Posts Tagged 'molecular biology'

Reduced seawater pH alters marine biofilms with impacts for marine polychaete larval settlement


• Reduced seawater pH strongly influences biofilm community composition, at both eukaryotic and prokaryotic level

• For older biofilms, biofilm age plays no role in community composition

• Incubation under different pH treatments results in variations in apparent colour and structural complexity of marine biofilms

• Incubation of marine biofilms under different pH treatments alters the settlement response in marine invertebrates

• The changes in marine biofilm community composition induced by seawater pH are most likely responsible for the changes observed in invertebrate settlement selectivity


Ocean acidification (OA) can negatively affect early-life stages of marine organisms, with the key processes of larval settlement and metamorphosis potentially vulnerable to reduced seawater pH. Settlement success depends strongly on suitable substrates and environmental cues, with marine biofilms as key settlement inducers for a range of marine invertebrate larvae. This study experimentally investigated (1) how seawater pH determines growth and community composition of marine biofilms, and (2) whether marine biofilms developed under different pH conditions can alter settlement success in the New Zealand serpulid polychaete Galeolaria hystrix. Biofilms were developed under six pH(T) treatments (spanning from 7.0 to 8.1 [ambient]) in a flow-through system for up to 14 months. Biofilms of different ages (7, 10 and 14 months) were used to assay successful settlement of competent G. hystrix larvae reared under ambient conditions. Biofilm microbiomes were characterized through amplicon sequencing of the small subunit ribosomal rRNA gene (16S and 18S). Biofilm community composition was stable over time within each pH treatment and biofilm age did not affect larval settlement selectivity. Seawater pH treatment strongly influenced biofilm community composition, as well as subsequent settlement success when biofilms were presented to competent Galeolaria larvae. Exposure to biofilms incubated under OA-treatments caused a decrease in larval settlement of up to 40% compared to the ambient treatments. We observed a decrease in settlement on biofilms relative to ambient pH for slides incubated at pH 7.9 and 7.7. This trend was reversed at pH 7.4, resulting in high settlement, comparable to ambient biofilms. Settlement decreased on biofilms from pH 7.2, and no settlement was observed on biofilms from pH 7.0. For the first time, we show that long-term incubation of marine biofilms under a wide range of reduced seawater pH treatments can alter marine biofilms in such a way that settlement success in marine invertebrates can be compromised.

Continue reading ‘Reduced seawater pH alters marine biofilms with impacts for marine polychaete larval settlement’

Effect of ocean acidification on bacterial metabolic activity and community composition in oligotrophic oceans, inferred from short-term bioassays

Increasing anthropogenic CO2 emissions in recent decades cause ocean acidification (OA), affecting carbon cycling in oceans by regulating eco-physiological processes of plankton. Heterotrophic bacteria play an important role in carbon cycling in oceans. However, the effect of OA on bacteria in oceans, especially in oligotrophic regions, was not well understood. In our study, the response of bacterial metabolic activity and community composition to OA was assessed by determining bacterial production, respiration, and community composition at the low-pCO2 (400 ppm) and high-pCO2 (800 ppm) treatments over the short term at two oligotrophic stations in the northern South China Sea. Bacterial production decreased significantly by 17.1–37.1 % in response to OA, since bacteria with high nucleic acid content preferentially were repressed by OA, which was less abundant under high-pCO2 treatment. Correspondingly, shifts in bacterial community composition occurred in response to OA, with a high fraction of the small-sized bacteria and high bacterial species diversity in a high-pCO2 scenario at K11. Bacterial respiration responded to OA differently at both stations, most likely attributed to different physiological responses of the bacterial community to OA. OA mitigated bacterial growth efficiency, and consequently, a larger fraction of DOC entering microbial loops was transferred to CO2.

