Flux balance analysis reveals acetate metabolism modulates cyclic electron flow and alternative glycolytic pathways in Chlamydomonas reinhardtii

Moderate high temperature is beneficial or detrimental depending on carbon availability in the green alga Chlamydomonas reinhardtii

High temperatures impair plant growth and reduce agricultural yields, but the underlying mechanisms remain elusive. The unicellular green alga Chlamydomonas reinhardtii is an excellent model to study heat responses in photosynthetic cells due to its fast growth rate, many similarities in cellular processes to land plants, simple and sequenced genome, and ample genetic and genomics resources. Chlamydomonas grows in light by photosynthesis and with externally supplied acetate as an organic carbon source. Understanding how organic carbon sources affect heat responses is important for the algal industry but remains understudied. We cultivated wild-type Chlamydomonas under highly controlled conditions in photobioreactors at 25 °C (control), 35 °C (moderate high temperature), or 40 °C (acute high temperature) with or without constant acetate supply for 1 or 4 day. Treatment at 35 °C increased algal growth with constant acetate supply but reduced algal growth without sufficient acetate. The overlooked and dynamic effects of 35 °C could be explained by induced acetate uptake and metabolism. Heat treatment at 40 °C for more than 2 day was lethal to algal cultures with or without constant acetate supply. Our findings provide insights to understand algal heat responses and help improve thermotolerance in photosynthetic cells.

Metabolomic analysis and pathway profiling of paramylon production in Euglena gracilis grown on different carbon sources

Paramylon (β-1,3-glucan) produced by Euglena gracilis displays antioxidant, antitumor, and hypolipidaemic functions. The biological properties of paramylon production by E. gracilis can be understood by elucidating the metabolic changes within the algae. In this study, the carbon sources in AF-6 medium were replaced with glucose, sodium acetate, glycerol, or ethanol, and the paramylon yield was measured. Adding 0.1260 g/L glucose to the culture medium resulted in the highest paramylon yield of 70.48 %. The changes in metabolic pathways in E. gracilis grown on glucose were assessed via non-targeted metabolomics analysis using ultra-high-performance liquid chromatography coupled to high-resolution quadrupole-Orbitrap mass spectrometry. We found that glucose, as a carbon source, regulated some differentially expressed metabolites, including l-glutamic acid, γ-aminobutyric acid (GABA), and l-aspartic acid. Pathway analysis using the Kyoto Encyclopedia of Genes and Genomes further showed that glucose regulated the carbon and nitrogen balance through the GABA shunt, which enhanced photosynthesis, regulated the flux of carbon and nitrogen into the tricarboxylic acid cycle, promoted glucose uptake, and increased the accumulation of paramylon. This study provides new insights into E. gracilis metabolism during paramylon synthesis.

Environmental and nuclear influences on microalgal chloroplast gene expression

Microalgal chloroplasts, such as those of the model organism Chlamydomonas reinhardtii, are emerging as a new platform to produce recombinant proteins, including industrial enzymes, diagnostics, as well as animal and human therapeutics. Improving transgene expression and final recombinant protein yields, at laboratory and industrial scales, require optimization of both environmental and cellular factors. Most studies on C. reinhardtii have focused on optimization of cellular factors. Here, we review the regulatory influences of environmental factors, including light (cycle time, intensity, and quality), carbon source (CO2 and organic), and temperature. In particular, we summarize their influence via the redox state, cis-elements, and trans-factors on biomass and recombinant protein production to support the advancement of emerging large-scale light-driven biotechnology applications.

The role of antioxidant response and nonphotochemical quenching of chlorophyll fluorescence in long-term adaptation to Cu-induced stress in Chlamydomonas reinhardtii

Copper is an essential micronutrient, but at supraoptimal concentrations it is also highly toxic, inducing oxidative stress and disrupting photosynthesis. The aim of the present study was to analyze selected protective mechanisms in strains of Chlamydomonas reinhardtii adapted and not adapted for growth in the presence of elevated copper concentrations. Two algal lines (tolerant and non-tolerant to high Cu²⁺ concentrations) were used in experiments to study photosynthetic pigment content, peroxidase activity, and non-photochemical quenching. The content of prenyllipids was studied in four different algal lines (two of the same as above and two new ones). The copper-adapted strains contained about 2.6 times more α-tocopherol and plastoquinol and about 1.7 times more total plastoquinone than non-tolerant strains. Exposure to excess copper led to oxidation of the plastoquinone pool in non-tolerant strains, whereas this effect was less pronounced or did not occur in copper-tolerant strains. Peroxidase activity was approximately 1.75 times higher in the tolerant strain than in the non-tolerant one. The increase in peroxidase activity in the tolerant strain was less pronounced when the algae were grown in dim light. In the tolerant line nonphotochemical quenching was induced faster and was usually about 20-30% more efficient than in the non-tolerant line. The improvement of antioxidant defense and photoprotection may be important factors in the evolutionary processes leading to tolerance to heavy metals.

