tagged 'molecular biology'

A potential role for epigenetic processes in the acclimation response to elevated pCO2 in the model diatom Phaeodactylum tricornutum

Understanding of the molecular responses underpinning diatom responses to ocean acidification is fundamental for predicting how important primary producers will be shaped by the continuous rise in atmospheric CO2. In this study, we have analyzed global transcriptomic changes of the model diatom Phaeodactylum tricornutum following growth for 15 generations in elevated pCO2 by strand-specific RNA sequencing (ssRNA-seq). Our results indicate that no significant effects of elevated pCO2 and associated carbonate chemistry changes on the physiological performance of the cells were observed after 15 generations whereas the expression of genes encoding histones and other genes involved in chromatin structure were significantly down-regulated, while the expression of transposable elements (TEs) and genes encoding histone acetylation enzymes were significantly up-regulated. Furthermore, we identified a series of long non-protein coding RNAs (lncRNAs) specifically responsive to elevated pCO2, suggesting putative regulatory roles for these largely uncharacterized genome components. Taken together, our integrative analyses reveal that epigenetic elements such as TEs, histone modifications and lncRNAs may have important roles in the acclimation of diatoms to elevated pCO2 over short time scales and thus may influence longer term adaptive processes in response to progressive ocean acidification.

Continue reading ‘A potential role for epigenetic processes in the acclimation response to elevated pCO2 in the model diatom Phaeodactylum tricornutum’

Microbial strains isolated from CO2-venting Kolumbo submarine volcano show enhanced co-tolerance to acidity and antibiotics


• The study investigates the effects of volcanic acidification to marine bacteria.

• Deep waters of Kolumbo submarine volcano are CO2-rich and more acidic.

• Pseudomonas strains from Kolumbo seafloor show higher tolerance to acidity.

• Strong correlation between acid and antibiotic tolerance of Pseudomonas species.

• Ocean acidification may lead to marine bacteria with increased antibiotic tolerance.


As ocean acidification intensifies, there is growing global concern about the impacts that future pH levels are likely to have on marine life and ecosystems. By analogy, a steep decrease of seawater pH with depth is encountered inside the Kolumbo submarine volcano (northeast Santorini) as a result of natural CO2 venting, making this system ideal for ocean acidification research. Here, we investigated whether the increase of acidity towards deeper layers of Kolumbo crater had any effect on relevant phenotypic traits of bacterial isolates. A total of 31 Pseudomonas strains were isolated from both surface- (SSL) and deep-seawater layers (DSL), with the latter presenting a significantly higher acid tolerance. In particular, the DSL strains were able to cope with H+ levels that were 18 times higher. Similarly, the DSL isolates exhibited a significantly higher tolerance than SSL strains against six commonly used antibiotics and As(III). More importantly, a significant positive correlation was revealed between antibiotics and acid tolerance across the entire set of SSL and DSL isolates. Our findings imply that Pseudomonas species with higher resilience to antibiotics could be favored by the prospect of acidifying oceans. Further studies are required to determine if this feature is universal across marine bacteria and to assess potential ecological impacts.

Continue reading ‘Microbial strains isolated from CO2-venting Kolumbo submarine volcano show enhanced co-tolerance to acidity and antibiotics’

Gene expression profiles of two coral species with varied resistance to ocean acidification

Recent studies have indicated that various corals might have different degrees of resistance to elevated CO2 levels. However, the underlying molecular mechanism accounting for these differences is still poorly understood. In this study, RNA-seq data were analyzed to identify differentially expressed genes in two coral species (Acropora austera and Acropora cerealis) in response to high CO2 levels. The calcification rates were higher in high CO2 treatment than the control in A. austera, but was not significantly different in A. cerealis. A KEGG database search revealed that in both coral species, most Ca2+ transporters were present in the calcium signaling pathway, which could be important in the CO2 regulation of coral calcification. The gene expression levels of many CO2 and HCO3 transporters were not affected by elevated CO2. Nevertheless, high CO2 levels did have an effect on the expression of certain Ca2+ transporters. The upregulation of Ca2+ transporters likely explained the higher resistance of A. austera to high CO2 than A. cerealis.

Continue reading ‘Gene expression profiles of two coral species with varied resistance to ocean acidification’

Low pH reduced survival of the oyster Crassostrea gigas exposed to the Ostreid herpesvirus 1 by altering the metabolic response of the host


  • The susceptibility of Crassostrea gigas to OsHV-1 increased at pH 7.8 in comparison to pH 8.1
  • The amount of OsHV-1 in oyster tissues was the same at both pH, suggesting the role of host metabolic response in differential survival
  • A lower activity of SOD and a basal activity of iNOS at pH 7.8, in comparison to pH 8.1, may have impaired the defence of oysters to OsHV-1 explaining the lower survival


Environmental change in the marine realm has been accompanied by emerging diseases as new pathogens evolve to take advantage of hosts weakened by environmental stress. Here we investigated how an exposure to reduced seawater pH influenced the response of the oyster Crassostrea gigas to an infection by the Ostreid herpesvirus type I (OsHV-1). Oysters were acclimated at pH 8.1 or pH 7.8 and then exposed to OsHV-1. Their survival was monitored and oyster tissues were sampled for biochemical analyses. The survival of oysters exposed to OsHV-1 at pH 7.8 was lower (33.5%) than that of their counterparts at pH 8.1 (44.8%) whereas levels of OsHV-1 DNA were similar. Energetic reserves, fatty acid composition and prostaglandin levels in oyster did not vary consistently with pH, infection or their interactions. However, there was a reduction in the activities of superoxide dismutase (SOD) and nitric oxide synthase (iNOS) in oysters at low pH, which is associated with the observed difference in survival.

