Posts Tagged 'molecular biology'

Sand smelt ability to cope and recover from ocean’s elevated CO2 levels


• Sand smelt larvae were exposed to short and long-term acidification scenarios.
• Cope and recover were assessed at behavioural, morphometric and biochemical levels.
• Exposure to high pCO2 induces different responses at distinct exposure times.
• Contrary to biochemical and morphometric responses, lateralization was unaffected.
• Larvae were not able to recover from acidified scenarios within the study period.


Considered a major environmental concern, ocean acidification has induced a recent research boost into effects on marine biodiversity and possible ecological, physiological, and behavioural impacts. Although the majority of literature indicate negative effects of future acidification scenarios, most studies are conducted for just a few days or weeks, which may be insufficient to detect the capacity of an organism to adjust to environmental changes through phenotypic plasticity. Here, the effects and the capacity of sand smelt larvae Atherina presbyter to cope and recover (through a treatment combination strategy) from short (15 days) and long-term exposure (45 days) to increasing pCO2 levels (control: ~515 μatm, pH = 8.07; medium: ~940 μatm, pH = 7.84; high: ~1500 μatm, pH = 7.66) were measured, addressing larval development traits, behavioural lateralization, and biochemical biomarkers related with oxidative stress and damage, and energy metabolism and reserves. Although behavioural lateralization was not affected by high pCO2 exposure, morphometric changes, energetic costs, and oxidative stress damage were impacted differently through different exposures periods. Generally, short-time exposures led to different responses to either medium or high pCO2 levels (e.g. development, cellular metabolism, or damage), while on the long-term the response patterns tend to become similar between them, with both acidification scenarios inducing DNA damage and tending to lower growth rates. Additionally, when organisms were transferred to lower acidified condition, they were not able to recover from the mentioned DNA damage impacts.

Overall, results suggest that exposure to future ocean acidification scenarios can induce sublethal effects on early life-stages of fish, but effects are dependent on duration of exposure, and are likely not reversible. Furthermore, to improve our understanding on species sensitivity and adaptation strategies, results reinforce the need to use multiple biological endpoints when assessing the effects of ocean acidification on marine organisms.

Continue reading ‘Sand smelt ability to cope and recover from ocean’s elevated CO2 levels’

Early life stages of Northern shrimp (Pandalus borealis) are sensitive to fish feed containing the anti-parasitic drug diflubenzuron


• Diflubenzuron is used in salmon aquaculture to remove parasitic lice.
• Salmon feed containing diflubenzuron increased mortality of shrimp larvae.
• Additive effects of diflubenzuron and ocean acidification/warming on mortality.
• More serious sublethal effects of diflubenzuron under future climate conditions.
• Use of diflubenzuron in salmon farms is a threat to non-target crustaceans.


Increasing use of fish feed containing the chitin synthesis inhibiting anti-parasitic drug diflubenzuron (DFB) in salmon aquaculture has raised concerns over its impact on coastal ecosystems. Larvae of Northern shrimp (Pandalus borealis) were exposed to DFB medicated feed under Control conditions (7.0 °C, pH 8.0) and under Ocean Acidification and Warming conditions (OAW, 9.5 °C and pH 7.6). Two weeks’ exposure to DFB medicated feed caused significantly increased mortality. The effect of OAW and DFB on mortality of shrimp larvae was additive; 10% mortality in Control, 35% in OAW, 66% in DFB and 92% in OAW + DFB. In OAW + DFB feeding and swimming activity were reduced for stage II larvae and none of the surviving larvae developed to stage IV. Two genes involved in feeding (GAPDH and PRLP) and one gene involved in moulting (DD9B) were significantly downregulated in larvae exposed to OAW + DFB relative to the Control. Due to a shorter intermoult period under OAW conditions, the OAW + DFB larvae were exposed throughout two instead of one critical pre-moult period. This may explain the more serious sub-lethal effects for OAW + DFB than DFB larvae. A single day exposure at 4 days after hatching did not affect DFB larvae, but high mortality was observed for OAW + DFB larvae, possibly because they were exposed closer to moulting. High mortality of shrimp larvae exposed to DFB medicated feed, indicates that the use of DFB in salmon aquaculture is a threat to crustacean zooplankton.