Continue reading ‘Effect of ocean acidification on bacterial metabolic activity and community composition in oligotrophic oceans, inferred from short-term bioassays’

Influence of acidification and warming of seawater on biofouling by bacteria grown over API 5L steel

The acidification and warming of seawater have several impacts on marine organisms, including over microorganisms. The influence of acidification and warming of seawater on biofilms grown on API 5L steel surfaces was evaluated by sequencing the 16S ribosomal gene. For this, three microcosms were designed, the first simulating the natural marine environment (MCC), the second with a decrease in pH from 8.1 to 7.9, and an increase in temperature by 2 °C (MMS), and the third with pH in around 7.7 and an increase in temperature of 4 °C (MES). The results showed that MCC was dominated by the Gammaproteobacteria class, mainly members of the Alteromonadales Order. The second most abundant group was Alphaproteobacteria, with a predominance of Rhodobacterales and Oceanospirillales. In the MMS system there was a balance between representatives of the Gammaproteobacteria and Alphaproteobacteria classes. In MES there was an inversion in the representations of the most prevalent classes previously described in MCC. In this condition, there was a predominance of members of the Alphaproteobacteria Class, in contrast to the decrease in the abundance of Gammaproteobacteria members. These results suggest that possible future climate changes may influence the dynamics of the biofouling process in surface metals.

Continue reading ‘Influence of acidification and warming of seawater on biofouling by bacteria grown over API 5L steel’

Evaluation of actin as a reference for quantitative gene expression studies in Emiliania huxleyi (Prymnesiophyceae) under ocean acidification conditions

Gene expression studies of marine phytoplankton under ocean acidification conditions are frequently based on relative measurements, with actin commonly used as a reference gene. Evidence from other organisms suggests that actin gene expression may be regulated by environmental conditions, compromising the role of actin as a reference gene. In this work the reliability of actin as a reference gene for ocean acidification experimental conditions (high CO2 vs low CO2) in two different metabolic states (acclimated metabolism vs perturbed metabolism) for the coccolithophore Emiliania huxleyi was tested. The transcriptional response of the actin (act) is compared with the expression of specific target genes associated with inorganic carbon uptake (α-carbonic anhydrase: αca1) and assimilation (RuBisCO: rbcL), which was regulated under the experimental conditions. Our results showed act expression instability in experimental conditions, evidencing that act is not a reliable reference gene for studies assessing the effect of ocean acidification on Emiliania huxleyi. Furthermore, when the act-based normalization was quantitatively tested, rbcL and αca1 expression were compromised, leading us to conclude that absolute gene expression quantification should be considered as a potentially reliable alternative for studying gene expression under ocean acidification conditions

Continue reading ‘Evaluation of actin as a reference for quantitative gene expression studies in Emiliania huxleyi (Prymnesiophyceae) under ocean acidification conditions’

Impaired antioxidant defenses and DNA damage in the European glass eel (Anguilla anguilla) exposed to ocean warming and acidification


  • European glass eels were lab-exposed to future warming and acidification conditions
  • Selected biomarkers were used to study physiological responses of glass eels
  • The antioxidant enzymatic machinery was impaired in the muscle and viscera
  • Heat shock response was different between tissues, increasing with temperature
  • The results emphasize the higher vulnerability of eels under climate change


The European eel (Anguilla anguilla) has attracted scientific inquiry for centuries due to its singular biological traits. Within the European Union, glass eel fisheries have declined sharply since 1980, from up to 2000 t (t) to 62.2 t in 2018, placing wild populations under higher risk of extinction. Among the major causes of glass eels collapse, climate change has become a growing worldwide issue, specifically ocean warming and acidification, but, to our knowledge, data on physiological and biochemical responses of glass eels to these stressors is limited. Within this context, we selected some representative biomarkers [e.g. glutathione peroxidase (GPx), catalase (CAT), total antioxidant capacity (TAC), heat shock proteins (HSP70), ubiquitin (Ub) and DNA damage] to study physiological responses of the European glass eel under distinct laboratory-climate change scenarios, such as increased water temperature (+ 4 °C) and pH reduction (− 0.4 units), for 12 weeks. Overall, the antioxidant enzymatic machinery was impaired, both in the muscle and viscera, manifested by significant changes in CAT, GPx and TAC. Heat shock response varied differently between tissues, increasing with temperature in the muscle, but not in the viscera, and decreasing in both tissues under acidification. The inability of HSP to maintain functional protein conformation was responsible for boosting the production of Ub, particularly under warming and acidification, as sole stressors. The overproduction of reactive oxygen species (ROS), either elicited by warming – due to increased metabolic demand – or acidification – through H+ interaction with O2, generating H2O2 – overwhelmed defense mechanisms, causing oxidative stress and consequently leading to protein and DNA damage. Our results emphasize the vulnerability of eels’ early life stages to climate change, with potential cascading consequences to adult stocks.

