Periodic Reporting for period 2 - SCOOBi (Seeking Constraints on Open Ocean Biocalcification)
Reporting period: 2024-06-01 to 2025-11-30
Why are the oceans supersaturated with respect to calcium carbonate? Foraminifera and coccolithophores generate over 2 billion tonnes of carbonate/yr1 but what limits this production? Our lack of understanding of the response of pelagic calcification to environmental change hinders any predictions of the future ocean carbon cycle and ecosystem.
This ground-breaking interdisciplinary project will transform our ability to predict the pelagic calcification response to future human “business as usual” or geoengineered perturbations. It will determine the historic and modern distribution of pelagic calcification rates, and how they are limited by environmental parameters quantitatively, and which factors accelerate calcification. Insights into the cost/benefit trade-off between calcification and growth will hint at emergence and origin of biomineralisation. By resolving mechanistically how cells partition energy and carbon between photosynthesis and calcification via genes and metabolites, and how the efficiency of these pathways is improved, SCOOBI opens the vista to engineering of these pathways including biomimetics and novel natural products.
The objectives are:
Ob1: Use innovative stable isotopic approaches applied to the natural laboratory of the geological record to identify the environmental parameters that trigger the highest pelagic adapted calcification efficiency (PIC/POC) in the modern and Cenozoic ocean.
Ob2: Document how different strategies of cell resource allocation affect the sensitivity of calcification to the environment in different coccolithophore species (Coccolithales versus Isochrysidales): Resolve whether there is a universal trade-off between growth rate and calcification.
Ob3: Detail the physiological and metabolic basis for the calcification efficiency of different species (PIC/POC) of coccolithophores and their sensitivity to environmental limitation and stress.
Ob4: Apply metabolite and large biomolecule composition, extracted from fossils, to document the environmental parameters that have driven changes in calcification efficiency over geological time and in the modern ocean
Ob5: Document the sensitivity of past community and organism-specific calcite production rates (PIC/POC*population size) to environmental parameters via a combination of cutting-edge genomic tools with sediment based estimates
Ob6: Investigate how the environmental sensitivity of calcite production rates, and their carbon isotopic composition, impacts understanding of the past and prediction of the future carbon cycle
This ground-breaking interdisciplinary project will transform our ability to predict the pelagic calcification response to future human “business as usual” or geoengineered perturbations. It will determine the historic and modern distribution of pelagic calcification rates, and how they are limited by environmental parameters quantitatively, and which factors accelerate calcification. Insights into the cost/benefit trade-off between calcification and growth will hint at emergence and origin of biomineralisation. By resolving mechanistically how cells partition energy and carbon between photosynthesis and calcification via genes and metabolites, and how the efficiency of these pathways is improved, SCOOBI opens the vista to engineering of these pathways including biomimetics and novel natural products.
The objectives are:
Ob1: Use innovative stable isotopic approaches applied to the natural laboratory of the geological record to identify the environmental parameters that trigger the highest pelagic adapted calcification efficiency (PIC/POC) in the modern and Cenozoic ocean.
Ob2: Document how different strategies of cell resource allocation affect the sensitivity of calcification to the environment in different coccolithophore species (Coccolithales versus Isochrysidales): Resolve whether there is a universal trade-off between growth rate and calcification.
Ob3: Detail the physiological and metabolic basis for the calcification efficiency of different species (PIC/POC) of coccolithophores and their sensitivity to environmental limitation and stress.
Ob4: Apply metabolite and large biomolecule composition, extracted from fossils, to document the environmental parameters that have driven changes in calcification efficiency over geological time and in the modern ocean
Ob5: Document the sensitivity of past community and organism-specific calcite production rates (PIC/POC*population size) to environmental parameters via a combination of cutting-edge genomic tools with sediment based estimates
Ob6: Investigate how the environmental sensitivity of calcite production rates, and their carbon isotopic composition, impacts understanding of the past and prediction of the future carbon cycle
We have pioneered culture experiments with omics, with innovative methods on the fossil record to uncover the mechanisms that govern calcification in modern coccolithophores and to explore their productivity in the past. Surprisingly, we have found that calcification may be more passive than has been previously considered, being used as an energy efficient process for cellular removal of Ca. We have discovered that the diffusion of CO2 into the cell is driven towards these highly alkaline vesicles, yielding the calcite preciptiation mechanism. This makes the process of calcification dependent on the diffusive supply rate of Co2 in the majority of species, although we have shown that G. huxleyi has the additional ability to use HCO3- for its calcification. It is likely that this process of calcification benefits photosynthesis by driving an inwards flux of carbon into the cells, where the process of calcite precipitation can drive the internal carbon levles closer to zero, which is a more efficient way of transporting carbon to the interior of the cell, than relying on the Rubisco enzyme which has a much lower affinity for carbon.