Continue reading ‘Early life stages of Northern shrimp (Pandalus borealis) are sensitive to fish feed containing the anti-parasitic drug diflubenzuron’

Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms


Despite recent work to characterize gene expression changes associated with larval development in oysters, the mechanism by which the larval shell is first formed is still largely unknown. In Crassostrea gigas, this shell forms within the first 24 h post fertilization, and it has been demonstrated that changes in water chemistry can cause delays in shell formation, shell deformations and higher mortality rates. In this study, we use the delay in shell formation associated with exposure to CO2-acidified seawater to identify genes correlated with initial shell deposition.


By fitting linear models to gene expression data in ambient and low aragonite saturation treatments, we are able to isolate 37 annotated genes correlated with initial larval shell formation, which can be categorized into 1) ion transporters, 2) shell matrix proteins and 3) protease inhibitors. Clustering of the gene expression data into co-expression networks further supports the result of the linear models, and also implies an important role of dynein motor proteins as transporters of cellular components during the initial shell formation process.


Using an RNA-Seq approach with high temporal resolution allows us to identify a conceptual model for how oyster larval calcification is initiated. This work provides a foundation for further studies on how genetic variation in these identified genes could affect fitness of oyster populations subjected to future environmental changes, such as ocean acidification.

Continue reading ‘Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms’

Effects of carbamazepine and cetirizine under an ocean acidification scenario on the biochemical and transcriptome responses of the clam Ruditapes philippinarum


• Drugs were bioconcentrated at both pH conditions (7.8 and 7.5).
• Uptake and BCF of CTZ decreased comparing low pH (7.5) with control pH (7.8).
• No oxidative stress was induced by drug exposure and/or pH.
• Exposure to drugs or low pH changed mRNA levels.
• Drug exposure and ocean acidification interaction change drugs toxicity.


Several works evaluated the toxicity of pharmaceutical drugs and climate related changes in invertebrates but few explored the combined effects of both stressors, namely considering their mode of action (MoA). Carbamazepine (CBZ) and cetirizine (CTZ) are pharmaceutical drugs detected in the environment and the toxicity derived from the combined effects of these drugs with ocean acidification (OA) is poorly explored. Thus, the present study investigated the biochemical parameters related to an oxidative stress response and the transcription of genes related to the MoA of CBZ (1.0 μg/L) and CTZ (0.6 μg/L) in the clam Ruditapes philippinarum chronically exposed (28 days) to control (7.8) and low (7.5) pH conditions. The results obtained showed that despite the clams accumulated both drugs, at low pH the clams exposed to CTZ decreased drug concentration and BCF values (CTZ uptake: 2.0 ± 0.5 ng/g fresh weight; BCF: 3.8 ± 0.9) in comparison with clams exposed to control pH (CTZ uptake: 2.9 ± 0.3 ng/g fresh weight; BCF: 5.5 ± 0.6). No oxidative stress was induced by the exposure to CBZ or CTZ at each pH level, but the transcription of several genes related with the MoA (neurotransmission, immunity and biomineralization) was altered by low pH, drug exposure and the combination of both stressors. At both pH conditions, CBZ increased the transcription of GABA receptor gene (neurotransmission) and CTZ led to a decrease of Perlucin gene (biomineralization) transcription. The transcription of MyD88 gene (immunity) decreased at low pH (7.5) combined with drug exposure (CBZ or CTZ). Thus, it was highlighted that the interaction of drug exposure and low pH conditions can change bivalves’ sensitivity to drugs or alter drugs toxicity.

Continue reading ‘Effects of carbamazepine and cetirizine under an ocean acidification scenario on the biochemical and transcriptome responses of the clam Ruditapes philippinarum’

Physiological stress response associated with elevated CO2 and dissolved iron in a phytoplankton community dominated by the coccolithophore Emiliania huxleyi

