Rubisco is a small fraction of total protein in marine phytoplankton

Temperature and nutrients drive distinct successions between diatoms and dinoflagellates over the past 40 years: Implications for climate warming and eutrophication

Diatoms and dinoflagellates are two typical functional groups of phytoplankton, playing important roles in ecosystem processes and biogeochemical cycles. Changes in diatoms and dinoflagellates are thought to be one of the possible mechanisms for the increase in harmful algal blooms (HABs), due to changing hydrological conditions associated with climate change and human activities. However, little is known about their ability to adapt to changing ocean environments, thus making it difficult to know whether and how they are adapting. By analyzing a 44-year monitoring dataset in the central Bohai Sea during 1978-2021, we found that the abundance ratio of diatoms to dinoflagellates showed a decreasing trend seasonally and ecologically, indicating that the phytoplankton community underwent distinct successional processes from diatom dominance to diatom-dinoflagellate co-dominance. These processes exhibited varying responses to temperature, nutrient concentrations and ratios, and their interactions, of which temperature primarily drove the seasonal succession whereas nutrients were responsible for the ecological succession. Specifically, diatoms showed a preference for lower temperatures and higher DIP concentrations, and were able to tolerate lower DIN at lower temperatures. In contrast, dinoflagellates tended to prevail at conditions of warming and high N/P ratios. These different traits of diatoms and dinoflagellates reflected the fact that warming as a result of rising temperature and eutrophication as a consequence of nutrient input would favor dinoflagellates over diatoms. Moreover, the increasing dominance of dinoflagellates indicated that dinoflagellate blooms were likely to become more frequent and intense in the central Bohai Sea.

Singular adaptations in the carbon assimilation mechanism of the polyextremophile cyanobacterium Chroococcidiopsis thermalis

Cyanobacteria largely contribute to the biogeochemical carbon cycle fixing ~ 25% of the inorganic carbon on Earth. However, the carbon acquisition and assimilation mechanisms in Cyanobacteria are still underexplored regardless of being of great importance for shedding light on the origins of autotropism on Earth and providing new bioengineering tools for crop yield improvement. Here, we fully characterized these mechanisms from the polyextremophile cyanobacterium Chroococcidiopsis thermalis KOMAREK 1964/111 in comparison with the model cyanobacterial strain, Synechococcus sp. PCC6301. In particular, we analyzed the Rubisco kinetics along with the in vivo photosynthetic CO₂ assimilation in response to external dissolved inorganic carbon, the effect of CO₂ concentrating mechanism (CCM) inhibitors on net photosynthesis and the anatomical particularities of their carboxysomes when grown under either ambient air (0.04% CO₂) or 2.5% CO₂-enriched air. Our results show that Rubisco from C. thermalis possess the highest specificity factor and carboxylation efficiency ever reported for Cyanobacteria, which were accompanied by a highly effective CCM, concentrating CO₂ around Rubisco more than 140-times the external CO₂ levels, when grown under ambient CO₂ conditions. Our findings provide new insights into the Rubisco kinetics of Cyanobacteria, suggesting that improved S_c/o values can still be compatible with a fast-catalyzing enzyme. The combination of Rubisco kinetics and CCM effectiveness in C. thermalis relative to other cyanobacterial species might indicate that the co-evolution between Rubisco and CCMs in Cyanobacteria is not as constrained as in other phylogenetic groups.

Effect of specific irradiance on productivity and pigment and protein production of Porphyridium purpureum (Rhodophyta) semi-continuous culture

Porphyridium purpureum is a promising microalga species due to the content of various valuable compounds. In this study, specific irradiance parameter, representing the amount of light energy per unit of microalgae biomass, was introduced. The growth characteristics and pigments and protein accumulation of P. purpureum culture were investigated under semi-continuous mode. Varying dilution rate and surface irradiance resulted in a specific irradiance of 0.2-6.7 W g^-1. Using mathematical modeling, we determined the patterns of changes in biomass, pigments, protein content and productivity of P. purpureum culture depending on specific irradiance. The content of target compounds was maximized under the lowest level of specific irradiance (0.2-1.2 W g^-1), while the highest productivity of this components was reached under 1.2-1.7 W g^-1. Overall, lower irradiance levels were favorable for P. purpureum cultivation based on the energy consumption and production characteristics of this species.

Transcriptomic analysis reveals distinct mechanisms of adaptation of a polar picophytoplankter under ocean acidification conditions

Human emissions of carbon dioxide are causing irreversible changes in our oceans and impacting marine phytoplankton, including a group of small green algae known as picochlorophytes. Picochlorophytes grown in natural phytoplankton communities under future predicted levels of carbon dioxide have been demonstrated to thrive, along with redistribution of the cellular metabolome that enhances growth rate and photosynthesis. Here, using next-generation sequencing technology, we measured levels of transcripts in a picochlorophyte Chlorella, isolated from the sub-Antarctic and acclimated under high and current ambient CO2 levels, to better understand the molecular mechanisms involved with its ability to acclimate to elevated CO2. Compared to other phytoplankton taxa that induce broad transcriptomic responses involving multiple parts of their cellular metabolism, the changes observed in Chlorella focused on activating gene regulation involved in different sets of pathways such as light harvesting complex binding proteins, amino acid synthesis and RNA modification, while carbon metabolism was largely unaffected. Triggering a specific set of genes could be a unique strategy of small green phytoplankton under high CO2 in polar oceans.

Photoacclimation of the polar diatom Chaetoceros neogracilis at low temperature

Polar microalgae face two major challenges: 1- growing at temperatures (-1.7 to 5°C) that limit enzyme kinetics; and 2- surviving and exploiting a wide range of irradiance. The objective of this study is to understand the adaptation of an Arctic diatom to its environment by studying its ability to acclimate to changes in light and temperature. We acclimated the polar diatom Chaetoceros neogracilis to various light levels at two different temperatures and studied its growth and photosynthetic properties using semi-continuous cultures. Rubisco content was high, to compensate for low catalytic rates, but did not change detectably with growth temperature. Contrary to what is observed in temperate species, in C. neogracilis, carbon fixation rate (20 min 14C incorporation) equaled net growth rate (μ) suggesting very low or very rapid (<20 min) re-oxidation of the newly fixed carbon. The comparison of saturation irradiances for electron transport, oxygen net production and carbon fixation revealed alternative electron pathways that could provide energy and reducing power to the cell without consuming organic carbon which is a very limiting product at low temperatures. High protein contents, low re-oxidation of newly fixed carbon and the use of electron pathways alternative to carbon fixation may be important characteristics allowing efficient growth under those extreme environmental conditions.

Mitochondrial phosphoenolpyruvate carboxylase contributes to carbon fixation in the diatom Phaeodactylum tricornutum at low inorganic carbon concentrations

Photosynthetic carbon fixation is often limited by CO₂ availability, which led to the evolution of CO₂ concentrating mechanisms (CCMs). Some diatoms possess CCMs that employ biochemical fixation of bicarbonate, similar to C₄ plants, but whether biochemical CCMs are commonly found in diatoms is a subject of debate. In the diatom Phaeodactylum tricornutum, phosphoenolpyruvate carboxylase (PEPC) is present in two isoforms, PEPC1 in the plastids and PEPC2 in the mitochondria. We used real-time quantitative polymerase chain reaction, Western blots, and enzymatic assays to examine PEPC expression and PEPC activity, under low and high concentrations of dissolved inorganic carbon (DIC). We generated and analyzed individual knockout cell lines of PEPC1 and PEPC2, as well as a PEPC1/2 double-knockout strain. While we could not detect an altered phenotype in the PEPC1 knockout strains at ambient, low or high DIC concentrations, PEPC2 and the double-knockout strains grown under ambient air or lower DIC availability conditions showed reduced growth and photosynthetic affinity for DIC while behaving similarly to wild-type (WT) cells at high DIC concentrations. These mutants furthermore exhibited significantly lower ¹³ C/¹² C ratios compared to the WT. Our data imply that in P. tricornutum at least parts of the CCM rely on biochemical bicarbonate fixation catalyzed by the mitochondrial PEPC2.