Continue reading ‘Low pH reduced survival of the oyster Crassostrea gigas exposed to the Ostreid herpesvirus 1 by altering the metabolic response of the host’

Divergent responses of Atlantic cod to ocean acidification and food limitation

In order to understand the effect of global change on marine fishes, it is imperative to quantify the effects on fundamental parameters such as survival and growth. Larval survival and recruitment of the Atlantic cod (Gadus morhua) was found to be heavily impaired by end‐of‐century levels of ocean acidification. Here, we analysed larval growth among 35‐36 days old surviving larvae, along with organ development and ossification of the skeleton. We combined CO2‐treatments (ambient: 503 μatm, elevated: 1179 μatm) with food availability in order to evaluate the effect of energy limitation in addition to the ocean acidification stressor. As expected, larval size (as a proxy for growth) and skeletogenesis were positively affected by high food availability. We found significant interactions between acidification and food availability. Larvae fed ad libitum showed little difference in growth and skeletogenesis due to the CO2 treatment. Larvae under energy limitation were significantly larger and had further developed skeletal structures in the elevated CO2 treatment compared to the ambient CO2 treatment. However, the elevated CO2 group revealed impairments in critically important organs, such as the liver, and had comparatively smaller functional gills indicating a mismatch between size and function. It is therefore likely that individual larvae that had survived acidification treatments, will suffer from impairments later during ontogeny. Our study highlights important allocation trade‐off between growth and organ development, which is critically important to interpret acidification effects on early life‐stages of fish.

Continue reading ‘Divergent responses of Atlantic cod to ocean acidification and food limitation’

Transgenerational exposure to ocean acidification induces biochemical distress in a keystone amphipod species (Gammarus locusta)


  • A transgenerational ocean acidification exposure was performed in Gammarus locusta
  • Biomarkers of cellular damage, protein repair and oxidative stress were quantified
  • Within- and transgenerational oxidative damage occurred under high CO2
  • Oxidative stress in F0-proteome may impair offspring’ DNA efficiency repair system
  • Increased vulnerability of wild G. locusta populations under ocean acidification


Atmospheric carbon dioxide (CO2) levels are increasing at the fastest rate ever recorded, causing higher CO2 dissolution in the ocean, leading to a process known as ocean acidification (OA). Unless anthropogenic CO2 emissions are reduced, they are expected to reach ~900 ppm by the century’s end, resulting in a 0.13-0.42 drop in the seawater pH levels. Since the transgenerational effects of high CO2 in marine organisms are still poorly understood at lower levels of biological organization (namely at the biochemical level), here we reared a key ecological relevant marine amphipod, Gammarus locusta, under control and high CO2 conditions for two generations. We measured several stress-related biochemical endpoints: i) oxidative damage [lipid peroxidation (LPO) and DNA damage]; ii) protein repair and removal mechanisms [heat shock proteins (HSPs) and ubiquitin (Ub)]; as well as iii) antioxidant responses [superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) and glutathione s-transferase (GST)] and total antioxidant capacity (TAC). The present results support the premise that exposure to high CO2 is expected to decrease survival rates in this species and cause within- and transgenerational oxidative damage. More specifically, the predicted upsurge of reactive oxygen and nitrogen species seemed to overwhelm the stimulated amphipod antioxidant machinery, which proved insufficient in circumventing protein damage within the parents. Additionally, negative effects of OA are potentially being inherited by the offspring, since the oxidative stress imposed in the parent’s proteome appears to be restricting DNA repair mechanisms efficiency within the offspring’s. Thus, we argue that a transgenerational exposure of G. locusta could further increase vulnerability to OA and may endanger the fitness and sustainability of natural populations.

Continue reading ‘Transgenerational exposure to ocean acidification induces biochemical distress in a keystone amphipod species (Gammarus locusta)’

Effects of ocean acidification on the transcriptome of larval Atlantic cod and impacts of parental acclimation

Ocean acidification, caused by the uptake of carbon dioxide (CO2) from the atmosphere, is impacting many marine organisms. This dissertation investigated the effects of direct exposure and parental acclimation to simulated ocean acidification on the larval stages of Atlantic cod (Gadus morhua, L.). For this, ocean acidification levels predicted for the year 2100 were applied on cod eggs from hatch to 36 days post hatch in in vivo laboratory experiments. The direct exposure experiment clearly showed that Atlantic cod larvae were severely affected by simulated ocean acidification on a phenotypic level (chapter 1). Changes in growth, bone and gill development as well as increased frequency of organ damages were observed under predicted ocean acidification levels compared to controls. Then, the underlying molecular phenotype was assessed, using whole transcriptome sequencing (RNA-Seq), to couple transcriptomic mechanisms to the observed phenotypes (chapter 2). Transcriptome analysis revealed 1413 differentially expressed genes in late larval stages, corresponding to the observed changes in growth and developmental patterns, leading to the conclusion that these changes represent an accelerated development under ocean acidification. Surprisingly, only few genes (3 and 16, respectively) were differentially expressed in the early larval stages. An experiment set to address the effects of long-term parental acclimation (5 month) was performed to assess whether or not this kind of acclimation can mediate the identified detrimental direct effects on the larvae (chapter 3). However, none of the previously observed phenotypes under ocean acidification were found in this experiment, making it impossible to draw any conclusion on the effectiveness of parental acclimation on larval susceptibility to simulated ocean acidification. A concluding meta-analysis between experiments shows that the larvae of Atlantic Cod are to be considered vulnerable to simulated ocean acidification.

Continue reading ‘Effects of ocean acidification on the transcriptome of larval Atlantic cod and impacts of parental acclimation’

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Ocean acidification in the IPCC AR5 WG II

OUP book