Urea as a source of nitrogen and carbon leads to increased photosynthesis rates in Chlamydomonas reinhardtii under mixotrophy

Microalgae is a potential source of bioproducts, including feedstock to biofuels. Urea has been pointed as potential N source for microalgae growth. Considering that urea metabolism releases HCO₃^- to the medium, we tested the hypothesis that this carbon source could improve photosynthesis and consequently growth rates of Chlamydomonas reinhardtii. In this sense, the metabolic responses of C. reinhardtii grown with ammonium and urea as nitrogen sources under mixotrophic and autotrophic conditions were investigated. Overall, the mixotrophy led to increased cell growth as well as to a higher accumulation of lipids independent of N source, followed by a decrease in photosynthesis over the growth phases. In mixotrophy, urea stimulates growth in terms of cell number and dry weight. Furthermore, higher photosynthesis was verified in late logarithmic phase compared to ammonium. Under autotrophy conditions, although cell number and biomass were reduced, there was higher production of starch independent of N source. Nonetheless, urea-based autotrophic treatments stimulated biomass production compared to ammonium-based treatment. Under mixotrophy higher input of carbon into the cell from acetate and urea optimized photosynthesis and consequently promoted cell growth. Together, these results suggest urea as alternative source of carbon, improving photosynthesis and cell growth in C. reinhardtii.

Metabolism of Scenedesmus obliquus cultivated with raw plant substrates

The potential benefits of adding raw, non-food, lignocellulosic plant material as a carbon source for mixotrophic growth of microalgae have previously been demonstrated. This approach has advantages over using traditional carbon sources like glucose or acetate due to wide-spread plant biomass availability and substrate recalcitrance to bacterial contamination. Here, we report the overall growth characteristics and explore the metabolic patterns of Scenedesmus obliquus cultured in the presence raw plant substrate. An initial screen of plant substrate candidates showed an increase in specific growth rate and biomass accumulation when S. obliquus was cultured in the presence of switchgrass or yard waste compared to media alone. We observed a near doubling of microalgal dry weight when S. obliquus was grown with 0.2% (w/v) switchgrass under ambient CO₂. Scanning electron microscopy (SEM) of corn stem after S. obliquus cultivation exhibited substantial phloem degradation. Transcriptomic analyses of S. obliquus during mid- and late-log phase growth revealed a dynamic metabolic landscape within many KEGG pathways. Notably, differential expression was observed for several potential glycosyl hydrolases. We also investigated the influence of switchgrass on the growth of S. obliquus at 50 L volume in mini raceway ponds to determine the scalability of this approach.

Photoprotective carbon redistribution in mixotrophic Haematococcus pluvialis under high light stress

Mixotrophy of Haematococcus pluvialis is a potential strategy for producing astaxanthin. However, this strategy has not been extensively commercialized because the mixotrophic mechanisms by which H. pluvialis overcomes high light stress are unclear. This study analyzed the biochemical compositions and differential proteomics of mixotrophic H. pluvialis under different light conditions. High light exposure substantially increased astaxanthin, carbohydrate, and fatty acid contents. A total of 119 and 81 proteins were significantly up- and down-regulated after two days of high light exposure. These proteins mainly enriched pathways for photosynthetic metabolism, glyoxylate cycle, and biosynthesis of secondary metabolites. This study proposed a regulatory model through which mixotrophic H. pluvialis copes with high light stress. The model includes pathways for modulating photosynthetic apparatus, increasing astaxanthin accumulation by enhancing photorespiration, pentose phosphate and Embden-Meyerhof-Parna pathways, while thickening the cell wall by malate-oxaloacetate shuttle.