Mass Cultivation of Microalgae: I. Experiences with Vertical Column Airlift Photobioreactors, Diatoms and CO2 Sequestration

From 2015 to 2021, we optimized mass cultivation of diatoms in our own developed vertical column airlift photobioreactors using natural and artificial light (LEDs). The project took place at the ferrosilicon producer Finnfjord AS in North Norway as a joint venture with UiT—The Arctic University of Norway. Small (0.1–6–14 m3) reactors were used for initial experiments and to produce inoculum cultures while upscaling experiments took place in a 300 m3 reactor. We here argue that species cultivated in reactors should be large since biovolume specific self-shadowing of light can be lower for large vs. small cells. The highest production, 1.28 cm3 L−1 biovolume (0.09–0.31 g DW day−1), was obtained with continuous culture at ca. 19% light utilization efficiency and 34% CO2 uptake. We cultivated 4–6 months without microbial contamination or biofouling, and this we argue was due to a natural antifouling (anti-biofilm) agent in the algae. In terms of protein quality all essential amino acids were present, and the composition and digestibility of the fatty acids were as required for feed ingredients. Lipid content was ca. 20% of ash-free DW with high EPA levels, and omega-3 and amino acid content increased when factory fume was added. The content of heavy metals in algae cultivated with fume was well within the accepted safety limits. Organic pollutants (e.g., dioxins and PCBs) were below the limits required by the European Union food safety regulations, and bioprospecting revealed several promising findings.

Enhancement of growth and biomolecules (carbohydrates, proteins, and chlorophylls) of isolated Chlorella thermophila using optimization tools

The production of multiple products from microalgae is essential for economic sustainability and the knowledge of optimum cultivation conditions for high growth and biomolecule synthesis of a microalgal strain is the prerequisite for its commercial production. In this work, optimization of nutrient concentrations for the cultivation of isolated Chlorella thermophila was performed by manipulating nine nutrients with the objectives of maximization of growth, carbohydrate, protein, and chlorophyll contents. Experiments were designed and effects of the parameters were studied using Taguchi orthogonal array (TOA). Experimental results of TOA were used for modeling artificial neural networks (ANN) followed by the optimization using genetic algorithm (GA) to find global optimal solutions. Results showed an increase of 36, 88, 36, and 88% for growth, carbohydrates, proteins, and chlorophylls, respectively, at optimal combinations of parameters given by TOA. Results obtained through the ANN-GA optimization were 9, 10, and 3% more compared to the TOA for biomass, carbohydrates, and chlorophylls, respectively with experimental verification. Nitrates and bicarbonate were found to play the most pivotal role in biomass and biomolecule synthesis of the isolated microalgal strain. Results of the current investigation can be used in the industrial scale-up for the production of multiple products using the biorefinery approach.

Carboxysome Mispositioning Alters Growth, Morphology, and Rubisco Level of the Cyanobacterium Synechococcus elongatus PCC 7942

Cyanobacteria are the prokaryotic group of phytoplankton responsible for a significant fraction of global CO2 fixation. Like plants, cyanobacteria use the enzyme ribulose 1,5-bisphosphate carboxylase/oxidase (Rubisco) to fix CO2 into organic carbon molecules via the Calvin-Benson-Bassham cycle. Unlike plants, cyanobacteria evolved a carbon-concentrating organelle called the carboxysome-a proteinaceous compartment that encapsulates and concentrates Rubisco along with its CO2 substrate. In the rod-shaped cyanobacterium Synechococcus elongatus PCC 7942, we recently identified the McdAB system responsible for uniformly distributing carboxysomes along the cell length. It remains unknown what role carboxysome positioning plays with respect to cellular physiology. Here, we show that a failure to distribute carboxysomes leads to slower cell growth, cell elongation, asymmetric cell division, and elevated levels of cellular Rubisco. Unexpectedly, we also report that even wild-type S. elongatus undergoes cell elongation and asymmetric cell division when grown at the cool, but environmentally relevant, growth temperature of 20°C or when switched from a high- to ambient-CO2 environment. The findings suggest that carboxysome positioning by the McdAB system functions to maintain the carbon fixation efficiency of Rubisco by preventing carboxysome aggregation, which is particularly important under growth conditions where rod-shaped cyanobacteria adopt a filamentous morphology. IMPORTANCE Photosynthetic cyanobacteria are responsible for almost half of global CO2 fixation. Due to eutrophication, rising temperatures, and increasing atmospheric CO2 concentrations, cyanobacteria have gained notoriety for their ability to form massive blooms in both freshwater and marine ecosystems across the globe. Like plants, cyanobacteria use the most abundant enzyme on Earth, Rubisco, to provide the sole source of organic carbon required for its photosynthetic growth. Unlike plants, cyanobacteria have evolved a carbon-concentrating organelle called the carboxysome that encapsulates and concentrates Rubisco with its CO2 substrate to significantly increase carbon fixation efficiency and cell growth. We recently identified the positioning system that distributes carboxysomes in cyanobacteria. However, the physiological consequence of carboxysome mispositioning in the absence of this distribution system remains unknown. Here, we find that carboxysome mispositioning triggers changes in cell growth and morphology as well as elevated levels of cellular Rubisco.

Carbon Dioxide Concentration Mechanisms in Natural Populations of Marine Diatoms: Insights From Tara Oceans

Marine diatoms, the most successful photoautotrophs in the ocean, efficiently sequester a significant part of atmospheric CO₂ to the ocean interior through their participation in the biological carbon pump. However, it is poorly understood how marine diatoms fix such a considerable amount of CO₂, which is vital information toward modeling their response to future CO₂ levels. The Tara Oceans expeditions generated molecular data coupled with in situ biogeochemical measurements across the main ocean regions, and thus provides a framework to compare diatom genetic and transcriptional flexibility under natural CO₂ variability. The current study investigates the interlink between the environmental variability of CO₂ and other physicochemical parameters with the gene and transcript copy numbers of five key enzymes of diatom CO₂ concentration mechanisms (CCMs): Rubisco activase and carbonic anhydrase (CA) as part of the physical pathway, together with phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, and malic enzyme as part of the potential C4 biochemical pathway. Toward this aim, we mined >200 metagenomes and >220 metatranscriptomes generated from samples of the surface layer of 66 globally distributed sampling sites and corresponding to the four main size fractions in which diatoms can be found: 0.8-5 μm, 5-20 μm, 20-180 μm, and 180-2,000 μm. Our analyses revealed that the transcripts for the enzymes of the putative C4 biochemical CCM did not in general display co-occurring profiles. The transcripts for CAs were the most abundant, with an order of magnitude higher values than the other enzymes, thus implying the importance of physical CCMs in diatom natural communities. Among the different classes of this enzyme, the most prevalent was the recently characterized iota class. Consequently, very little information is available from natural diatom assemblages about the distribution of this class. Biogeographic distributions for all the enzymes show different abundance hotspots according to the size fraction, pointing to the influence of cell size and aggregation in CCMs. Environmental correlations showed a complex pattern of responses to CO₂ levels, total phytoplankton biomass, temperature, and nutrient concentrations. In conclusion, we propose that biophysical CCMs are prevalent in natural diatom communities.

