Posts Tagged 'molecular biology'

Projected near-future ocean acidification decreases mercury toxicity in marine copepods


  • Copepods were subjected to OA and Hg pollution under multigenerational exposure.
  • OA reduced Hg accumulation and its toxicity to the growth/reproduction in copepods.
  • Copepod proteome enabled its physiological resilience to decreasing pH.
  • Proteomics indicated many toxic events, ensuring Hg toxicity to the copepod’s traits.
  • Proteome compensation was accounting for the alleviative effect of OA on Hg toxicity.


Here, we examined the combinational effect of ocean acidification (OA) and mercury (Hg) in the planktonic copepod Pseudodiaptomus annandalei in cross-factored response to different pCO2 (400, 800 μatm) and Hg (control, 1.0 and 2.5 μg/L) exposures for three generations (F0-F2), followed by single-generation recovery (F3) under clean condition. Several phenotypic traits and Hg accumulation were analyzed for F0-F3. Furthermore, shotgun-based quantitative proteomics was performed for F0 and F2. Our results showed that OA insignificantly influenced the traits. During F0-F2, combined exposure reduced Hg accumulation as compared with the counterpart Hg treatment, supporting the mitigating effect of OA on Hg toxicity in copepods. Proteomics analysis indicated that the copepods probably increased energy production/storage and stress response to ensure physiological resilience against OA. However, Hg induced many toxic events (e.g., energy depletion and degenerated organomorphogenesis/embryogenesis for F0; cell cycle arrest and detrimental stress-defense for F2), which were translated to the population-level adverse outcome, i.e., compromised growth/reproduction. Particularly, compensatory proteome response was identified (e.g., increased immune defense for F0; energetic compensation and enhanced embryogenesis for F2), accounting for a negative interaction between OA and Hg. Together, this study provides the molecular mechanisms behind the effects of OA and Hg pollution in marine copepods.

Continue reading ‘Projected near-future ocean acidification decreases mercury toxicity in marine copepods’

Impacts of multiple stressors on a benthic foraminiferal community: a long-term experiment assessing response to ocean acidification, hypoxia and warming

Ocean chemistry is changing as a result of human activities. Atmospheric carbon dioxide (CO2) concentrations are increasing, causing an increase in oceanic pCO2 that drives a decrease in oceanic pH, a process called ocean acidification (OA). Higher CO2 concentrations are also linked to rising global temperatures that can result in more stratified surface waters, reducing the exchange between surface and deep waters; this stronger stratification, along with nutrient pollution, contributes to an expansion of oxygen-depleted zones (so called hypoxia or deoxygenation). Determining the response of marine organisms to environmental changes is important for assessments of future ecosystem functioning. While many studies have assessed the impact of individual or paired stressors, fewer studies have assessed the combined impact of pCO2, O2, and temperature. A long-term experiment (∼10 months) with different treatments of these three stressors was conducted to determine their sole or combined impact on the abundance and survival of a benthic foraminiferal community collected from a continental-shelf site. Foraminifera are well suited to such study because of their small size, relatively rapid growth, varied mineralogies and physiologies. Inoculation materials were collected from a ∼77-m deep site south of Woods Hole, MA. Very fine sediments (<53 μm) were used as inoculum, to allow the entire community to respond. Thirty-eight morphologically identified taxa grew during the experiment. Multivariate statistical analysis indicates that hypoxia was the major driving factor distinguishing the yields, while warming was secondary. Species responses were not consistent, with different species being most abundant in different treatments. Some taxa grew in all of the triple-stressor samples. Results from the experiment suggest that foraminiferal species’ responses will vary considerably, with some being negatively impacted by predicted environmental changes, while other taxa will tolerate, and perhaps even benefit, from deoxygenation, warming and OA.

Continue reading ‘Impacts of multiple stressors on a benthic foraminiferal community: a long-term experiment assessing response to ocean acidification, hypoxia and warming’

Regulation of apoptosis by Pacific oyster Crassostrea gigas reveals acclimation strategy to CO2 driven acidification


  • Apoptosis ratio increased and caspase-3/9 was activated under short-term CO2 exposure.
  • Opposite phenomenon was observed under long-term CO2 exposure.
  • CgBcl-XL mRNA level displayed significant up-regulation under long term CO2 exposure.
  • In vivo knock down of CgBcl-XL demonstrated its anti-apoptotic role.
  • The protein level of CgBcl-XL increased significantly under long-term CO2 exposure.