Reducing culture medium nitrogen supply coupled with replenishing carbon nutrient simultaneously enhances the biomass and lipid production of Chlamydomonas reinhardtii

Chlamydomonas reinhardtii is a model strain to explore algal lipid metabolism mechanism, and exhibits great potentials in large-scale production of lipids. Completely lacking nitrogen is an efficient strategy to trigger the lipid synthesis in microalgal cells, while it always leads to the obvious reduction in the biomass. To illustrate the optimal culture substrate carbon (C) and nitrogen (N) levels to simultaneously stimulate the growth and lipid production of C. reinhardtii, cells were cultivated under altered C and N concentrations. Results showed that replenishing 6 g/L sodium acetate (NaAc) could increase 1.50 and 1.53 times biomass and lipid productivity compared with 0 g/L NaAc treatment (the control), but total lipid content slightly decreased. Reducing 75% of basic medium (TAP) N level (0 g/L NaAc + 0.09 g/L NH₄Cl treatment) could promote 21.57% total lipid content in comparison with the control (containing 0.38 g/L NH₄Cl), but decrease 44.45% biomass and 34.15% lipid productivity. The result of the central composite design (CCD) experiment suggested the optimum total lipid content together with higher biomass and lipid productivity could be obtained under the condition of 4.12 g/L NaAc and 0.20 g/L NH₄Cl. They reached 32.14%, 1.68 g/L and 108.21 mg/L/d, and increased by 36.77%, 93.10% and 1.75 times compared with the control, respectively. It suggests moderately increasing C supply and decreasing N levels could synchronously improve the biomass and lipid content of C. reinhardtii.

Interactions Between Carbon Metabolism and Photosynthetic Electron Transport in a Chlamydomonas reinhardtii Mutant Without CO2 Fixation by RuBisCO

A Chlamydomonas reinhardtii RuBisCO-less mutant, ΔrbcL, was used to study carbohydrate metabolism without fixation of atmospheric carbon. The regulatory mechanism(s) that control linear electron flow, known as "photosynthetic control," are amplified in ΔrbcL at the onset of illumination. With the aim to understand the metabolites that control this regulatory response, we have correlated the kinetics of primary carbon metabolites to chlorophyll fluorescence induction curves. We identify that ΔrbcL in the absence of acetate generates adenosine triphosphate (ATP) via photosynthetic electron transfer reactions. Also, metabolites of the Calvin Benson Bassham (CBB) cycle are responsive to the light. Indeed, ribulose 1,5-bisphosphate (RuBP), the last intermediate before carboxylation by Ribulose-1,5-bisphosphate carboxylase-oxygenase, accumulates significantly with time, and CBB cycle intermediates for RuBP regeneration, dihydroxyacetone phosphate (DHAP), pentose phosphates and ribose-5-phosphate (R5P) are rapidly accumulated in the first seconds of illumination, then consumed, showing that although the CBB is blocked, these enzymes are still transiently active. In opposition, in the presence of acetate, consumption of CBB cycle intermediates is strongly diminished, suggesting that the link between light and primary carbon metabolism is almost lost. Phosphorylated hexoses and starch accumulate significantly. We show that acetate uptake results in heterotrophic metabolism dominating phototrophic metabolism, with glyoxylate and tricarboxylic acid (TCA) cycle intermediates being the most highly represented metabolites, specifically succinate and malate. These findings allow us to hypothesize which metabolites and metabolic pathways are relevant to the upregulation of processes like cyclic electron flow that are implicated in photosynthetic control mechanisms.

Trophic state alters the mechanism whereby energetic coupling between photosynthesis and respiration occurs in Euglena gracilis

The coupling between mitochondrial respiration and photosynthesis plays an important role in the energetic physiology of green plants and some secondary-red photosynthetic eukaryotes (diatoms), allowing an efficient CO₂ assimilation and optimal growth. Using the flagellate Euglena gracilis, we first tested if photosynthesis-respiration coupling occurs in this species harbouring secondary green plastids (i.e. originated from an endosymbiosis between a green alga and a phagotrophic euglenozoan). Second, we tested how the trophic state (mixotrophy and photoautotrophy) of the cell alters the mechanisms involved in the photosynthesis-respiration coupling. Energetic coupling between photosynthesis and respiration was determined by testing the effect of respiratory inhibitors on photosynthesis, and measuring the simultaneous variation of photosynthesis and respiration rates as a function of temperature (i.e. thermal response curves). The mechanism involved in the photosynthesis-respiration coupling was assessed by combining proteomics, biophysical and cytological analyses. Our work shows that there is photosynthesis-respiration coupling and membrane contacts between mitochondria and chloroplasts in E. gracilis. However, whereas in mixotrophy adjustment of the chloroplast ATP/NADPH ratio drives the interaction, in photoautotrophy the coupling is conditioned by CO₂ limitation and photorespiration. This indicates that maintenance of photosynthesis-respiration coupling, through plastic metabolic responses, is key to E. gracilis functioning under changing environmental conditions.