Continue reading ‘Impaired antioxidant defenses and DNA damage in the European glass eel (Anguilla anguilla) exposed to ocean warming and acidification’

Gene expression responses of larval gopher (Sebastes carnatus) and blue (S. mystinus) rockfish to ocean acidification and hypoxia

Global climate change is driving shifts in ocean chemistry, which combined with intensification of coastal upwelling, reduces ocean pH and dissolved oxygen (DO) content in the nearshore habitats of the California Current System. Physiological plasticity, within and across generations, might be especially important for long-lived, late-to-mature species, like rockfishes (genus Sebastes), that may be unable to keep pace with climate change via genetic adaptation. Rockfishes exhibit matrotrophic viviparity and may be able to buffer their offspring from environmental stress through early developmental exposure or transgenerational plasticity (non-genetic inheritance of phenotypes). In this study, mature female gopher (S. carnatus) and blue (S. mystinus) rockfish were pre-exposed to one of four treatments; 1) control conditions, 2) low pH, 3) low DO, or 4) combined low pH/DO stressors during embryonic growth (i.e. fertilization and gestation), followed by a 5-day larval exposure after birth in either the same or a different treatment received by mothers. I used RNA sequencing to determine how the maternal environment affected larval rockfish gene expression (GE) at birth, after the 5-day larval exposure in either the same maternal treatment or a novel pH/DO environment, and between larvae sampled at birth and after the 5-day larval exposure within each treatment. For both species, I found that the maternal exposure drove larval GE patterns regardless of sampling time point or treatment. Furthermore, the maternal environment continued to strongly influence larval GE for at least the first five days after birth. In gopher rockfish, larvae differentially expressed fewer genes at birth between the control and hypoxic groups than larvae that gestated in and remained in the same treatment and were sampled after the 5-day larval exposure. Gene functions also shifted; at day 5, there was an increase in differentially expressed genes that were related to metabolic pathways, implying that the larvae in the hypoxic treatment are responding to the stressor. In both species, I found that larvae which experienced a pH and/or hypoxic stressor during the maternal exposure had fewer differentially expressed genes across time compared to larvae that experienced control conditions. This pattern remained consistent, even if the larvae were placed into control conditions for the 5-day larval exposure, indicating that exposure to low pH/DO stressors might cause a delay in development. These data suggest that rockfish may not be able to buffer their offspring from environmental stressors, highlighting the important role of the maternal environment during gestation. Between the two species, however, blue rockfish may in fact fare better in future conditions as their reproductive season occurs before the onset of strong spring upwelling, when more hypoxic and low pH water intrudes the nearshore. However, if future climate models are correct, shifts in the timing and intensity of upwelling season may overlap with the reproductive season in blue rockfish. Elucidating the critical role of the maternal environment on offspring physiology can help us better understand how economically and ecologically important species will fare in the face of climate change.

Continue reading ‘Gene expression responses of larval gopher (Sebastes carnatus) and blue (S. mystinus) rockfish to ocean acidification and hypoxia’

Effect of environmental history on the habitat-forming kelp Macrocystis pyrifera responses to ocean acidification and warming: a physiological and molecular approach

The capacity of marine organisms to adapt and/or acclimate to climate change might differ among distinct populations, depending on their local environmental history and phenotypic plasticity. Kelp forests create some of the most productive habitats in the world, but globally, many populations have been negatively impacted by multiple anthropogenic stressors. Here, we compare the physiological and molecular responses to ocean acidification (OA) and warming (OW) of two populations of the giant kelp Macrocystis pyrifera from distinct upwelling conditions (weak vs strong). Using laboratory mesocosm experiments, we found that juvenile Macrocystis sporophyte responses to OW and OA did not differ among populations: elevated temperature reduced growth while OA had no effect on growth and photosynthesis. However, we observed higher growth rates and NO3 assimilation, and enhanced expression of metabolic-genes involved in the NO3 and CO2 assimilation in individuals from the strong upwelling site. Our results suggest that despite no inter-population differences in response to OA and OW, intrinsic differences among populations might be related to their natural variability in CO2, NO3 and seawater temperatures driven by coastal upwelling. Further work including additional populations and fluctuating climate change conditions rather than static values are needed to precisely determine how natural variability in environmental conditions might influence a species’ response to climate change.