Elevated CO2 concentration alleviates UVR-induced inhibition of photosynthetic light reactions and growth in an intertidal red macroalga

The commercially important red macroalga Pyropia (formerly Porphyra) yezoensis is, in its natural intertidal environment, subjected to high levels of both photosynthetically active and ultraviolet radiation (PAR and UVR, respectively). In the present work, we investigated the effects of a plausibly increased global CO₂ concentration on quantum yields of photosystems II (PSII) and I (PSI), as well as photosynthetic and growth rates of P. yezoensis grown under natural solar irradiance regimes with or without the presence of UV-A and/or UV-B. Our results showed that the high-CO₂ treatment (~1000 μbar, which also caused a drop of 0.3 pH units in the seawater) significantly increased both CO₂ assimilation rates (by 35%) and growth (by 18%), as compared with ambient air of ~400 μbar CO₂. The inhibition of growth by UV-A (by 26%) was reduced to 15% by high-CO₂ concentration, while the inhibition by UV-B remained at ~6% under both CO₂ concentrations. Homologous results were also found for the maximal relative photosynthetic electron transport rates (rETR_max), the maximum quantum yield of PSII (F_v/F_m), as well as the midday decrease in effective quantum yield of PSII (YII) and concomitant increased non-photochemical quenching (NPQ). A two-way ANOVA analysis showed an interaction between CO₂ concentration and irradiance quality, reflecting that UVR-induced inhibition of both growth and YII were alleviated under the high-CO₂ treatment. Contrary to PSII, the effective quantum yield of PSI (YI) showed higher values under high-CO₂ condition, and was not significantly affected by the presence of UVR, indicating that it was well protected from this radiation. Both the elevated CO₂ concentration and presence of UVR significantly induced UV-absorbing compounds. These results suggest that future increasing CO₂ conditions will be beneficial for photosynthesis and growth of P. yezoensis even if UVR should remain at high levels.

Effects of multiple drivers of ocean global change on the physiology and functional gene expression of the coccolithophore Emiliania huxleyi

Ongoing ocean global change due to anthropogenic activities is causing multiple chemical and physical seawater properties to change simultaneously, which may affect the physiology of marine phytoplankton. The coccolithophore Emiliania huxleyi is a model species often employed in the study of the marine carbon cycle. The effect of ocean acidification (OA) on coccolithophore calcification has been extensively studied; however, physiological responses to multiple environmental drivers are still largely unknown. Here we examined two-way and multiple driver effects of OA and other key environmental drivers-nitrate, phosphate, irradiance, and temperature-on the growth, photosynthetic, and calcification rates, and the elemental composition of E. huxleyi. In addition, changes in functional gene expression were examined to understand the molecular mechanisms underpinning the physiological responses. The single driver manipulation experiments suggest decreased nitrate supply being the most important driver regulating E. huxleyi physiology, by significantly reducing the growth, photosynthetic, and calcification rates. In addition, the interaction of OA and decreased nitrate supply (projected for year 2100) had more negative synergistic effects on E. huxleyi physiology than all other two-way factorial manipulations, suggesting a linkage between the single dominant driver (nitrate) effects and interactive effects with other drivers. Simultaneous manipulation of all five environmental drivers to the conditions of the projected year 2100 had the largest negative effects on most of the physiological metrics. Furthermore, functional genes associated with inorganic carbon acquisition (RubisCO, AEL1, and δCA) and calcification (CAX3, AEL1, PATP, and NhaA2) were most downregulated by the multiple driver manipulation, revealing linkages between responses of functional gene expression and associated physiological metrics. These findings together indicate that for more holistic projections of coccolithophore responses to future ocean global change, it is necessary to understand the relative importance of environmental drivers both individually (i.e., mechanistic understanding) and interactively (i.e., cumulative effect) on coccolithophore physiology.

Rubisco and carbon-concentrating mechanism co-evolution across chlorophyte and streptophyte green algae

Green algae expressing a carbon-concentrating mechanism (CCM) are usually associated with a Rubisco-containing micro-compartment, the pyrenoid. A link between the small subunit (SSU) of Rubisco and pyrenoid formation in Chlamydomonas reinhardtii has previously suggested that specific RbcS residues could explain pyrenoid occurrence in green algae. A phylogeny of RbcS was used to compare the protein sequence and CCM distribution across the green algae and positive selection in RbcS was estimated. For six streptophyte algae, Rubisco catalytic properties, affinity for CO₂ uptake (K_0.5 ), carbon isotope discrimination (δ¹³ C) and pyrenoid morphology were compared. The length of the βA-βB loop in RbcS provided a phylogenetic marker discriminating chlorophyte from streptophyte green algae. Rubisco kinetic properties in streptophyte algae have responded to the extent of inducible CCM activity, as indicated by changes in inorganic carbon uptake affinity, δ¹³ C and pyrenoid ultrastructure between high and low CO₂ conditions for growth. We conclude that the Rubisco catalytic properties found in streptophyte algae have coevolved and reflect the strength of any CCM or degree of pyrenoid leakiness, and limitations to inorganic carbon in the aquatic habitat, whereas Rubisco in extant land plants reflects more recent selective pressures associated with improved diffusive supply of the terrestrial environment.

Extraction of proteins from the microalga Scenedesmus obliquus BR003 followed by lipid extraction of the wet deproteinized biomass using hexane and ethyl acetate

A current problem of the lipid extraction from wet biomass is the formation of emulsions during the mixing of the microalgal biomass and organic solvents. It has been suggested that microalgal proteins play an important role in the formation and stability of such emulsions. Herein, the extraction of proteins of the freshwater microalga Scenedesmus obliquus BR003 was optimized for further extraction of lipids from the wet deproteinized biomass. The optimal (pH 12 at 60 °C for 3 h) and moderate (pH 10.5 at 50 °C for 2 h) conditions of protein extraction resulted in protein yields of 20.6% and 15.4%, respectively. Wet lipid extraction of deproteinized biomass resulted in a less stable emulsion that released twice the solvent than the control biomass. However, the faster separation of phases that occurred during the wet lipid extraction of the deproteinized biomass resulted in a lipid yield twice lower than the control biomass.

Effects of Temperature and Nutrient Supply on Resource Allocation, Photosynthetic Strategy, and Metabolic Rates of Synechococcus sp

Temperature and nutrient supply are key factors that control phytoplankton ecophysiology, but their role is commonly investigated in isolation. Their combined effect on resource allocation, photosynthetic strategy, and metabolism remains poorly understood. To characterize the photosynthetic strategy and resource allocation under different conditions, we analyzed the responses of a marine cyanobacterium (Synechococcus PCC 7002) to multiple combinations of temperature and nutrient supply. We measured the abundance of proteins involved in the dark (RuBisCO, rbcL) and light (Photosystem II, psbA) photosynthetic reactions, the content of chlorophyll a, carbon and nitrogen, and the rates of photosynthesis, respiration, and growth. We found that rbcL and psbA abundance increased with nutrient supply, whereas a temperature-induced increase in psbA occurred only in nutrient-replete treatments. Low temperature and abundant nutrients caused increased RuBisCO abundance, a pattern we observed also in natural phytoplankton assemblages across a wide latitudinal range. Photosynthesis and respiration increased with temperature only under nutrient-sufficient conditions. These results suggest that nutrient supply exerts a stronger effect than temperature upon both photosynthetic protein abundance and metabolic rates in Synechococcus sp. and that the temperature effect on photosynthetic physiology and metabolism is nutrient dependent. The preferential resource allocation into the light instead of the dark reactions of photosynthesis as temperature rises is likely related to the different temperature dependence of dark-reaction enzymatic rates versus photochemistry. These findings contribute to our understanding of the strategies for photosynthetic energy allocation in phytoplankton inhabiting contrasting environments.