Lutein production with Chlorella sorokiniana MB-1-M12 using novel two-stage cultivation strategies - metabolic analysis and process improvement

Microalgae-derived carotenoids have increasingly been considered as feasible green alternatives for synthetic antioxidants. In this study, the lutein high-yielding strain (Chlorella sorokiniana MB-1; henceforth MB-1) and its mutant derivative (C. sorokiniana MB-1-M12; henceforth M12) were evaluated for their growth, biomass production, and lutein accumulation in three different cultivation modes - photoautotrophy, mixotrophy, and heterotrophy. M12 could grow effectively under heterotrophic conditions, but the lutein content was lower, indicating the necessity of photo-induction for lutein accumulation. Metabolic analysis of MB-1 and M12 in autotrophic growth in the presence of carbon dioxide indicated that carbon assimilation and channeling of the fixed metabolites towards carotenoid accumulation was elevated in M12 compared to MB-1. Novel two-stage alternative cultivation strategies (Autotrophic/Heterotrophic and Mixotrophic/Heterotrophic cultures) were applied for enhancing lutein production in M12. Maximum lutein quantity (6.17 mg/g) and production (33.64 mg/L) were obtained with the TSHM strategy that is considered the best two-stage operation.

Mixotrophic Growth of Chlorella sorokiniana on Acetate and Butyrate: Interplay Between Substrate, C:N Ratio and pH

Microalgae can be cultivated on waste dark fermentation effluents containing volatile fatty acids (VFA) such as acetate or butyrate. These VFA can however inhibit microalgae growth at concentrations above 0.5-1 g_C.L^-1. This study used the model strain Chlorella sorokiniana to investigate the effects of acetate or butyrate concentration on biomass growth rates and yields alongside C:N:P ratios and pH control. Decreasing undissociated acid levels by raising the initial pH to 8.0 allowed growth without inhibition up to 5 g_C.L^-1 VFAs. However, VFA concentration strongly affected biomass yields irrespective of pH control or C:N:P ratios. Biomass yields on 1.0 g_C.L^-1 acetate were around 1.3-1.5 g_C.g_C ^-1 but decreased by 26-48% when increasing initial acetate to 2.0 g_C.L^-1. This was also observed for butyrate with yields decreasing up to 25%. This decrease in yield in suggested to be due to the prevalence of heterotrophic metabolism at high organic acid concentration, which reduced the amount of carbon fixed by autotrophy. Finally, the effects of C:N:P on biomass, lipids and carbohydrates production dynamics were assessed using a mixture of both substrates. In nutrient replete conditions, C. sorokiniana accumulated up to 20.5% carbohydrates and 16.4% lipids while nutrient limitation triggered carbohydrates accumulation up to 45.3%.

Consequences of Mixotrophy on Cell Energetic Metabolism in Microchloropsis gaditana Revealed by Genetic Engineering and Metabolic Approaches

Algae belonging to the Microchloropsis genus are promising organisms for biotech purposes, being able to accumulate large amounts of lipid reserves. These organisms adapt to different trophic conditions, thriving in strict photoautotrophic conditions, as well as in the concomitant presence of light plus reduced external carbon as energy sources (mixotrophy). In this work, we investigated the mixotrophic responses of Microchloropsis gaditana (formerly Nannochloropsis gaditana). Using the Biolog growth test, in which cells are loaded into multiwell plates coated with different organic compounds, we could not find a suitable substrate for Microchloropsis mixotrophy. By contrast, addition of the Lysogeny broth (LB) to the inorganic growth medium had a benefit on growth, enhancing respiratory activity at the expense of photosynthetic performances. To further dissect the role of respiration in Microchloropsis mixotrophy, we focused on the mitochondrial alternative oxidase (AOX), a protein involved in energy management in other algae prospering in mixotrophy. Knocking-out the AOX1 gene by transcription activator-like effector nuclease (TALE-N) led to the loss of capacity to implement growth upon addition of LB supporting the hypothesis that the effect of this medium was related to a provision of reduced carbon. We conclude that mixotrophic growth in Microchloropsis is dominated by respiratory rather than by photosynthetic energetic metabolism and discuss the possible reasons for this behavior in relationship with fatty acid breakdown via β-oxidation in this oleaginous alga.