We have collected data on the cellular response of coccolithophores to varying; temperature, pH, light, Mg/Ca ratio, C availability, Ca concentration and growth phase (i.e. exponential versus stationary growth). We have adopted methods which combine high resolution physiology data on core metabolic activities including growth, photosynthesis, respiration and calcification with modern molecular approaches (proteomics and transcriptomics) to advance understanding on the cellular regulation of coccolithophores and altering performance of central metabolism under the environmental perturbations described. Much of this work has been published or is in preparation for submission to review and represents a first-of-its-kind study for this group of phytoplankton.
Intracellular calcification in coccolithophores has been thought to be energy-intensive, necessitating precise energy regulation for the import of substrates and export of coccoliths. Here we apply varied conditions of Mg availability via Mg/Ca ratios, due to its dual interactions with the cellular C cycling and calcification pathways of coccolithophores, to interrogate the physiological context of calcification. We reveal a complex interplay between cellular carbon metabolism and calcification in the ubiquitous coccolithophore species Gephyrocapsa huxleyi (formerly Emiliania huxleyi). Notably, we identify that two energy thresholds for calcification exist: with sufficient energy to initiate calcification being reached between Mg/Ca ratios of 0 and 0.5 and energy to optimize the performance of calcification being attained between Mg/Ca ratios of 0.5 and 5. In energy-limited conditions, the allocation of carbon and energy towards cell growth and core metabolic activities is prioritised over calcification When sufficient energy is present, variations in substrate availability at the site of calcification override any cellular regulation. Beyond the required energy threshold, there is no feedback between calcification performance and cell physiology. It further suggests that as long as the environmental conditions are sufficient to reach the fairly low energy demand, globally G. huxleyi calcification intensity will depend on substrate availability subsequently impacting the global carbon cycle (Ma et al., in prep).
Proteomic analysis revealed a significant modification of the E. huxleyi cellular proteome as temperatures increased: at lower temperature, ribosomal proteins and photosynthetic machinery appeared abundant, as rates of protein translation and photosynthetic performance are restricted by low temperatures. As temperatures increased, evidence of heat stress was observed in the photosystem, characterized by a relative down-regulation of the Photosystem II oxygen evolving complex and ATP synthase. Acclimation to elevated warming (28°C) revealed a substantial alteration to carbon metabolism. Here, E. huxleyi made use of the glyoxylate cycle and succinate metabolism to optimize carbon use, maintain growth and maximize ATP production in heat-damaged mitochondria, enabling cultures to maintain growth at levels significantly higher than those recorded in the control (17°C). Based on the metabolic changes observed, we can predict that warming may benefit photosynthetic carbon fixation by E. huxleyi in the sub-optimal to optimal thermal range. Past the thermal optima, increasing rates of respiration and costs of repair will likely constrain growth, causing a possible decline in the contribution of this species to the oceanic carbon sink depending on the evolvability of these temperature thresholds.
In the geological record, we have developed tools and methods for extracting signals on the physiology of the cells in the past.
We have generated and integrated a dataset consisting of carbon isotope ratios of size-separated coccolith calcite from marine sediments with a cell-scale model to interrogate cellular carbon fluxes and pCO2 through the Eocene (~55–34 Ma), Earth’s hottest interval of the past 100 million years. We show that the large coccolithophores that rose to dominate the oceans through the Eocene have higher calcification-to-carbon fixation ratios than their predecessors while the opposite is true for smaller coccolithophores. These changes, which occurred in the context of increasing ocean alkalization, may have played a role in an apparent positive carbon cycle feedback to decreasing pCO2. Our approach also provides independent support of multiproxy-based evidence for general decline through the Eocene in step with temperature. Together, this challenges the emerging view that a general decline in pCO2 reduces calcification on evolutionary timescales (Claxton et al., 2022).
We have also explored the extraction of polysaccharides from liths preserved in the geological record and measured their isotopic composition. Coccoliths can be taxonomically separated by size and identified, often to species level, prior to CAP extraction, providing a species-specific record. Coccolith morphology and composition are important additional sources of information, which are then unambiguously associated with the extracted CAPs. We found that carbon isotope ratios of CAPs changed in response to the environmental changes associated with a glacial cycle, which we attribute to temperature-driven changes in average growth rate. Once the underlying biosynthetic processes and the associated isotope effects are better understood, this archive of pristine organic matter has the potential to provide insight into phytoplankton growth rates and atmospheric pCO far beyond the Cenozoic, to when the first coccolithophores inhabited the surface ocean over 200 million years ago.