Continue reading ‘Effect of environmental history on the habitat-forming kelp Macrocystis pyrifera responses to ocean acidification and warming: a physiological and molecular approach’

American lobster postlarvae alter gene regulation in response to ocean warming and acidification

Anthropogenic carbon emissions released into the atmosphere is driving rapid, concurrent increases in temperature and acidity across the world’s oceans. Disentangling the interactive effects of warming and acidification on vulnerable life stages is important to our understanding of responses of marine species to climate change. This study evaluates the interactive effects of these stressors on the acute response of gene expression of postlarval American lobster (Homarus americanus), a species whose geographic range is warming and acidifying faster than most of the world’s oceans. In the context of our experiment, we found two especially noteworthy results: First, although physiological end points have consistently been shown to be more responsive to warming in similar experimental designs, our study found gene regulation to be considerably more responsive to elevated pCO2. Furthermore, the combined effect of both stressors on gene regulation was significantly greater than either stressor alone. Using a full factorial experimental design, lobsters were raised in control and elevated pCO2 concentrations (400 ppm and 1,200 ppm) and temperatures (16°C and 19°C). A transcriptome was assembled from an identified 414,517 unique transcripts. Overall, 1,108 transcripts were differentially expressed across treatments, several of which were related to stress response and shell formation. When temperature alone was elevated (19°C), larvae downregulated genes related to cuticle development; when pCO2 alone was elevated (1,200 ppm), larvae upregulated chitinase as well as genes related to stress response and immune function. The joint effects of end‐century stressors (19°C, 1,200 ppm) resulted in the upregulation of those same genes, as well as cellulase, the downregulation of calcified cuticle proteins, and a greater upregulation of genes related to immune response and function. These results indicate that changes in gene expression in larval lobster provide a mechanism to respond to stressors resulting from a rapidly changing environment.

Continue reading ‘American lobster postlarvae alter gene regulation in response to ocean warming and acidification’

Genomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece

Although the rise of antibiotic and multidrug resistant bacteria is one of the biggest current threats to human health, our understanding of the mechanisms involved in antibiotic resistance selection remains scarce. We performed whole genome sequencing of 21 Pseudomonas strains, previously isolated from an active submarine volcano of Greece, the Kolumbo volcano. Our goal was to identify the genetic basis of the enhanced co-tolerance to antibiotics and acidity of these Pseudomonas strains. Pangenome analysis identified 10,908 Gene Clusters (GCs). It revealed that the numbers of phage-related GCs and sigma factors, which both provide the mechanisms of adaptation to environmental stressors, were much higher in the high tolerant Pseudomonas strains compared to the rest ones. All identified GCs of these strains were associated with antimicrobial and multidrug resistance. The present study provides strong evidence that the CO2-rich seawater of the volcano associated with low pH might be a reservoir of microorganisms carrying multidrug efflux-mediated systems and pumps. We, therefore, suggest further studies of other extreme environments (or ecosystems) and their associated physicochemical parameters (or factors) in the rise of antibiotic resistance.

Continue reading ‘Genomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece’

Ocean acidification boosts reproduction in fish via indirect effects

Ocean acidification affects species populations and biodiversity through direct negative effects on physiology and behaviour. The indirect effects of elevated CO2 are less well known and can sometimes be counterintuitive. Reproduction lies at the crux of species population replenishment, but we do not know how ocean acidification affects reproduction in the wild. Here, we use natural CO2 vents at a temperate rocky reef and show that even though ocean acidification acts as a direct stressor, it can indirectly increase energy budgets of fish to stimulate reproduction at no cost to physiological homeostasis. Female fish maintained energy levels by compensation: They reduced activity (foraging and aggression) to increase reproduction. In male fish, increased reproductive investment was linked to increased energy intake as mediated by intensified foraging on more abundant prey. Greater biomass of prey at the vents was linked to greater biomass of algae, as mediated by a fertilisation effect of elevated CO2 on primary production. Additionally, the abundance and aggression of paternal carers were elevated at the CO2 vents, which may further boost reproductive success. These positive indirect effects of elevated CO2 were only observed for the species of fish that was generalistic and competitively dominant, but not for 3 species of subordinate and more specialised fishes. Hence, species that capitalise on future resource enrichment can accelerate their reproduction and increase their populations, thereby altering species communities in a future ocean.

Continue reading ‘Ocean acidification boosts reproduction in fish via indirect effects’

Subscribe to the RSS feed

Powered by FeedBurner

Follow AnneMarin on Twitter

Blog Stats

  • 1,428,870 hits


Ocean acidification in the IPCC AR5 WG II

OUP book