Optimisation of microalgal cultivation via nutrient-enhanced strategies: the biorefinery paradigm

BACKGROUND

The production of microalgal biofuels, despite their sustainable and renowned potential, is not yet cost-effective compared to current conventional fuel technologies. However, the biorefinery concept increases the prospects of microalgal biomass as an economically viable feedstock suitable for the co-production of multiple biofuels along with value-added chemicals. To integrate biofuels production within the framework of a microalgae biorefinery, it is not only necessary to exploit multi-product platforms, but also to identify optimal microalgal cultivation strategies maximising the microalgal metabolites from which biofuels are obtained: starch and lipids. Whilst nutrient limitation is widely known for increasing starch and lipid formation, this cultivation strategy can greatly reduce microalgal growth. This work presents an optimisation framework combining predictive modelling and experimental methodologies to effectively simulate and predict microalgal growth dynamics and identify optimal cultivation strategies.

RESULTS

Microalgal cultivation strategies for maximised starch and lipid formation were successfully established by developing a multi-parametric kinetic model suitable for the prediction of mixotrophic microalgal growth dynamics co-limited by nitrogen and phosphorus. The model's high predictive capacity was experimentally validated against various datasets obtained from laboratory-scale cultures of Chlamydomonas reinhardtii CCAP 11/32C subject to different initial nutrient regimes. The identified model-based optimal cultivation strategies were further validated experimentally and yielded significant increases in starch (+ 270%) and lipid (+ 74%) production against a non-optimised strategy.

CONCLUSIONS

The optimised microalgal cultivation scenarios for maximised starch and lipids, as identified by the kinetic model presented here, highlight the benefits of exploiting modelling frameworks as optimisation tools that facilitate the development and commercialisation of microalgae-to-fuel technologies.

Algae-Bacteria Consortia as a Strategy to Enhance H2 Production

Biological hydrogen production by microalgae is a potential sustainable, renewable and clean source of energy. However, many barriers limiting photohydrogen production in these microorganisms remain unsolved. In order to explore this potential and make biohydrogen industrially affordable, the unicellular microalga Chlamydomonas reinhardtii is used as a model system to solve barriers and identify new approaches that can improve hydrogen production. Recently, Chlamydomonas–bacteria consortia have opened a new window to improve biohydrogen production. In this study, we review the different consortia that have been successfully employed and analyze the factors that could be behind the improved H₂ production.

Reconstruction and analysis of a carbon-core metabolic network for Dunaliella salina

BACKGROUND

The green microalga Dunaliella salina accumulates a high proportion of β-carotene during abiotic stress conditions. To better understand the intracellular flux distribution leading to carotenoid accumulation, this work aimed at reconstructing a carbon core metabolic network for D. salina CCAP 19/18 based on the recently published nuclear genome and its validation with experimental observations and literature data.

RESULTS

The reconstruction resulted in a network model with 221 reactions and 212 metabolites within three compartments: cytosol, chloroplast and mitochondrion. The network was implemented in the MATLAB toolbox CellNetAnalyzer and checked for feasibility. Furthermore, a flux balance analysis was carried out for different light and nutrient uptake rates. The comparison of the experimental knowledge with the model prediction revealed that the results of the stoichiometric network analysis are plausible and in good agreement with the observed behavior. Accordingly, our model provides an excellent tool for investigating the carbon core metabolism of D. salina.

CONCLUSIONS

The reconstructed metabolic network of D. salina presented in this work is able to predict the biological behavior under light and nutrient stress and will lead to an improved process understanding for the optimized production of high-value products in microalgae.

The phosphite oxidoreductase gene, ptxD as a bio-contained chloroplast marker and crop-protection tool for algal biotechnology using Chlamydomonas

Edible microalgae have potential as low-cost cell factories for the production and oral delivery of recombinant proteins such as vaccines, anti-bacterials and gut-active enzymes that are beneficial to farmed animals including livestock, poultry and fish. However, a major economic and technical problem associated with large-scale cultivation of microalgae, even in closed photobioreactors, is invasion by contaminating microorganisms. Avoiding this requires costly media sterilisation, aseptic techniques during set-up and implementation of 'crop-protection' strategies during cultivation. Here, we report a strain improvement approach in which the chloroplast of Chlamydomonas reinhardtii is engineered to allow oxidation of phosphite to its bio-available form: phosphate. We have designed a synthetic version of the bacterial gene (ptxD)-encoding phosphite oxidoreductase such that it is highly expressed in the chloroplast but has a Trp→Opal codon reassignment for bio-containment of the transgene. Under mixotrophic conditions, the growth rate of the engineered alga is unaffected when phosphate is replaced with phosphite in the medium. Furthermore, under non-sterile conditions, growth of contaminating microorganisms is severely impeded in phosphite medium. This, therefore, offers the possibility of producing algal biomass under non-sterile conditions. The ptxD gene can also serve as a dominant marker for genetic engineering of any C. reinhardtii strain, thereby avoiding the use of antibiotic resistance genes as markers and allowing the 'retro-fitting' of existing engineered strains. As a proof of concept, we demonstrate the application of our ptxD technology to a strain expressing a subunit vaccine targeting a major viral pathogen of farmed fish.