We exposed a natural phytoplankton community to combined present (390 µatm, low carbon [LC]) and future CO2 levels predicted for the year 2100 (900 µatm, high carbon [HC]), and ambient (4.5 nM, -DFB [desferoxamine B]) and high (12 nM, +DFB) dissolved iron (dFe) levels, for 25 d in mesocosms. We report on the physiological response of the community dominated by the coccolithophore Emiliania huxleyi. The community structure shifted on Day 10, leading to 2 different phases (1 and 2), i.e. before and after Day 10, respectively. We focussed on the massive bloom of E. huxleyi that developed in Phase 2, in the LC+DFB treatment. In high dFe conditions, pigments and photosynthetic parameters increased compared to the control (LC-DFB). Cell death was only detected during the community shift (Days 10-12) and mostly increased in the presence of high CO2. The accumulation of reactive oxygen species (ROS) decreased under high dFe, pointing to an efficient, rather than a stressed, metabolism. DNA lesions, caused by excess irradiance, were minimised under high Fe. E. huxleyi is known for its low Fe requirements for growth. However, we demonstrate that Fe is essential to E. huxleyi for DNA repair and ROS management, and to maintain optimal functioning of the photosynthetic machinery, with implications for carbon cycling and future ecosystem functioning.

Continue reading ‘Physiological stress response associated with elevated CO2 and dissolved iron in a phytoplankton community dominated by the coccolithophore Emiliania huxleyi’

Intraspecific variation in the response of the scleractinian coral Acropora digitifera to ocean acidification

To examine the possible variation in responses of corals to ocean acidification (OA) among populations, we compared the sensitivity of two Okinawan populations (Sesoko and Bise) of the scleractinian coral Acropora digitifera to high pCO2. We found that both light and dark calcification rates of Sesoko corals did not change with an increase in seawater pCO2, while the calcification rates of Bise corals significantly decreased. Additionally, calcification rate of Sesoko corals was significantly lower than Bise corals at control conditions. Expressions of two putative calcification-related genes (BAT: bicarbonate transporter and galaxin) were up-regulated at high CO2 compared to the control and expression of the BAT gene was significantly higher in Sesoko compared to Bise corals. Consequently, differences in the calcification rate between populations and differences in the expression of genes related to inorganic carbon transport regulation could be reasons that explain the difference in the response to OA between the two populations. Furthermore, taking into account that Sesoko corals were located in relatively nearshore areas where the environmental conditions are more variable, while Bise corals were located in the forereef which shows more stable conditions, plasticity for coral calcification in response to different environmental conditions and/or acclimation response to changes such as seawater pCO2 may lead to differences in sensitivity between the two populations to high seawater pCO2. Studies considering the potential variability in corals sensitivity to OA among local populations from different habitats are important to predict the potential effects of climate change on reef ecosystems.

Continue reading ‘Intraspecific variation in the response of the scleractinian coral Acropora digitifera to ocean acidification’

Expression of homing endonuclease gene and insertion-like element in sea anemone mitochondrial genomes: lesson learned from Anemonia viridis


• We report complete mitochondrial genome sequences and corresponding mito-transcriptomes of the two related sea anemone species Anemonia viridis and Anemonia majano
• We describe structural features of group I introns in the NADH dehydrogenase 5 gene and the cytochrome oxidase I (COI) gene, the latter containing a homing endonuclease gene
• We provide support of that the intron homing endonuclease gene is expressed in a gene-fusion strategy involving exon 1 of the COI gene
• We show that the insertion-like element orfA is well expressed from sea anemone mitochondrial geneomes
• Long-term environmental stress due to low-seawater pH conditions results in up-regulation of COI and orfA gene expressions in Anemonia viridis


The mitochondrial genomes of sea anemones are dynamic in structure. Invasion by genetic elements, such as self-catalytic group I introns or insertion-like sequences, contribute to sea anemone mitochondrial genome expansion and complexity. By using next generation sequencing we investigated the complete mtDNAs and corresponding transcriptomes of the temperate sea anemone Anemonia viridis and its closer tropical relative Anemonia majano. Two versions of fused homing endonuclease gene (HEG) organization were observed among the Actiniidae sea anemones; in-frame gene fusion and pseudo-gene fusion. We provided support for the pseudo-gene fusion organization in Anemonia species, resulting in a repressed HEG from the COI-884 group I intron. orfA, a putative protein-coding gene with insertion-like features, was present in both Anemonia species. Interestingly, orfA and COI expression were significantly up-regulated upon long-term environmental stress corresponding to low seawater pH conditions. This study provides new insights to the dynamics of sea anemone mitochondrial genome structure and function.

Continue reading ‘Expression of homing endonuclease gene and insertion-like element in sea anemone mitochondrial genomes: lesson learned from Anemonia viridis’

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Ocean acidification in the IPCC AR5 WG II

OUP book