Posts Tagged 'individualmodeling'

Integrated regulatory and metabolic networks of the marine diatom Phaeodactylum tricornutum predict the response to rising CO2 levels

Diatoms are eukaryotic microalgae that are responsible for up to 40% of the ocean’s primary productivity. How diatoms respond to environmental perturbations such as elevated carbon concentrations in the atmosphere is currently poorly understood. We developed a transcriptional regulatory network based on various transcriptome sequencing expression libraries for different environmental responses to gain insight into the marine diatom’s metabolic and regulatory interactions and provide a comprehensive framework of responses to increasing atmospheric carbon levels. This transcriptional regulatory network was integrated with a recently published genome-scale metabolic model of Phaeodactylum tricornutum to explore the connectivity of the regulatory network and shared metabolites. The integrated regulatory and metabolic model revealed highly connected modules within carbon and nitrogen metabolism. P. tricornutum’s response to rising carbon levels was analyzed by using the recent genome-scale metabolic model with cross comparison to experimental manipulations of carbon dioxide.

IMPORTANCE: Using a systems biology approach, we studied the response of the marine diatom Phaeodactylum tricornutum to changing atmospheric carbon concentrations on an ocean-wide scale. By integrating an available genome-scale metabolic model and a newly developed transcriptional regulatory network inferred from transcriptome sequencing expression data, we demonstrate that carbon metabolism and nitrogen metabolism are strongly connected and the genes involved are coregulated in this model diatom. These tight regulatory constraints could play a major role during the adaptation of P. tricornutum to increasing carbon levels. The transcriptional regulatory network developed can be further used to study the effects of different environmental perturbations on P. tricornutum’s metabolism.

Continue reading ‘Integrated regulatory and metabolic networks of the marine diatom Phaeodactylum tricornutum predict the response to rising CO2 levels’

Sensitivity of sea urchin fertilization to pH varies across a natural pH mosaic

In the coastal ocean, temporal fluctuations in pH vary dramatically across biogeographic ranges. How such spatial differences in pH variability regimes might shape ocean acidification resistance in marine species remains unknown. We assessed the pH sensitivity of the sea urchin Strongylocentrotus purpuratus in the context of ocean pH variability. Using unique male–female pairs, originating from three sites with similar mean pH but different variability and frequency of low pH (pHT ≤ 7.8) exposures, fertilization was tested across a range of pH (pHT 7.61–8.03) and sperm concentrations. High fertilization success was maintained at low pH via a slight right shift in the fertilization function across sperm concentration. This pH effect differed by site. Urchins from the site with the narrowest pH variability regime exhibited the greatest pH sensitivity. At this site, mechanistic fertilization dynamics models support a decrease in sperm–egg interaction rate with decreasing pH. The site differences in pH sensitivity build upon recent evidence of local pH adaptation in S. purpuratus and highlight the need to incorporate environmental variability in the study of global change biology.

Continue reading ‘Sensitivity of sea urchin fertilization to pH varies across a natural pH mosaic’

Light and temperature control physiological responses of Halimeda to ocean acidification

The oceans have absorbed excess carbon dioxide (CO2) resulting from anthropogenic activities such as the burning of fossil fuels and deforestation. As a result, seawater chemistry has shifted causing an increase in bicarbonate ions (HCO32-) and hydrogen ions (H+) and leading to a reduction in carbonate (CO32-) concentration. This shift in seawater chemistry leads to a decrease in aragonite saturation state and pH. Eventually, the ocean will accumulate most of the extra CO2 produced over many years resulting in extreme acidified conditions where aragonite saturation levels will not support the chemical process of calcification that is vital to marine calcifiers. This thesis investigates the combined effects of elevated pCO2 with temperature and light on the calcification and photosynthesis of the green calcareous algae Halimeda. Halimeda, is a major contributor to sediment production for coral reef accretion and island reef formation. Based on carbonate data from biologists and geologists it is estimated that vertical accretion of CaCO3 by Halimeda ranges between 0.18 to 5.9 m in 1000 years. The role that light plays in the coupling between photosynthesis and calcification in Halimeda macroloba was investigated experimentally through a combination of two pCO2 levels (360 and 1200 uatm) and three irradiances (80, 150, and 595 μmol quanta m-2 s-1). A decrease in calcification at low light intensity and elevated pCO2 suggests that light is a limiting factor for the physiology of H. macroloba. The effects of elevated pCO2 and temperature on the photosynthesis and calcification of Halimeda incrassata were tested through two experiments using two pCO2 levels (390 and 900 uatm) and four temperatures (26, 29, 30 and 34 °C). Elevated temperature can mitigate the effects Ocean Acidification (OA) in H. incrassata. An estimate of current carbonate production by H. incrassata in Key Biscayne Florida Lagoon was obtained from biomass, CaCO3 content and turnover rate. Calcification rates from laboratory experiments were used to estimate future (200 years from now) seasonal carbonate production rates, which were then compared against current summer carbonate production. Future summer carbonate production rates were not affected by elevated pCO2 in relationship to current summer carbonate production. Elevated temperatures ~2 °C above summer maximum average could promote calcification of H. incrassata under ocean acidification conditions and, therefore, overall carbonate production of the reef. Results throughout the thesis revealed that the tolerance of the green calcareous algae Halimeda to OA could change depending on light and temperature conditions. In a more acidic future ocean, growth rates and sediment production of Halimeda will be affected under low light and temperature and will be enhanced under high light and and moderate elevated temperatures.