Metabolic modelling and simulation of the light and dark metabolism of Chlamydomonas reinhardtii

A metabolic network model of the green microalga Chlamydomonas reinhardtii was used to characterize photoautotrophic and heterotrophic (i.e. growth on stored compounds) growth under light and dark, respectively. The metabolic network comprised 2514 reactions distributed among nine intracellular compartments and the extracellular space. The metabolic network included all the key biochemical pathways for synthesis and metabolism of starch and triacylglycerols (TAGs). Under light and nitrogen limitation, the model simulated the accumulation of the energy-rich compounds (TAGs and starch) in the cell. In the dark, the model could simulate cell growth and maintenance on stored compounds. The model-predicted consumption rates of storage compounds (starch or TAGs) to enable growth in the dark, were found to be greater than the rates of synthesis under light. This implied utilization of the storage compounds for cell maintenance in the dark. Under constant illumination, the simulations of cell growth and intracellular starch content agreed closely with independent experimental data. In other simulations, compared with the case without photorespiration, light uptake rate increased 1.04-fold when the ratio of the rates of oxygenation and carboxylation (Rubisco) was 0.1. Although extensive experimental work exists on culture and physiology of microalgae, it does not allow quantitative predictions of the influence of dark metabolism on the productivity of metabolites to be made. This limitation is overcome using the present model. A metabolic network model of Chlamydomonas reinhardtii is shown to simulate growth and synthesis of energy-rich compounds (triacylglycerols and starch) under light. The same model also simulates dark growth and maintenance through consumption of the stored energy-rich compounds.

Advances in metabolic flux analysis toward genome-scale profiling of higher organisms

Methodological and technological advances have recently paved the way for metabolic flux profiling in higher organisms, like plants. However, in comparison with omics technologies, flux profiling has yet to provide comprehensive differential flux maps at a genome-scale and in different cell types, tissues, and organs. Here we highlight the recent advances in technologies to gather metabolic labeling patterns and flux profiling approaches. We provide an opinion of how recent local flux profiling approaches can be used in conjunction with the constraint-based modeling framework to arrive at genome-scale flux maps. In addition, we point at approaches which use metabolomics data without introduction of label to predict either non-steady state fluxes in a time-series experiment or flux changes in different experimental scenarios. The combination of these developments allows an experimentally feasible approach for flux-based large-scale systems biology studies.

Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA

In this work we present new concepts of VANESA, a tool for modeling and simulation in systems biology. We provide a convenient way to handle mathematical expressions and take physical units into account. Simulation and result management has been improved, and syntax and consistency checks, based on physical units, reduce modeling errors. As a proof of concept, essential components of the aerobic carbon metabolism of the green microalga Chlamydomonas reinhardtii are modeled and simulated. The modeling process is based on xHPN Petri net formalism and simulation is performed with OpenModelica, a powerful environment and compiler for Modelica. VANESA, as well as OpenModelica, is open source, free-of-charge for non-commercial use, and is available at: http://agbi.techfak.uni-bielefeld.de/vanesa.

Algal-bacterial cooperation improves algal photolysis-mediated hydrogen production

In this study, bacterium Pseudomonas sp. strain D was proved to be the main partner assisting Chlamydomonas reinhardtii in improving photolysis-mediated H₂ production and a good partner for promoting H₂ production by the green algae Chlorella and Scenedesmus. In strain D partnered algal-bacterial co-culture, the relative O₂ content in the headspace plus the dissolved oxygen in the culture medium were rapidly consumed by bacterial growth, resulting in a completely anaerobic environment that proved suitable for the activation of algal hydrogenase. Moreover, algal-bacterial cooperation was able to slow the reduction of chlorophyll, enhance starch accumulation, and maintain protein content, which are the potential factors whose control provides an opportunity for improving algal H₂ production. This study systematically analyzed the main pathway responsible for H₂ production by algal-bacterial cooperation and the potential mechanisms for improvement, and proposed an efficient and durable algal-bacterial cooperation system for improving photolysis-mediated H₂ production by green algae.