Microalgae proteins: production, separation, isolation, quantification, and application in food and feed

Many countries have been experienced an increase in protein consumption due to the population growth and adoption of protein-rich dietaries. Unfortunately, conventional-based protein agroindustry is associated with environmental impacts that might aggravate as the humankind increase. Thus, it is important to screen for novel protein sources that are environmentally friendly. Microalgae farming is a promising alternative to couple the anthropic emissions with the production of food and feed. Some microalgae show protein contents two times higher than conventional protein sources. The use of whole microalgae biomass as a protein source in food and feed is simple and well-established. Conversely, the production of microalgae protein supplements and isolates requires the development of feasible and robust processes able to fractionate the microalgae biomass in different value-added products. Since most of the proteins are inside the microalgae cells, several techniques of disruption have been proposed to increase the efficiency to extract them. After the disruption of the microalgae cells, the proteins can be extracted, concentrated, isolated or purified allowing the development of different products. This critical review addresses the current state of the production of microalgae proteins for multifarious applications, and possibilities to concatenate the production of proteins and advanced biofuels.

Agro-industrial by-product in photoheterotrophic and mixotrophic culture of Tetradesmus obliquus: Production of ω3 and ω6 essential fatty acids with biotechnological importance

In recent years, researchers have highlighted the role of low cost-efficient agro-industrial by-products used as supplements in algal culture media. The aim of the study was to identify and characterize the basic metabolic pathways in Tetradesmus obliquus cells induced by supplementation with beet molasses in photoheterotrophic and mixotrophic culture conditions. To assess the impact of the nutritional strategy in unicellular algae, growth curves were plotted and lipid, carbohydrate, and protein levels were determined. Fourier Transform Infrared Spectroscopy was applied to measure the Tetradesmus obliquus cell composition. Additionally, the C16-C18 fatty acid profile of Tetradesmus obliquus was determined by gas chromatograph/mass spectrometry. The switch from autotrophy to photoheterotrophy and mixotrophy contributes to shortening of the adaptation growth phase. The highest protein content was obtained in the mixotrophic growth. This study has demonstrated high content of 18:1, cisΔ₉, 18:2, cisΔ_9,12, ω6, and 18:3, cisΔ_9,12,15, ω3 in photoheterotrophic and mixotrophic culture conditions. High levels of proteins and essential fatty acids make Tetradesmus obliquus cell biomass important for human and animals health.

Microalgal kinetics - a guideline for photobioreactor design and process development

Kinetics generally describes bio‐(chemical) reaction rates in dependence on substrate concentrations. Kinetics for microalgae is often adapted from heterotrophs and lacks mechanistic foundation, e.g. for light harvesting. Using and understanding kinetic equations as the representation of intracellular mechanisms is essential for reasonable comparisons and simulations of growth behavior. Summarizing growth kinetics in one equation does not yield reliable models. Piecewise linear or rational functions may mimic photosynthesis irradiance response curves, but fail to represent the mechanisms. Our modeling approach for photoautotrophic growth comprises physical and kinetic modules with mechanistic foundation extracted from the literature. Splitting the light submodel into the modules for light distribution, light absorption, and photosynthetic sugar production with independent parameters allows the transfer of kinetics between different reactor designs. The consecutive anabolism depends among others on nutrient concentrations. The nutrient uptake kinetics largely impacts carbon partitioning in the reviewed stoichiometry range of cellular constituents. Consecutive metabolic steps mask each other and demand a maximum value understandable as the minimum principle of growth. These fundamental modules need to be clearly distinguished, but may be modified or extended based on process conditions and progress in research. First, discussion of kinetics helps to understand the physiological situation, for which ranges of parameter values are given. Second, kinetics should be used for photobioreactor design, but also for gassing and nutrient optimization. Numerous examples are given for both aspects. Finally, measuring kinetics more comprehensively and precisely will help in improved process development.

The singular properties of photosynthetic cytochrome c550 from the diatom Phaeodactylum tricornutum suggest new alternative functions

Cytochrome c₅₅₀ is an extrinsic component in the luminal side of photosystem II (PSII) in cyanobacteria, as well as in eukaryotic algae from the red photosynthetic lineage including, among others, diatoms. We have established that cytochrome c₅₅₀ from the diatom Phaeodactylum tricornutum can be obtained as a complete protein from the membrane fraction of the alga, although a C-terminal truncated form is purified from the soluble fractions of this diatom as well as from other eukaryotic algae. Eukaryotic cytochromes c₅₅₀ show distinctive electrostatic features as compared with cyanobacterial cytochrome c₅₅₀ . In addition, co-immunoseparation and mass spectrometry experiments, as well as immunoelectron microscopy analyses, indicate that although cytochrome c₅₅₀ from P. tricornutum is mainly located in the thylakoid domain of the chloroplast - where it interacts with PSII - , it can also be found in the chloroplast pyrenoid, related with proteins linked to the CO₂ concentrating mechanism and assimilation. These results thus suggest new alternative functions of this heme protein in eukaryotes.

Heterotrophic carbon metabolism and energy acquisition in Candidatus Thioglobus singularis strain PS1, a member of the SUP05 clade of marine Gammaproteobacteria

A hallmark of the SUP05 clade of marine Gammaproteobacteria is the ability to use energy obtained from reduced inorganic sulfur to fuel autotrophic fixation of carbon using RuBisCo. However, some SUP05 also have the genetic potential for heterotrophic growth, raising questions about the roles of SUP05 in the marine carbon cycle. We used genomic reconstructions, physiological growth experiments and proteomics to characterize central carbon and energy metabolism in Candidatus Thioglobus singularis strain PS1, a representative from the SUP05 clade that has the genetic potential for autotrophy and heterotrophy. Here, we show that the addition of individual organic compounds and 0.2 μm filtered diatom lysate significantly enhanced the growth of this bacterium. This positive growth response to organic substrates, combined with expression of a complete TCA cycle, heterotrophic pathways for carbon assimilation, and methylotrophic pathways for energy conversion demonstrate strain PS1's capacity for heterotrophic growth. Further, our inability to verify the expression of RuBisCO suggests that carbon fixation was not critical for growth. These results highlight the metabolic diversity of the SUP05 clade that harbours both primary producers and consumers of organic carbon in the oceans and expand our understanding of specific pathways of organic matter oxidation by the heterotrophic SUP05.

The global mass and average rate of rubisco

Rubisco is often claimed to be the most abundant protein on Earth, yet the quantitative evidence to support the estimate of its global mass are scarce. Here we provide a robust and detailed estimate of the global mass of Rubisco, which is an order of magnitude larger than previous estimates. We use this estimate to derive the time-average rate of terrestrial and marine Rubisco and show that they are, respectively, 100-fold and sevenfold lower than the in vitro measured k_cat of Rubisco at 25 °C.