We have collected data on the cellular response of coccolithophores to varying; temperature, pH, light, Mg/Ca ratio, C availability, Ca concentration and growth phase (i.e. exponential versus stationary growth). We have adopted methods which combine high resolution physiology data on core metabolic activities including growth, photosynthesis, respiration and calcification with modern molecular approaches (proteomics and transcriptomics) to advance understanding on the cellular regulation of coccolithophores and altering performance of central metabolism under the environmental perturbations described. Much of this work has been published or is in preparation for submission to review and represents a first-of-its-kind study for this group of phytoplankton.
Intracellular calcification in coccolithophores has been thought to be energy-intensive, necessitating precise energy regulation for the import of substrates and export of coccoliths. Here we apply varied conditions of Mg availability via Mg/Ca ratios, due to its dual interactions with the cellular C cycling and calcification pathways of coccolithophores, to interrogate the physiological context of calcification. We reveal a complex interplay between cellular carbon metabolism and calcification in the ubiquitous coccolithophore species Gephyrocapsa huxleyi (formerly Emiliania huxleyi). Notably, we identify that two energy thresholds for calcification exist: with sufficient energy to initiate calcification being reached between Mg/Ca ratios of 0 and 0.5 and energy to optimize the performance of calcification being attained between Mg/Ca ratios of 0.5 and 5. In energy-limited conditions, the allocation of carbon and energy towards cell growth and core metabolic activities is prioritised over calcification When sufficient energy is present, variations in substrate availability at the site of calcification override any cellular regulation. Beyond the required energy threshold, there is no feedback between calcification performance and cell physiology. It further suggests that as long as the environmental conditions are sufficient to reach the fairly low energy demand, globally G. huxleyi calcification intensity will depend on substrate availability subsequently impacting the global carbon cycle (Ma et al., in prep).
Proteomic analysis revealed a significant modification of the E. huxleyi cellular proteome as temperatures increased: at lower temperature, ribosomal proteins and photosynthetic machinery appeared abundant, as rates of protein translation and photosynthetic performance are restricted by low temperatures. As temperatures increased, evidence of heat stress was observed in the photosystem, characterized by a relative down-regulation of the Photosystem II oxygen evolving complex and ATP synthase. Acclimation to elevated warming (28°C) revealed a substantial alteration to carbon metabolism. Here, E. huxleyi made use of the glyoxylate cycle and succinate metabolism to optimize carbon use, maintain growth and maximize ATP production in heat-damaged mitochondria, enabling cultures to maintain growth at levels significantly higher than those recorded in the control (17°C). Based on the metabolic changes observed, we can predict that warming may benefit photosynthetic carbon fixation by E. huxleyi in the sub-optimal to optimal thermal range. Past the thermal optima, increasing rates of respiration and costs of repair will likely constrain growth, causing a possible decline in the contribution of this species to the oceanic carbon sink depending on the evolvability of these temperature thresholds.
In the geological record, we have developed tools and methods for extracting signals on the physiology of the cells in the past.
We have generated and integrated a dataset consisting of carbon isotope ratios of size-separated coccolith calcite from marine sediments with a cell-scale model to interrogate cellular carbon fluxes and pCO2 through the Eocene (~55–34 Ma), Earth’s hottest interval of the past 100 million years. We show that the large coccolithophores that rose to dominate the oceans through the Eocene have higher calcification-to-carbon fixation ratios than their predecessors while the opposite is true for smaller coccolithophores. These changes, which occurred in the context of increasing ocean alkalization, may have played a role in an apparent positive carbon cycle feedback to decreasing pCO2. Our approach also provides independent support of multiproxy-based evidence for general decline through the Eocene in step with temperature. Together, this challenges the emerging view that a general decline in pCO2 reduces calcification on evolutionary timescales (Claxton et al., 2022).
We have also explored the extraction of polysaccharides from liths preserved in the geological record and measured their isotopic composition. Coccoliths can be taxonomically separated by size and identified, often to species level, prior to CAP extraction, providing a species-specific record. Coccolith morphology and composition are important additional sources of information, which are then unambiguously associated with the extracted CAPs. We found that carbon isotope ratios of CAPs changed in response to the environmental changes associated with a glacial cycle, which we attribute to temperature-driven changes in average growth rate. Once the underlying biosynthetic processes and the associated isotope effects are better understood, this archive of pristine organic matter has the potential to provide insight into phytoplankton growth rates and atmospheric pCO far beyond the Cenozoic, to when the first coccolithophores inhabited the surface ocean over 200 million years ago.