Mixotrophic cultivation of microalgae to enhance the quality of lipid for biodiesel application: effects of scale of cultivation and light spectrum on reduction of α-linolenic acid

The research on microalgal biodiesel is focused not only on getting the highest lipid productivity but also desired quality of lipid. The experiments were initially conducted on flask scale (1L) using acetate carbon source at different concentrations viz. 0.5, 2, 3 and 4 g L^-1. The optimum concentration of acetate was considered for further experiments in two airlift photobioreactors (10 L) equipped separately with red and white LED lights. The Feasibility Index (FI) was derived to analyze the scalability of mixotrophic cultivation based on net carbon fixation in biomass per consumption of total organic carbon. The experimental strategy under mixotrophic mode of cultivation lowered the α-linolenic acid content of lipid by 60-80% as compared to autotrophic cultivation for Scenedesmus abundans species and yielded the highest biomass and lipid productivities, 59 ± 2 and 17 ± 1.8 mg L^-1 day^-1, respectively. The TOC, nitrate, and phosphate reduction rates were 74.6 ± 3.0, 11.5 ± 1.4, 9.6 ± 2.4 mg L^-1 day^-1, respectively. The significant change was observed in lipid compositions due to the scale, mode of cultivation, and light spectra. As compared to phototrophic cultivation, biodiesel obtained under mixotrophic cultivation only met standard biodiesel properties. The FI data showed that the mixotrophic cultivation was feasible on moderate concentrations of acetate (2-3 g L^-1).

Cyclic decomposition explains a photosynthetic down regulation for Chlamydomonas reinhardtii

The regulation of metabolic networks has been shown to be distributed and shared through the action of metabolic cycles. Biochemical cycles play important roles in maintaining flux and substrate availability for multiple pathways to supply cellular energy and contribute to dynamic stability. By understanding the cyclic and acyclic flows of matter through a network, we are closer to understanding how complex dynamic systems distribute flux along interconnected pathways. In this work, we have applied a cycle decomposition algorithm to a genome-scale metabolic model of Chlamydomonas reinhardtii to analyse how acetate supply affects the distribution of fluxes that sustain cellular activity. We examined the role of metabolic cycles which explain the down regulation of photosynthesis that is observed when cells are grown in the presence of acetate. Our results suggest that acetate modulates changes in global metabolism, with the pentose phosphate pathway, the Calvin-Benson cycle and mitochondrial respiration activity being affected whilst reducing photosynthesis. These results show how the decomposition of metabolic flux into cyclic and acyclic components helps to understand the impact of metabolic cycling on organismal behaviour at the genome scale.

Identification and Metabolite Profiling of Chemical Activators of Lipid Accumulation in Green Algae

Microalgae are proposed as feedstock organisms useful for producing biofuels and coproducts. However, several limitations must be overcome before algae-based production is economically feasible. Among these is the ability to induce lipid accumulation and storage without affecting biomass yield. To overcome this barrier, a chemical genetics approach was employed in which 43,783 compounds were screened against Chlamydomonas reinhardtii, and 243 compounds were identified that increase triacylglyceride (TAG) accumulation without terminating growth. Identified compounds were classified by structural similarity, and 15 were selected for secondary analyses addressing impacts on growth fitness, photosynthetic pigments, and total cellular protein and starch concentrations. TAG accumulation was verified using gas chromatography-mass spectrometry quantification of total fatty acids, and targeted TAG and galactolipid measurements were performed using liquid chromatography-multiple reaction monitoring/mass spectrometry. These results demonstrated that TAG accumulation does not necessarily proceed at the expense of galactolipid. Untargeted metabolite profiling provided important insights into pathway shifts due to five different compound treatments and verified the anabolic state of the cells with regard to the oxidative pentose phosphate pathway, Calvin cycle, tricarboxylic acid cycle, and amino acid biosynthetic pathways. Metabolite patterns were distinct from nitrogen starvation and other abiotic stresses commonly used to induce oil accumulation in algae. The efficacy of these compounds also was demonstrated in three other algal species. These lipid-inducing compounds offer a valuable set of tools for delving into the biochemical mechanisms of lipid accumulation in algae and a direct means to improve algal oil content independent of the severe growth limitations associated with nutrient deprivation.