Photosynthetic carbon assimilation enables energy storage in the living world and produces most of the biomass in the biosphere. Rubisco (d-ribulose 1,5-bisphosphate carboxylase/oxygenase) is responsible for the vast majority of global carbon fixation and has been claimed to be the most abundant protein on Earth. Here we provide an updated and rigorous estimate for the total mass of Rubisco on Earth, concluding it is ≈0.7 Gt, more than an order of magnitude higher than previously thought. We find that >90% of Rubisco enzymes are found in the ≈2 × 10¹⁴ m² of leaves of terrestrial plants, and that Rubisco accounts for ≈3% of the total mass of leaves, which we estimate at ≈30 Gt dry weight. We use our estimate for the total mass of Rubisco to derive the effective time-averaged catalytic rate of Rubisco of ≈0.03 s⁻¹ on land and ≈0.6 s⁻¹ in the ocean. Compared with the maximal catalytic rate observed in vitro at 25 °C, the effective rate in the wild is ≈100-fold slower on land and sevenfold slower in the ocean. The lower ambient temperature, and Rubisco not working at night, can explain most of the difference from laboratory conditions in the ocean but not on land, where quantification of many more factors on a global scale is needed. Our analysis helps sharpen the dramatic difference between laboratory and wild environments and between the terrestrial and marine environments.

A Potential Role for Epigenetic Processes in the Acclimation Response to Elevated pCO2 in the Model Diatom Phaeodactylum tricornutum

Understanding of the molecular responses underpinning diatom responses to ocean acidification is fundamental for predicting how important primary producers will be shaped by the continuous rise in atmospheric CO2. In this study, we have analyzed global transcriptomic changes of the model diatom Phaeodactylum tricornutum following growth for 15 generations in elevated pCO2 by strand-specific RNA sequencing (ssRNA-seq). Our results indicate that no significant effects of elevated pCO2 and associated carbonate chemistry changes on the physiological performance of the cells were observed after 15 generations whereas the expression of genes encoding histones and other genes involved in chromatin structure were significantly down-regulated, while the expression of transposable elements (TEs) and genes encoding histone acetylation enzymes were significantly up-regulated. Furthermore, we identified a series of long non-protein coding RNAs (lncRNAs) specifically responsive to elevated pCO2, suggesting putative regulatory roles for these largely uncharacterized genome components. Taken together, our integrative analyses reveal that epigenetic elements such as TEs, histone modifications and lncRNAs may have important roles in the acclimation of diatoms to elevated pCO2 over short time scales and thus may influence longer term adaptive processes in response to progressive ocean acidification.

Structural and functional analyses of Rubisco from arctic diatom species reveal unusual posttranslational modifications

The catalytic performance of the major CO₂-assimilating enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), restricts photosynthetic productivity. Natural diversity in the catalytic properties of Rubisco indicates possibilities for improvement. Oceanic phytoplankton contain some of the most efficient Rubisco enzymes, and diatoms in particular are responsible for a significant proportion of total marine primary production as well as being a major source of CO₂ sequestration in polar cold waters. Until now, the biochemical properties and three-dimensional structures of Rubisco from diatoms were unknown. Here, diatoms from arctic waters were collected, cultivated, and analyzed for their CO₂-fixing capability. We characterized the kinetic properties of five and determined the crystal structures of four Rubiscos selected for their high CO₂-fixing efficiency. The DNA sequences of the rbcL and rbcS genes of the selected diatoms were similar, reflecting their close phylogenetic relationship. The V_max and K_m for the oxygenase and carboxylase activities at 25 °C and the specificity factors (S_c/o) at 15, 25, and 35 °C were determined. The S_c/o values were high, approaching those of mono- and dicot plants, thus exhibiting good selectivity for CO₂ relative to O₂ Structurally, diatom Rubiscos belong to form I C/D, containing small subunits characterized by a short βA-βB loop and a C-terminal extension that forms a β-hairpin structure (βE-βF loop). Of note, the diatom Rubiscos featured a number of posttranslational modifications of the large subunit, including 4-hydroxyproline, β-hydroxyleucine, hydroxylated and nitrosylated cysteine, mono- and dihydroxylated lysine, and trimethylated lysine. Our studies suggest adaptation toward achieving efficient CO₂ fixation in arctic diatom Rubiscos.

Separation Options for Phosphorylated Osteopontin from Transgenic Microalgae Chlamydomonas reinhardtii

Correct folding and post-translational modifications are vital for therapeutic proteins to elicit their biological functions. Osteopontin (OPN), a bone regenerative protein present in a range of mammalian cells, is an acidic phosphoprotein with multiple potential phosphorylation sites. In this study, the ability of unicellular microalgae, Chlamydomonas reinhardtii, to produce phosphorylated recombinant OPN in its chloroplast is investigated. This study further explores the impact of phosphorylation and expression from a “plant-like” algae on separation of OPN. Chromatography resins ceramic hydroxyapatite (CHT) and Gallium-immobilized metal affinity chromatography (Ga-IMAC) were assessed for their binding specificity to phosphoproteins. Non-phosphorylated recombinant OPN expressed in E. coli was used to compare the specificity of interaction of the resins to phosphorylated OPN. We observed that CHT binds OPN by multimodal interactions and was better able to distinguish phosphorylated proteins in the presence of 250 mM NaCl. Ga-IMAC interaction with OPN was not selective to phosphorylation, irrespective of salt, as the resin bound OPN from both algal and bacterial sources. Anion exchange chromatography proved an efficient capture method to partially separate major phosphorylated host cell protein impurities such as Rubisco from OPN.

Physiological response of a red tide alga (Skeletonema costatum) to nitrate enrichment, with special reference to inorganic carbon acquisition

A classical red tide alga Skeletonema costatum was cultured under various nitrate levels to investigate its physiological response to nitrate enrichment combined with CO₂ limitation. The higher nitrate levels increased content of photosynthetic pigments (Chl a and Chl c), electron transport rate in photosystem II, photosynthetic O₂ evolution, and thus growth rate in S. costatum. On the other hand, the lower CO₂ levels (3.5-4.4 μmol kg^-1 seawater) and higher pH (8.56-8.63) values in seawater were observed under higher nitrate conditions. Redox activity of plasma membrane and carbonic anhydrase in S. costatum was enhanced to address the reduced CO₂ level at higher nitrate levels. In addition, the pH compensation point was enhanced and direct HCO₃^- use was induced at higher nitrate levels. These findings indicate that nitrate enrichment would stimulate the breakout of S. costatum dominated red tides via enhancing its photosynthetic performances, and maintain a quick growth rate under CO₂ limitation conditions through improving its inorganic carbon acquisition capability. Our study sheds light on the mechanisms of S. costatum defeating CO₂ limitation during algal bloom.

The role of external carbonic anhydrase in photosynthesis during growth of the marine diatom Chaetoceros muelleri

Carbon dioxide concentrating mechanisms (CCMs) act to improve the supply of CO₂ at the active site of ribulose-1,5-bisphosphate carboxylase/oxygenase. There is substantial evidence that in some microalgal species CCMs involve an external carbonic anhydrase (CA_ext ) and that CA_ext activity is induced by low CO₂ concentrations in the growth medium. However, much of this work has been conducted on cells adapted to air-equilibrium concentrations of CO₂ , rather than to changing CO₂ conditions caused by growing microalgal populations. We investigated the role of CA_ext in inorganic carbon (C_i ) acquisition and photosynthesis at three sampling points during the growth cycle of the cosmopolitan marine diatom Chaetoceros muelleri. We observed that CA_ext activity increased with decreasing C_i , particularly CO₂ , concentration, supporting the idea that CA_ext is modulated by external CO₂ concentration. Additionally, we found that the contribution of CA_ext activity to carbon acquisition for photosynthesis varies over time, increasing between the first and second sampling points before decreasing at the last sampling point, where external pH was high. Lastly, decreases in maximum quantum yield of photosystem II (F_v /F_m ), chlorophyll, maximum relative electron transport rate, light harvesting efficiency (α) and maximum rates of C_i - saturated photosynthesis (V_max ) were observed over time. Despite this decrease in photosynthetic capacity an up-regulation of CCM activity, indicated by a decreasing half-saturation constant for CO₂ (K_0.5 CO₂ ), occurred over time. The flexibility of the CCM during the course of growth in C. muelleri may contribute to the reported dominance and persistence of this species in phytoplankton blooms.