The exact molecular mechanisms which direct and control coccolith formation are unknown. In this study, we report on the presence and functional features of proteins within the coccoliths produced by a range of model coccolithophore species including: the globally abundant and well-studied Gephyrocapsa huxleyi (formerly Emiliania huxleyi) and related Gephyrocapsa oceanica, as well as the larger and more heavily calcified Coccolithus braarudii. Protein features were compared between species and against biomineralisation proteins previously identified in other marine calcifying organisms. Notably, several protein features were consistently seen across the examined coccolithophore species, including the cell signalling 14-3-3 domain, chromosome segregation SMC ATPase domain, as well as proteins involved in protein processing and protease inhibition. The copper-binding cupredoxin domain was observed in both Gephyrocapsa species, as well as other marine calcifiers, suggestive of a requirement of Cu in biomineralisation. Building consensus with existing work, we highlight the pentapeptide repeat as a feature which is associated with the coccolith matrix, being identified in all three examined species, and propose that this structural motif may play a role in controlling coccolith growth. This preliminary study provides insight towards the functional diversity of calcification machinery in coccolithophores and presents a number of candidates for future research towards understanding the biochemical controls which direct coccolithogenesis. (Dedman et al., 2024).
We have reported an integrated morphological, ecological and genomic survey across globally distributed G. huxleyi strains to reconstruct evolutionary relationships between morphotypes in relation to their habitats. While G. huxleyi has been considered a single cosmopolitan species, our analyses demonstrate that it has evolved to comprise at least three distinct species, which led us to formally revise the taxonomy of the G. huxleyi complex. Moreover, the first speciation event occurred before the onset of the last interglacial period (~140 ka), while the second followed during this interglacial. Then, further rapid diversifications occurred during the most recent ice-sheet expansion of the last glacial period and established morphotypes as dominant populations across environmental clines. These results suggest that glacial-cycle dynamics contributed to the isolation of ocean basins and the segregations of oceans fronts as extrinsic drivers of micro-evolutionary radiations in extant marine phytoplankton (Bendif et al., 2023).
We have shown that pH and CO2 driven vital effects and fractionation into organic matter indicate the residence time for carbon in the intracellular carbon pool, where the size of the pool is proportional to cell size. Due to the increased buffering afforded by a larger pool, C. leptoporus and C. carterae may have elevated intracellular pH which minimises CO2 leakage, whereas vital effects in G. huxleyi and G. oceanica are caused by CO2 diffusion in or out of their small internal carbon pool with limited buffering capacity owing to its small size (Chauhan and Rickaby, 2024).
We have pioneered methods to extract biologically relevant molecules from liths both in culture experiments, and from sediments down-core. We have extracted polsyaccharides from fossil ltihs to explore what their isotopic compositions say about the growth and photosynthesis of coccolithophores in the past (McClelland et al, 2025). We have also extracted proteins from cultured liths to identify likely candidates controlling calcification (Dedman et al., 2024).
We have reported an integrated morphological, ecological and genomic survey across globally distributed G. huxleyi strains to reconstruct evolutionary relationships between morphotypes in relation to their habitats. While G. huxleyi has been considered a single cosmopolitan species, our analyses demonstrate that it has evolved to comprise at least three distinct species, which led us to formally revise the taxonomy of the G. huxleyi complex. Moreover, the first speciation event occurred before the onset of the last interglacial period (~140 ka), while the second followed during this interglacial. Then, further rapid diversifications occurred during the most recent ice-sheet expansion of the last glacial period and established morphotypes as dominant populations across environmental clines. These results suggest that glacial-cycle dynamics contributed to the isolation of ocean basins and the segregations of oceans fronts as extrinsic drivers of micro-evolutionary radiations in extant marine phytoplankton (Bendif et al., 2023).
We have shown that pH and CO2 driven vital effects and fractionation into organic matter indicate the residence time for carbon in the intracellular carbon pool, where the size of the pool is proportional to cell size. Due to the increased buffering afforded by a larger pool, C. leptoporus and C. carterae may have elevated intracellular pH which minimises CO2 leakage, whereas vital effects in G. huxleyi and G. oceanica are caused by CO2 diffusion in or out of their small internal carbon pool with limited buffering capacity owing to its small size (Chauhan and Rickaby, 2024).
We have pioneered methods to extract biologically relevant molecules from liths both in culture experiments, and from sediments down-core. We have extracted polsyaccharides from fossil ltihs to explore what their isotopic compositions say about the growth and photosynthesis of coccolithophores in the past (McClelland et al, 2025). We have also extracted proteins from cultured liths to identify likely candidates controlling calcification (Dedman et al., 2024).