Continue reading ‘Light and temperature control physiological responses of Halimeda to ocean acidification’

Proton pumping accompanies calcification in foraminifera

Ongoing ocean acidification is widely reported to reduce the ability of calcifying marine organisms to produce their shells and skeletons. Whereas increased dissolution due to acidification is a largely inorganic process, strong organismal control over biomineralization influences calcification and hence complicates predicting the response of marine calcifyers. Here we show that calcification is driven by rapid transformation of bicarbonate into carbonate inside the cytoplasm, achieved by active outward proton pumping. Moreover, this proton flux is maintained over a wide range of pCO2 levels. We furthermore show that a V-type H+ ATPase is responsible for the proton flux and thereby calcification. External transformation of bicarbonate into CO2 due to the proton pumping implies that biomineralization does not rely on availability of carbonate ions, but total dissolved CO2 may not reduce calcification, thereby potentially maintaining the current global marine carbonate production.

Continue reading ‘Proton pumping accompanies calcification in foraminifera’

Mechanistic understanding of ocean acidification impacts on larval feeding physiology and energy budgets of the mussel Mytilus californianus

Ocean acidification (OA)—a process describing the ocean’s increase in dissolved carbon dioxide ( pCO2) and a reduction in pH and aragonite saturation state (Ωar) due to higher concentrations of atmospheric CO2—is considered a threat to bivalve mollusks and other marine calcifiers. While many studies have focused on the effects of OA on shell formation and growth, we present findings on the separate effects of pCO2, Ωar, and pH on larval feeding physiology (initiation of feeding, gut fullness, and ingestion rates) of the California mussel Mytilus californianus. We found that elevated pCO2 delays initiation of feeding, while gut fullness and ingestion rates were best predicted by Ωar; however, pH was not found to have a significant effect on these feeding processes under the range of OA conditions tested. We also modeled how OA impacts on initial shell development and how feeding physiology might subsequently affect larval energy budget components (e.g. scope for growth) and developmental rate to 260 µm shell length, a size at which larvae typically become pediveligers. Our model predicted that Ωar impacts on larval shell size and ingestion rates over the initial 48 h period of development would result in a developmental delay to the pediveliger stage of >4 d, compared with larvae initially developing in supersaturated conditions (Ωar > 1). Collectively, these results suggest that predicted increases in pCO2 and reduced Ωar values may negatively impact feeding activity and energy balances of bivalve larvae, reducing their overall fitness and recruitment success.

Continue reading ‘Mechanistic understanding of ocean acidification impacts on larval feeding physiology and energy budgets of the mussel Mytilus californianus’

Coral biomineralization, climate proxies and the sensitivity of coral reefs to CO2-driven climate change

Scleractinian corals extract calcium (Ca2+) and carbonate (CO2−3) ions from seawater to construct their calcium carbonate (CaCO3) skeletons. Key to the coral biomineralization process is the active elevation of the CO2−3 concentration of the calcifying fluid to achieve rapid nucleation and growth of CaCO3 crystals. Coral skeletons contain valuable records of past climate variability and contribute to the formation of coral reefs. However, limitations in our understanding of coral biomineralization hinder the accuracy of (1) coral-based reconstructions of past climate, and (2) predictions of coral reef futures as anthropogenic CO2 emissions drive declines in seawater CO2−3 concentration. In this thesis, I investigate the mechanism of coral biomineralization and evaluate the sensitivity of coral reef CaCO3 production to seawater carbonate chemistry. First, I conducted abiogenic CaCO3 precipitation experiments that identified the U/Ca ratio as a proxy for fluid CO2−3 concentration. Based on these experimental results, I developed a quantitative coral biomineralization model that predicts temperature can be reconstructed from coral skeletons by combining Sr/Ca – which is sensitive to both temperature and CO2−3 – with U/Ca into a new proxy called “Sr-U”. I tested this prediction with 14 corals from the Pacific Ocean and the Red Sea spanning mean annual temperatures of 25.7-30.1°C and found that Sr-U has uncertainty of only 0.5°C, twice as accurate as conventional coral-based thermometers. Second, I investigated the processes that differentiate reef-water and open-ocean carbonate chemistry, and the sensitivity of ecosystem-scale calcification to these changes. On Dongsha Atoll in the northern South China Sea, metabolic activity of resident organisms elevates reef-water CO2−3 twice as high as the surrounding open ocean, driving rates of ecosystem calcification higher than any other coral reef studied to date. When high temperatures stressed the resident coral community, metabolic activity slowed, with dramatic effects on reef-water chemistry and ecosystem calcification. Overall, my thesis highlights how the modulation of CO2−3, by benthic communities on the reef and individual coral polyps in the colony, controls the sensitivity of coral reefs to future ocean acidification and influences the climate records contained in the skeleton.

Continue reading ‘Coral biomineralization, climate proxies and the sensitivity of coral reefs to CO2-driven climate change’

European sea bass show behavioural resilience to near-future ocean acidification

Ocean acidification (OA)—caused by rising concentrations of carbon dioxide (CO2)—is thought to be a major threat to marine ecosystems and has been shown to induce behavioural alterations in fish. Here we show behavioural resilience to near-future OA in a commercially important and migratory marine finfish, the Sea bass (Dicentrarchus labrax). Sea bass were raised from eggs at 19°C in ambient or near-future OA (1000 µatm pCO2) conditions and n = 270 fish were observed 59–68 days post-hatch using automated tracking from video. Fish reared under ambient conditions, OA conditions, and fish reared in ambient conditions but tested in OA water showed statistically similar movement patterns, and reacted to their environment and interacted with each other in comparable ways. Thus our findings indicate behavioural resilience to near-future OA in juvenile sea bass. Moreover, simulated agent-based models indicate that our analysis methods are sensitive to subtle changes in fish behaviour. It is now important to determine whether the absences of any differences persist under more ecologically relevant circumstances and in contexts which have a more direct bearing on individual fitness.

Continue reading ‘European sea bass show behavioural resilience to near-future ocean acidification’

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Ocean acidification in the IPCC AR5 WG II

OUP book