Ocean acidification (OA) has posed formidable threats to marine calcifiers. In response to elevated CO2 levels, marine calcifiers have developed multiple strategies to survive, such as taking advantage of apoptosis, but its regulation mechanism remains largely unknown. Here, we used the Pacific oyster Crassostrea gigas as model to understand the apoptotic responses and regulation mechanism at short- (7 d) to long-term (56 d) CO2 exposure (pH = 7.50). The apoptosis of hemocytes was significantly induced after short-term treatment (7–21 d) but was suppressed under long-term CO2 exposure (42–56 d). Similarly, caspase-3 and caspase-9 were also increased post short-term exposure and fell back to normal levels after long-term exposure. These data together indicated diverse regulation mechanisms of apoptosis through different exposure periods. Through analysis of the B-cell lymphoma 2 (Bcl-2) family mitochondrial apoptosis regulators, we showed that only CgBcl-XL’s expression kept at high levels after 42- and 56-day CO2 exposure. CgBcl-XL shared sequence, and structural similarity with its mammalian counterpart, and knockdown of CgBcl-XL in hemocytes via RNA interference promoted apoptosis. The protein level of CgBcl-XL was significantly increased after long-term CO2 exposure (28–56 d), and its distribution in hemocytes became more concentrated and dense. Therefore, CgBcl-XL serves as an essential anti-apoptotic protein for tipping the balance of cell apoptosis, which may play a key role in survival under long-term CO2 exposure. These results reveal a potential adaptation strategy of oysters towards OA and the variable environment changes through the modulation of apoptosis.

Continue reading ‘Regulation of apoptosis by Pacific oyster Crassostrea gigas reveals acclimation strategy to CO2 driven acidification’

Natural CO2 seeps reveal adaptive potential to ocean acidification in fish

Volcanic CO2 seeps are natural laboratories that can provide insights into the adaptation of species to ocean acidification. Whilst many species are challenged by reduced pH levels, some species benefit from the altered environment and thrive. Here, we explore the molecular mechanisms of adaptation to ocean acidification in a population of a temperate fish species that experiences increased population sizes under elevated CO2. Fish from CO2 seeps exhibited an overall increased gene expression in gonad tissue compared to those from ambient CO2 sites. Up‐regulated genes at CO2 seeps are possible targets of adaptive selection as they can directly influence the physiological performance of fishes exposed to ocean acidification. Most of the up‐regulated genes at seeps were functionally involved in the maintenance of pH homeostasis and increased metabolism, and presented a deviation from neutral evolution expectations in their patterns of DNA polymorphisms, providing evidence for adaptive selection to ocean acidification. The targets of this adaptive selection are likely regulatory sequences responsible for the increased expression of these genes which would allow a fine‐tuned physiological regulation to maintain homeostasis and thrive at CO2 seeps. Our findings reveal that standing genetic variation in DNA sequences regulating the expression of genes in response to a reduced pH environment could provide for adaptive potential to near‐future ocean acidification in fishes. Moreover, with this study we provide a forthright methodology combining transcriptomics and genomics which can be applied to infer the adaptive potential to different environmental conditions in wild marine populations.

Continue reading ‘Natural CO2 seeps reveal adaptive potential to ocean acidification in fish’

Ocean acidification induces changes in virus–host relationships in Mediterranean benthic ecosystems

Acidified marine systems represent “natural laboratories”, which provide opportunities to investigate the impacts of ocean acidification on different living components, including microbes. Here, we compared the benthic microbial response in four naturally acidified sites within the Southern Tyrrhenian Sea characterized by different acidification sources (i.e., CO2 emissions at Ischia, mixed gases at Panarea and Basiluzzo and acidified freshwater from karst rocks at Presidiana) and pH values. We investigated prokaryotic abundance, activity and biodiversity, viral abundance and prokaryotic infections, along with the biochemical composition of the sediment organic matter. We found that, despite differences in local environmental dynamics, viral life strategies change in acidified conditions from mainly lytic to temperate lifestyles (e.g., chronic infection), also resulting in a lowered impact on prokaryotic communities, which shift towards (chemo)autotrophic assemblages, with lower organic matter consumption. Taken together, these results suggest that ocean acidification exerts a deep control on microbial benthic assemblages, with important feedbacks on ecosystem functioning.