Inorganic carbon availability in benthic diatom communities: photosynthesis and migration

Diatom-dominated microphytobenthos (MPB) is the main primary producer of many intertidal and shallow subtidal environments, being therefore of critical importance to estuarine and coastal food webs. Owing to tidal cycles, intertidal MPB diatoms are subjected to environmental conditions far more variable than the ones experienced by pelagic diatoms (e.g. light, temperature, salinity, desiccation and nutrient availability). Nevertheless, benthic diatoms evolved adaptation mechanisms to these harsh conditions, including the capacity to move within steep physical and chemical gradients, allowing them to perform photosynthesis efficiently. In this contribution, we will review present knowledge on the effects of dissolved inorganic carbon (DIC) availability on photosynthesis and productivity of diatom-dominated MPB. We present evidence of carbon limitation of photosynthesis in benthic diatom mats and highly productive MPB natural communities. Furthermore, we hypothesize that active vertical migration of epipelic motile diatoms could overcome local depletion of DIC in the photic layer, providing the cells alternately with light and inorganic carbon supply. The few available longer-term experiments on the effects of inorganic carbon enrichment on the productivity of diatom-dominated MPB have yielded inconsistent results. Therefore, further studies are needed to properly assess the response of MPB communities to increased CO2 and ocean acidification related to climate change.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.

Mechanisms of carbon dioxide acquisition and CO2 sensing in marine diatoms: a gateway to carbon metabolism

Diatoms are one of the most successful marine eukaryotic algal groups, responsible for up to 20% of the annual global CO2 fixation. The evolution of a CO2-concentrating mechanism (CCM) allowed diatoms to overcome a number of serious constraints on photosynthesis in the marine environment, particularly low [CO2]aq in seawater relative to concentrations required by the CO2 fixing enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), which is partly due to the slow diffusion rate of CO2 in water and a limited CO2 formation rate from [Formula: see text] in seawater. Diatoms use two alternative strategies to take up dissolved inorganic carbon (DIC) from the environment: one primarily relies on the direct uptake of [Formula: see text] through plasma-membrane type solute carrier (SLC) 4 family [Formula: see text] transporters and the other is more reliant on passive diffusion of CO2 formed by an external carbonic anhydrase (CA). Bicarbonate taken up into the cytoplasm is most likely then actively transported into the chloroplast stroma by SLC4-type transporters on the chloroplast membrane system. Bicarbonate in the stroma is converted into CO2 only in close proximity to RubisCO preventing unnecessary CO2 leakage. CAs play significant roles in mobilizing DIC as it is progressively moved towards the site of fixation. However, the evolutionary types and subcellular locations of CAs are not conserved between different diatoms, strongly suggesting that this DIC mobilization strategy likely evolved multiple times with different origins. By contrast, the recent discovery of the thylakoid luminal θ-CA indicates that the strategy to supply CO2 to RubisCO in the pyrenoid may be very similar to that of green algae, and strongly suggests convergent coevolution in CCM function of the thylakoid lumen not only among diatoms but among eukaryotic algae in general. In this review, both experimental and corresponding theoretical models of the diatom CCMs are discussed.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.

Increased temperature and CO2 alleviate photoinhibition in Desmarestia anceps: from transcriptomics to carbon utilization

Ocean acidification and warming are affecting polar regions with particular intensity. Rocky shores of the Antarctic Peninsula are dominated by canopy-forming Desmarestiales. This study investigates the physiological and transcriptomic responses of the endemic macroalga Desmarestia anceps to a combination of different levels of temperature (2 and 7 °C), dissolved CO2 (380 and 1000 ppm), and irradiance (65 and 145 µmol photons m-2 s-1). Growth and photosynthesis increased at high CO2 conditions, and strongly decreased at 2 °C plus high irradiance, in comparison to the other treatments. Photoinhibition at 2 °C plus high irradiance was evidenced by the photochemical performance and intensive release of dissolved organic carbon. The highest number of differentially regulated transcripts was observed in thalli exposed to 2 °C plus high irradiance. Algal 13C isotopic discrimination values suggested an absence of down-regulation of carbon-concentrating mechanisms at high CO2. CO2 enrichment induced few transcriptomic changes. There was high and constitutive gene expression of many photochemical and inorganic carbon utilization components, which might be related to the strong adaptation of D. anceps to the Antarctic environment. These results suggest that increased temperature and CO2 will allow D. anceps to maintain its productivity while tolerating higher irradiances than at present conditions.

The role of Rubisco kinetics and pyrenoid morphology in shaping the CCM of haptophyte microalgae

The haptophyte algae are a cosmopolitan group of primary producers that contribute significantly to the marine carbon cycle and play a major role in paleo-climate studies. Despite their global importance, little is known about carbon assimilation in haptophytes, in particular the kinetics of their Form 1D CO2-fixing enzyme, Rubisco. Here we examine Rubisco properties of three haptophytes with a range of pyrenoid morphologies (Pleurochrysis carterae, Tisochrysis lutea, and Pavlova lutheri) and the diatom Phaeodactylum tricornutum that exhibit contrasting sensitivities to the trade-offs between substrate affinity (Km) and turnover rate (kcat) for both CO2 and O2. The pyrenoid-containing T. lutea and P. carterae showed lower Rubisco content and carboxylation properties (KC and kCcat) comparable with those of Form 1D-containing non-green algae. In contrast, the pyrenoid-lacking P. lutheri produced Rubisco in 3-fold higher amounts, and displayed a Form 1B Rubisco kCcat-KC relationship and increased CO2/O2 specificity that, when modeled in the context of a C3 leaf, supported equivalent rates of photosynthesis to higher plant Rubisco. Correlation between the differing Rubisco properties and the occurrence and localization of pyrenoids with differing intracellular CO2:O2 microenvironments has probably influenced the divergent evolution of Form 1B and 1D Rubisco kinetics.

The potential for co-evolution of CO2-concentrating mechanisms and Rubisco in diatoms

Diatoms are a diverse group of unicellular algae that contribute significantly to global photosynthetic carbon fixation and export in the modern ocean, and are an important source of microfossils for paleoclimate reconstructions. Because of their importance in the environment, diatoms have been a focus of study on the physiology and ecophysiology of carbon fixation, in particular their CO2-concentrating mechanisms (CCMs) and Rubisco characteristics. While carbon fixation in diatoms is not as well understood as in certain model aquatic photoautotrophs, a greater number of species have been examined in diatoms. Recent work has highlighted a large diversity in the function, physiology, and kinetics of both the CCM and Rubisco between different diatom species. This diversity was unexpected since it has generally been assumed that CCMs and Rubiscos were similar within major algal lineages as the result of selective events deep in evolutionary history, and suggests a more recent co-evolution between the CCM and Rubisco within diatoms. This review explores our current understanding of the diatom CCM and highlights the diversity of both the CCM and Rubisco kinetics. We will suggest possible environmental, physiological, and evolutionary drivers for the co-evolution of the CCM and Rubisco in diatoms.