Carbon Supply and Photoacclimation Cross Talk in the Green Alga Chlamydomonas reinhardtii

Photosynthetic organisms are exposed to drastic changes in light conditions, which can affect their photosynthetic efficiency and induce photodamage. To face these changes, they have developed a series of acclimation mechanisms. In this work, we have studied the acclimation strategies of Chlamydomonas reinhardtii, a model green alga that can grow using various carbon sources and is thus an excellent system in which to study photosynthesis. Like other photosynthetic algae, it has evolved inducible mechanisms to adapt to conditions where carbon supply is limiting. We have analyzed how the carbon availability influences the composition and organization of the photosynthetic apparatus and the capacity of the cells to acclimate to different light conditions. Using electron microscopy, biochemical, and fluorescence measurements, we show that differences in CO₂ availability not only have a strong effect on the induction of the carbon-concentrating mechanisms but also change the acclimation strategy of the cells to light. For example, while cells in limiting CO₂ maintain a large antenna even in high light and switch on energy-dissipative mechanisms, cells in high CO₂ reduce the amount of pigments per cell and the antenna size. Our results show the high plasticity of the photosynthetic apparatus of C. reinhardtii This alga is able to use various photoacclimation strategies, and the choice of which to activate strongly depends on the carbon availability.

Synergism between Inositol Polyphosphates and TOR Kinase Signaling in Nutrient Sensing, Growth Control, and Lipid Metabolism in Chlamydomonas

The networks that govern carbon metabolism and control intracellular carbon partitioning in photosynthetic cells are poorly understood. Target of Rapamycin (TOR) kinase is a conserved growth regulator that integrates nutrient signals and modulates cell growth in eukaryotes, though the TOR signaling pathway in plants and algae has yet to be completely elucidated. We screened the unicellular green alga Chlamydomonas reinhardtii using insertional mutagenesis to find mutants that conferred hypersensitivity to the TOR inhibitor rapamycin. We characterized one mutant, vip1-1, that is predicted to encode a conserved inositol hexakisphosphate kinase from the VIP family that pyrophosphorylates phytic acid (InsP₆) to produce the low abundance signaling molecules InsP₇ and InsP₈ Unexpectedly, the rapamycin hypersensitive growth arrest of vip1-1 cells was dependent on the presence of external acetate, which normally has a growth-stimulatory effect on Chlamydomonas. vip1-1 mutants also constitutively overaccumulated triacylglycerols (TAGs) in a manner that was synergistic with other TAG inducing stimuli such as starvation. vip1-1 cells had reduced InsP₇ and InsP₈, both of which are dynamically modulated in wild-type cells by TOR kinase activity and the presence of acetate. Our data uncover an interaction between the TOR kinase and inositol polyphosphate signaling systems that we propose governs carbon metabolism and intracellular pathways that lead to storage lipid accumulation.

Cytochrome b 6 f function and localization, phosphorylation state of thylakoid membrane proteins and consequences on cyclic electron flow

Both the structure and the protein composition of thylakoid membranes have an impact on light harvesting and electron transfer in the photosynthetic chain. Thylakoid membranes form stacks and lamellae where photosystem II and photosystem I localize, respectively. Light-harvesting complexes II can be associated to either PSII or PSI depending on the redox state of the plastoquinone pool, and their distribution is governed by state transitions. Upon state transitions, the thylakoid ultrastructure and lateral distribution of proteins along the membrane are subject to significant rearrangements. In addition, quinone diffusion is limited to membrane microdomains and the cytochrome b 6 f complex localizes either to PSII-containing grana stacks or PSI-containing stroma lamellae. Here, we discuss possible similarities or differences between green algae and C3 plants on the functional consequences of such heterogeneities in the photosynthetic electron transport chain and propose a model in which quinones, accepting electrons either from PSII (linear flow) or NDH/PGR pathways (cyclic flow), represent a crucial control point. Our aim is to give an integrated description of these processes and discuss their potential roles in the balance between linear and cyclic electron flows.

Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN) models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms, and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA), experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e., (i) lumped networks, (ii) compartment per guild networks, (iii) bi-level optimization simulations, and (iv) dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach) are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial interactions can be used to analyze complex “omics” data and to infer and optimize metabolic processes. Thereby, SMN models are suitable to capitalize on advances in high-throughput molecular and metabolic data generation. SMN models are starting to be applied to describe microbial interactions during wastewater treatment, in-situ bioremediation, microalgae blooms methanogenic fermentation, and bioplastic production. Despite their current challenges, we envisage that SMN models have future potential for the design and development of novel growth media, biochemical pathways and synthetic microbial associations.