Continue reading ‘Ocean acidification induces changes in virus–host relationships in Mediterranean benthic ecosystems’

Bacterial communities are more sensitive to ocean acidification than fungal communities in estuarine sediments

Ocean acidification (OA) in estuaries is becoming a global concern, and may affect microbial characteristics in estuarine sediments. Bacterial communities in response to acidification in this habitat have been well discussed; however, knowledge about how fungal communities respond to OA remains poorly understood. Here, we explored the effects of acidification on bacterial and fungal activities, structures and functions in estuarine sediments during a 50-day incubation experiment. Under acidified conditions, activities of three extracellular enzymes related to nutrient cycling were inhibited and basal respiration rates were decreased. Acidification significantly altered bacterial communities and their interactions, while weak alkalization had a minor impact on fungal communities. We distinguished pH-sensitive/tolerant bacteria and fungi in estuarine sediments, and found that only pH-sensitive/tolerant bacteria had strong correlations with sediment basal respiration activity. FUNGuild analysis indicated that animal pathogen abundances in sediment were greatly increased by acidification, while plant pathogens were unaffected. High-throughput quantitative PCR-based SmartChip analysis suggested that the nutrient cycling-related multifunctionality of sediments was reduced under acidified conditions. Most functional genes associated with nutrient cycling were identified in bacterial communities and their relative abundances were decreased by acidification. These new findings highlight that acidification in estuarine regions affects bacterial and fungal communities differently, increases potential pathogens and disrupts bacteria-mediated nutrient cycling.

Continue reading ‘Bacterial communities are more sensitive to ocean acidification than fungal communities in estuarine sediments’

Tissue comparison of transcriptional response to acute acidification stress of barramundi Lates calcarifer in coastal and estuarine areas


  • Assessed tissues response of barramundi in acidification stress by RNA-seq analysis
  • Acidification inhibited the immune function of barramundi in different tissues.
  • Provided insights for susceptible physiological processes to acidification stress


In order to explore the common and unique physiological changes in tissues of juvenile barramundi Lates calcarifer in acidified water environment, RNA sequence analysis was used to analyze the molecular responses of liver, head kidney, and gill of juvenile barramundi in pH 7.4 and pH 8.1 seawater environment. The number of differential expression genes identified in liver, head kidney and gill were 860, 388 and 1792, respectively. Through functional enrichment analysis, the differential expression genes common to the three tissues were all related to immunity. Among the unique differential genes in the liver, pathways related to digestion, endocrine, and metabolism were enriched. Among the unique differential expression genes in gill, pathways related to genetic information processing, immunity and metabolism were enriched. The findings of the present study uncover the transcriptional changes in fish correspond to environmental pH change, and provide a better understanding on the biological process at molecular level to environmental pH adapting. This work highlights that assessments for the potential of estuarine fishes to cope with environmental pH change to develop the future conservation strategies.

Continue reading ‘Tissue comparison of transcriptional response to acute acidification stress of barramundi Lates calcarifer in coastal and estuarine areas’

Transgenerational responses to seawater pH in the edible oyster, with implications for the mariculture of the species under future ocean acidification


• Larval offspring of C. hongkongensis were resilient to OA exposure

• Phenotypic traits in out-planted juveniles improved with parental exposure

• Positive carry-over effect from exposed parents persisted and manifested in the estuary

• Linking multiple life stages is vital to assess OA-induced carry-over capacity

• OA exposure at early life stages revealed potential mariculture application and species fitness