The possible evolution and future of CO2-concentrating mechanisms

CO2-concentrating mechanisms (CCMs), based either on active transport of inorganic carbon (biophysical CCMs) or on biochemistry involving supplementary carbon fixation into C4 acids (C4 and CAM), play a major role in global primary productivity. However, the ubiquitous CO2-fixing enzyme in autotrophs, Rubisco, evolved at a time when atmospheric CO2 levels were very much higher than today and O2 was very low and, as CO2 and O2 approached (by no means monotonically), today's levels, at some time subsequently many organisms evolved a CCM that increased the supply of CO2 and decreased Rubisco oxygenase activity. Given that CO2 levels and other environmental factors have altered considerably between when autotrophs evolved and the present day, and are predicted to continue to change into the future, we here examine the drivers for, and possible timing of, evolution of CCMs. CCMs probably evolved when CO2 fell to 2-16 times the present atmospheric level, depending on Rubisco kinetics. We also assess the effects of other key environmental factors such as temperature and nutrient levels on CCM activity and examine the evidence for evolutionary changes in CCM activity and related cellular processes as well as limitations on continuity of CCMs through environmental variations.

Diversity of CO2-concentrating mechanisms and responses to CO2 concentration in marine and freshwater diatoms

The presence of CO2-concentrating mechanisms (CCMs) is believed to be one of the characteristics that allows diatoms to thrive in many environments and to be major contributors to global productivity. Here, the type of CCM and the responses to variable CO2 concentration were studied in marine and freshwater diatoms. At 400 ppm, there was a large diversity in physiological and biochemical mechanisms among the species. While Phaeodactylum tricornutum mainly used HCO3-, Thalassiosira pseudonana mainly used CO2. Carbonic anhydrase was an important component of the CCM in all species and C4 metabolism was absent, even with T. weissflogii. For all species, at 20 000 ppm, the affinity for dissolved inorganic carbon was lower than at 400 ppm CO2 and the reliance on CO2 was higher. Despite the difference in availability of inorganic carbon in marine and fresh waters, there were only small differences in CCMs between species from the two environments, and Navicula pelliculosa behaved similarly when grown in the two environments. The results suggest that species-specific differences are great, and more important than environmental differences in determining the nature and effectiveness of the CCM in diatoms.

The effects of pH and pCO2 on photosynthesis and respiration in the diatom Thalassiosira weissflogii

The response of marine phytoplankton to the ongoing increase in atmospheric pCO₂ reflects the consequences of both increased CO₂ concentration and decreased pH in surface seawater. In the model diatom Thalassiosira weissflogii, we explored the effects of varying pCO₂ and pH, independently and in concert, on photosynthesis and respiration by incubating samples in water enriched in H₂¹⁸O. In long-term experiments (~6-h) at saturating light intensity, we observed no effects of pH or pCO₂ on growth rate, photosynthesis or respiration. This absence of a measurable response reflects the very small change in energy used by the carbon concentrating mechanism (CCM) compared to the energy used in carbon fixation. In short-term experiments (~3 min), we also observed no effects of pCO₂ or pH, even under limiting light intensity. We surmise that in T. weissflogii, it is the photosynthetic production of NADPH and ATP, rather than the CO₂-saturation of Rubisco that controls the rate of photosynthesis at low irradiance. In short-term experiments, we observed a slightly higher respiration rate at low pH at the onset of the dark period, possibly reflecting the energy used for exporting H⁺ and maintaining pH homeostasis. Based on what is known of the biochemistry of marine phytoplankton, our results are likely generalizable to other diatoms and a number of other eukaryotic species. The direct effects of ocean acidification on growth, photosynthesis and respiration in these organisms should be small over the range of atmospheric pCO₂ predicted for the twenty-first century.

The relative availability of inorganic carbon and inorganic nitrogen influences the response of the dinoflagellate Protoceratium reticulatum to elevated CO2

This work originates from three facts: (i) changes in CO₂ availability influence metabolic processes in algal cells; (ii) Spatial and temporal variations of nitrogen availability cause repercussions on phytoplankton physiology; (iii) Growth and cell composition are dependent on the stoichiometry of nutritional resources. In this study, we assess whether the impact of rising pCO₂ is influenced by N availability, through the impact that it would have on the C/N stoichiometry, in conditions of N sufficiency. Our experiments used the dinoflagellate Protoceratium reticulatum, which we cultured under three CO₂ regimes (400, 1,000, and 5,000 ppmv, pH of 8.1) and either variable (the NO₃^- concentration was always 2.5 mmol · L^-1 ) or constant (NO₃^- concentration varied to maintain the same C_i /NO₃^- ratio at all pCO₂ ) C_i /NO₃^- ratio. Regardless of N availability, cells had higher specific growth rates, but lower cell dry weight and C and N quotas, at elevated CO₂ . The carbohydrate pool size and the C/N was unaltered in all treatments. The lipid content only decreased at high pCO₂ at constant C_i /NO₃^- ratio. In the variable C_i /NO₃^- conditions, the relative abundance of Rubisco (and other proteins) also changed; this did not occur at constant C_i /NO₃^- . Thus, the biomass quality of P. reticulatum for grazers was affected by the C_i /NO₃^- ratio in the environment and not only by the pCO₂ , both with respect to the size of the main organic pools and the composition of the expressed proteome.

Rubisco Extraction and Purification from Diatoms

This protocol describes a method to extract ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco) from diatoms (Bacillariophyta) to determine catalytic performance. This protocol has been adapted from use in cyanobacteria and higher plants (Andrews, 1988; Whitney and Sharwood, 2007). First part (steps A1-A3) of the extraction provides a crude extract of Rubisco that is sufficient for carboxylation assays to measure the Michaelis constant for CO₂ (K_C) and the catalytic turnover rate ( k_cat ^c ). However, the further purification steps outlined (steps B1-B4) are needed for measurements of Rubisco CO₂/O₂ Specificity (S_C/O, [ Kane et al., 1994 ]).

Ocean acidification modulates expression of genes and physiological performance of a marine diatom

Ocean Acidification (OA) is known to affect various aspects of physiological performances of diatoms, but little is known about the underlining molecular mechanisms involved. Here, we show that in the model diatom Phaeodactylum tricornutum, the expression of key genes associated with photosynthetic light harvesting as well as those encoding Rubisco, carbonic anhydrase, NADH dehydrogenase and nitrite reductase, are modulated by OA (1000 μatm, pHnbs 7.83). Growth and photosynthetic carbon fixation were enhanced by elevated CO2. OA treatment decreased the expression of β-carbonic anhydrase (β-ca), which functions in balancing intracellular carbonate chemistry and the CO2 concentrating mechanism (CCM). The expression of the genes encoding fucoxanthin chlorophyll a/c protein (lhcf type (fcp)), mitochondrial ATP synthase (mtATP), ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit gene (rbcl) and NADH dehydrogenase subunit 2 (ndh2), were down-regulated during the first four days (< 8 generations) after the cells were transferred from LC (cells grown under ambient air condition; 390 μatm; pHnbs 8.19) to OA conditions, with no significant difference between LC and HC treatments with the time elapsed. The expression of nitrite reductase (nir) was up-regulated by the OA treatment. Additionally, the genes for these proteins (NiR, FCP, mtATP synthase, β-CA) showed diel expression patterns. It appeared that the enhanced photosynthetic and growth rates under OA could be attributed to stimulated nitrogen assimilation, increased CO2 availability or saved energy from down-regulation of the CCM and consequently lowered cost of protein synthesis versus that of non-nitrogenous cell components.