The majority of common edible oysters are projected to grow more slowly and have smaller impaired shells because of anthropogenic CO2-induced reductions in seawater carbonate ion concentration and pH, a process called ocean acidification (OA). Recent evidence has shown that OA has carryover effects, for example, larvae exposed to OA will also exhibit either positive or negative effects after metamorphosis. This study examined the hidden carryover effects of OA exposure during parental and larval stages on post-metamorphic traits of the commercially important oyster species Crassostrea hongkongensis. Adults of C. hongkongensis were exposed to control pH (pHNBS 8.0) and OA-induced low pH (pHNBS 7.4) conditions. Their larval offspring were then exposed to the same aquarium conditions before being out-planted as post-metamorphic juveniles at a mariculture site for 10 months. Initially, larval offspring were resilient to low pH with or without parental exposure. The larvae exposed to low pH had significantly faster development and higher percentage of settlement success compared to control groups. The out-planted juveniles with parental exposure had improved survival and growth compared to juveniles without parental exposure, regardless of the larval exposure history. This implies that transgenerational effects due to parental exposure not only persists but also have a greater influence than the within-generational effects of larval exposure. Our results shed light on the importance of linking the various life history stages when assessing the OA-induced carryover capacity of C. hongkongensis in the natural environment. Understanding these linked relationships helps us better predict the species rapid adaptation responses in the face of changing coastal conditions due to OA.

Continue reading ‘Transgenerational responses to seawater pH in the edible oyster, with implications for the mariculture of the species under future ocean acidification’

Ocean acidification but not hypoxia alters the gonad performance in the thick shell mussel Mytilus coruscus


  • Ocean acidification adversely affects the gonadal performance of mussels.
  • Hypoxia does not have effects on fecundity of mussels.
  • Steroids and Wnt/β-catenin gene expressions have weak correlations with fecundity in mussels.


Ocean acidification and hypoxia have become increasingly severe in coastal areas, and their co-occurrence poses emerging threats to coastal ecosystems. Here, we investigated the combined effects of ocean acidification and hypoxia on the reproductive capacity of the thick-shelled mussel Mytilus coruscus. Our results demonstrated low pH but not low oxygen induced decreased gonadosomatic index (GSI) in mussels. Male mussels had a lower level of sex steroids (estradiol, testosterone, and progesterone) when kept at low pH. Expression of genes related to reproduction were also impacted by low pH with a downregulation of genes involved in gonad development in males (β-catenin and Wnt-7b involved in males) and an upregulation of testosterone synthesis inhibition-related gene (Wnt-4) in females. Overall, our results suggest that ocean acidification has an impact on the gonadal development through an alternation of gene expression and level of steroids while hypoxia had no significant effect.

Continue reading ‘Ocean acidification but not hypoxia alters the gonad performance in the thick shell mussel Mytilus coruscus’

Ocean acidification effects on the stress response in a calcifying Antarctic coastal organism: the case of Nacella concinna ecotypes


• An ocean acidification experiment with the two ecotypes of Nacella concinna

• No noticeable low-pH effects on the stress response in the Antarctic limpet

• Adaptation of both ecotypes to natural pH fluctuations in the fjord might be occurring


Ocean acidification (OA) could become a serious threat for the Antarctic marine ecosystem over coming years, as the solubility of atmospheric CO2 and CaCO3 minerals increases at lower temperatures. We evaluated the effect of OA on the stress response of the limpet Nacella concinna by measuring gene expression levels. The experiment was performed with the two ecotypes (Littoral and Sublittoral) of the species during 54 days (IPCC, 2019 scenario RCP8.5; control, ~375 ppm; low-pH treatment, ~923 ppm). Exposure to low-pH treatment during 15 days triggered the down-regulation of two heat-shock protein genes (HSP70A, HSP70B) only in sublittoral individuals. Little variation in the relative expression values of all genes in both ecotypes was observed probably, due to a historical exposure to the substantial daily natural pH fluctuations recorded in the study area during the experiment. This study provides relevant baseline data for future OA experiments on coastal species in Antarctica.

Continue reading ‘Ocean acidification effects on the stress response in a calcifying Antarctic coastal organism: the case of Nacella concinna ecotypes’

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Ocean acidification in the IPCC AR5 WG II

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