Interactive effects of nitrogen and light on growth rates and RUBISCO content of small and large centric diatoms

Among marine phytoplankton groups, diatoms span the widest range of cell size, with resulting effects upon their nitrogen uptake, photosynthesis and growth responses to light. We grew two strains of marine centric diatoms differing by ~4 orders of magnitude in cell biovolume in high (enriched artificial seawater with ~500 µmol L^-1 µmol L^-1 NO₃^-) and lower-nitrogen (enriched artificial seawater with <10 µmol L^-1 NO₃^-) media, across a range of growth light levels. Nitrogen and total protein per cell decreased with increasing growth light in both species when grown under the lower-nitrogen media. Cells growing under lower-nitrogen media increased their cellular allocation to RUBISCO and their rate of electron transport away from PSII, for the smaller diatom under low growth light and for the larger diatom across the range of growth lights. The smaller coastal diatom Thalassiosira pseudonana is able to exploit high nitrogen in growth media by up-regulating growth rate, but the same high-nitrogen growth media inhibits growth of the larger diatom species.

Decreased photosynthesis and growth with reduced respiration in the model diatom Phaeodactylum tricornutum grown under elevated CO2 over 1800 generations

Studies on the long-term responses of marine phytoplankton to ongoing ocean acidification (OA) are appearing rapidly in the literature. However, only a few of these have investigated diatoms, which is disproportionate to their contribution to global primary production. Here we show that a population of the model diatom Phaeodactylum tricornutum, after growing under elevated CO₂ (1000 μatm, HCL, pH_T : 7.70) for 1860 generations, showed significant differences in photosynthesis and growth from a population maintained in ambient CO₂ and then transferred to elevated CO₂ for 20 generations (HC). The HCL population had lower mitochondrial respiration, than did the control population maintained in ambient CO₂ (400 μatm, LCL, pH_T : 8.02) for 1860 generations. Although the cells had higher respiratory carbon loss within 20 generations under the elevated CO₂ , being consistent to previous findings, they downregulated their respiration to sustain their growth in longer duration under the OA condition. Responses of phytoplankton to OA may depend on the timescale for which they are exposed due to fluctuations in physiological traits over time. This study provides the first evidence that populations of the model species, P. tricornutum, differ phenotypically from each other after having been grown for differing spans of time under OA conditions, suggesting that long-term changes should be measured to understand responses of primary producers to OA, especially in waters with diatom-dominated phytoplankton assemblages.

Will an algal CO2-concentrating mechanism work in higher plants?

Many algae use a biophysical carbon concentrating mechanism for active accumulation and retention of inorganic carbon within chloroplasts, with CO2 fixation by RuBisCO within a micro-compartment, the pyrenoid. Engineering such mechanisms into higher plant chloroplasts is a possible route to augment RuBisCO operating efficiency and photosynthetic rates. Significant progress has been made recently in characterising key algal transporters and identifying factors responsible for the aggregation of RuBisCO into the pyrenoid. Several transporters have now also been successfully incorporated into higher plant chloroplasts. Consistent with the predictions from modelling, regulation of higher plant plastidic carbonic anhydrases and some form of RuBisCO aggregation will be needed before the mechanism delivers potential benefits. Key research priorities include a better understanding of the regulation of the algal carbon concentrating mechanism, advancing the fundamental characterisation of known components, evaluating whether higher plant chloroplasts can accommodate a pyrenoid, and, ultimately, testing transgenic lines under realistic growth conditions.

Phosphorus Deficiency Inhibits Cell Division But Not Growth in the Dinoflagellate Amphidinium carterae

Phosphorus (P) is an essential nutrient element for the growth of phytoplankton. How P deficiency affects population growth and the cell division cycle in dinoflagellates has only been studied in some species, and how it affects photosynthesis and cell growth remains poorly understood. In the present study, we investigated the impact of P deficiency on the cell division cycle, the abundance of the carbon-fixing enzyme Rubisco, and other cellular characteristics in the Gymnodiniales peridinin-plastid species Amphidinium carterae. We found that under P-replete condition, the cell cycle actively progressed in the culture in a 24-h diel cycle with daily growth rates markedly higher than the P-deficient cultures, in which cells were arrested in the G1 phase and cell size significantly enlarged. The results suggest that, as in previously studied dinoflagellates, P deficiency likely disenables A. carterae to complete DNA duplication or check-point protein phosphorylation. We further found that under P-deficient condition, overall photosystem II quantum efficiency (Fv/Fm ratio) and Rubisco abundance decreased but not significantly, while cellular contents of carbon, nitrogen, and proteins increased significantly. These observations indicated that under P-deficiency, this dinoflagellate was able to continue photosynthesis and carbon fixation, such that proteins and photosynthetically fixed carbon could accumulate resulting in continued cell growth in the absence of division. This is likely an adaptive strategy thereby P-limited cells can be ready to resume the cell division cycle upon resupply of phosphorus.

Large variation in the Rubisco kinetics of diatoms reveals diversity among their carbon-concentrating mechanisms

While marine phytoplankton rival plants in their contribution to global primary productivity, our understanding of their photosynthesis remains rudimentary. In particular, the kinetic diversity of the CO2-fixing enzyme, Rubisco, in phytoplankton remains unknown. Here we quantify the maximum rates of carboxylation (k cat (c)), oxygenation (k cat (o)), Michaelis constants (K m) for CO2 (K C) and O2 (K O), and specificity for CO2 over O2 (SC/O) for Form I Rubisco from 11 diatom species. Diatom Rubisco shows greater variation in K C (23-68 µM), SC/O (57-116mol mol(-1)), and K O (413-2032 µM) relative to plant and algal Rubisco. The broad range of K C values mostly exceed those of C4 plant Rubisco, suggesting that the strength of the carbon-concentrating mechanism (CCM) in diatoms is more diverse, and more effective than previously predicted. The measured k cat (c) for each diatom Rubisco showed less variation (2.1-3.7s(-1)), thus averting the canonical trade-off typically observed between K C and k cat (c) for plant Form I Rubisco. Uniquely, a negative relationship between K C and cellular Rubisco content was found, suggesting variation among diatom species in how they allocate their limited cellular resources between Rubisco synthesis and their CCM. The activation status of Rubisco in each diatom was low, indicating a requirement for Rubisco activase. This work highlights the need to better understand the correlative natural diversity between the Rubisco kinetics and CCM of diatoms and the underpinning mechanistic differences in catalytic chemistry among the Form I Rubisco superfamily.

Response of Spring Diatoms to CO2 Availability in the Western North Pacific as Determined by Next-Generation Sequencing

Next-generation sequencing (NGS) technologies have enabled us to determine phytoplankton community compositions at high resolution. However, few studies have adopted this approach to assess the responses of natural phytoplankton communities to environmental change. Here, we report the impact of different CO₂ levels on spring diatoms in the Oyashio region of the western North Pacific as estimated by NGS of the diatom-specific rbcL gene (DNA), which encodes the large subunit of RubisCO. We also examined the abundance and composition of rbcL transcripts (cDNA) in diatoms to assess their physiological responses to changing CO₂ levels. A short-term (3-day) incubation experiment was carried out on-deck using surface Oyashio waters under different pCO₂ levels (180, 350, 750, and 1000 μatm) in May 2011. During the incubation, the transcript abundance of the diatom-specific rbcL gene decreased with an increase in seawater pCO₂ levels. These results suggest that CO₂ fixation capacity of diatoms decreased rapidly under elevated CO₂ levels. In the high CO₂ treatments (750 and 1000 μatm), diversity of diatom-specific rbcL gene and its transcripts decreased relative to the control treatment (350 μatm), as well as contributions of Chaetocerataceae, Thalassiosiraceae, and Fragilariaceae to the total population, but the contributions of Bacillariaceae increased. In the low CO₂ treatment, contributions of Bacillariaceae also increased together with other eukaryotes. These suggest that changes in CO₂ levels can alter the community composition of spring diatoms in the Oyashio region. Overall, the NGS technology provided us a deeper understanding of the response of diatoms to changes in CO₂ levels in terms of their community composition, diversity, and photosynthetic physiology.