The biodiversity of carbon assimilation

As all plastids that have been investigated so far can be traced back to endosymbiotic uptake of cyanobacteria by heterotrophic host cells, they accordingly show a high similarity regarding photosynthesis, which includes both the photosystems and the biochemical reactions around the CO2 fixation via the Calvin-Bassham cycle. Major differences between the different algal and plant groups may include the presence or absence of carbon concentrating mechanisms, pyrenoids, Rubisco activases, carbonic anhydrases as well as differences in the regulation of the Calvin-Bassham cycle. This review describes the diversity of primary carbon fixation steps in algae and plants and the respective regulatory mechanisms.

Redox changes accompanying inorganic carbon limitation in Synechocystis sp. PCC 6803

Inorganic carbon (Ci) is the major sink for photosynthetic reductant in organisms capable of oxygenic photosynthesis. In the absence of abundant Ci, the cyanobacterium Synechocystis sp. strain PCC6803 expresses a high affinity Ci acquisition system, the CO2-concentrating mechanisms (CCM), controlled by the transcriptional regulator CcmR and the metabolites NADP+ and α-ketoglutarate, which act as co-repressors of CcmR by modulating its DNA binding. The CCM thus responds to internal cellular redox changes during the transition from Ci-replete to Ci-limited conditions. However, the actual changes in the metabolic state of the NADPH/NADP+ system that occur during the transition to Ci-limited conditions remain ill-defined. Analysis of changes in the redox state of cells experiencing Ci limitation reveals systematic changes associated with physiological adjustments and a trend towards the quinone and NADP pools becoming highly reduced. A rapid and persistent increase in F0 was observed in cells reaching the Ci-limited state, as was the induction of photoprotective fluorescence quenching. Systematic changes in the fluorescence induction transients were also observed. As with Chl fluorescence, a transient reduction of the NADPH pool ('M' peak), is assigned to State 2→State 1 transition associated with increased electron flow to NADP+. This was followed by a characteristic decline, which was abolished by Ci limitation or inhibition of the Calvin-Benson-Bassham (CBB) cycle and is thus assigned to the activation of the CBB cycle. The results are consistent with the proposed regulation of the CCM and provide new information on the nature of the Chl and NADPH fluorescence induction curves.

Improving microalgae for biotechnology - From genetics to synthetic biology - Moving forward but not there yet

Microalgae are a diverse group of photosynthetic organisms that can be exploited for the production of different compounds, ranging from crude biomass and biofuels to high value-added biochemicals and synthetic proteins. Traditionally, algal biotechnology relies on bioprospecting to identify new highly productive strains and more recently, on forward genetics to further enhance productivity. However, it has become clear that further improvements in algal productivity for biotechnology is impossible without combining traditional tools with the arising molecular genetics toolkit. We review recent advantages in developing high throughput screening methods, preparing genome-wide mutant libraries, and establishing genome editing techniques. We discuss how algae can be improved in terms of photosynthetic efficiency, biofuel and high value-added compound production. Finally, we critically evaluate developments over recent years and explore future potential in the field.

Changes in pH and dissolved inorganic carbon in water affect the growth, saxitoxins production and toxicity of the cyanobacterium Raphidiopsis raciborskii ITEP-A1

Raphidiopsis raciborskii is a widely distributed, potentially toxic cyanobacterium described as a tropical-subtropical species. However, its occurrence in temperate regions has been expanding. Understanding the environmental factors underlying the expansion and colonization success of Raphidiopsis has been the object of numerous studies. However, less is known regarding its responses to pH and inorganic carbon in water. Thus, the aim of the present study was to investigate the effects of changes in pH and dissolved inorganic carbon on growth and saxitoxins production in the strain R. raciborskii ITEP-A1. We incubated batch cultures with different unbuffered and buffered pH (neutral-acid and alkaline) and inorganic carbon availability (CO₂-rich air bubbling and the addition of NaHCO₃) to assess the effect of these factors on the growth, toxin production as well as saxitoxins composition of the cyanobacterium. The carbon concentrating mechanism (CCM) system of ITEP-A1 was also characterized by an in silico analysis of its previously sequenced genome. The growth and saxitoxins production of R. raciborskii were affected. The addition of sodium bicarbonate and air bubbling enhanced the growth of the cyanobacterium in alkaline pH. In contrast, saxitoxins production and relative toxicity were decreased. Moreover, significant changes in the cellular composition of saxitoxins were strongly related to pH changes. ITEP-A1 potentially expresses the low-flux bicarbonate transporter BicA, an efficient CCM which uptakes most of its carbon from HCO₃^-. Hence, increasing the diffusion of CO₂ in alkaline eutrophic lakes is likely to increase R. raciborskii dominance, but produce less toxic blooms.

Evaluation of photosynthetic efficacy and CO2 removal of microalgae grown in an enriched bicarbonate medium

Bicarbonate species in the aqueous phase is the primary source for CO₂ for the growth of microalgae. The potential of carbon dioxide (CO₂) fixation by Chlorella pyrenoidosa in enriched bicarbonate medium was evaluated. In the present study, effects of parameters such as pH, sodium bicarbonate concentration and inoculum size were assessed for the removal of CO₂ by C. pyrenoidosa under mixotrophic condition. Central composite design tool from response surface methodology was used to validate statistical methods in order to study the influence of these parameters. The obtained results reveal that the maximum removal of CO₂ was attained at pH 8 with sodium bicarbonate concentration of 3.33 g/l, and inoculum size of 30 %. The experimental results were statistically significant with R ² value of 0.9527 and 0.960 for CO₂ removal and accumulation of chlorophyll content, respectively. Among the various interactions, interactive effects between the parameters pH and inoculum size was statistically significant (P < 0.05) for CO₂ removal and chlorophyll accumulation. Based on the studies, the application of C. pyrenoidosa as a potential source for carbon dioxide removal at alkaline pH from bicarbonate source is highlighted.

Coordination between photorespiration and carbon concentrating mechanism in Chlamydomonas reinhardtii: transcript and protein changes during light-dark diurnal cycles and mixotrophy conditions

Carbon concentrating mechanism (CCM) and photorespiration (PR) are interlinked and co-regulated in Chlamydomonas reinhardtii, but conditions where co-regulation alters are not sufficiently explored. Here, we uncover that PR gene transcripts, like CCM transcripts, are induced even in the dark when both processes are not active. Such diurnal cycles show that transcript levels peak in the middle of 12 h day, decline by early part of 12-h dark followed by their onset again at mid-dark. Interestingly, the onset in the mid-dark phase is sensitive to high CO₂, implying that the active carbon sensing mechanism operates even in the dark. The rhythmic alterations of both CCM and PR transcript levels are unlinked to circadian clock: the "free-running state" reveals no discernible rhythmicity in transcript changes. Only continuous light leads to high transcript levels but no detectable transcripts were observed in continuous dark. Asynchronous continuous light cultures, upon shifting to low from high CO₂ exhibit only transient induction of PR transcripts/proteins while CCM transcript induction is stable, indicating the loss of co-regulation between PR and CCM gene transcription. Lastly, we also describe that both CCM and PR transcripts/proteins are induced in low CO₂ even in mixotrophic cultures, but only in high light, the same being attenuated in high CO₂, implying that high light is a mandatory "trigger" for CCM and PR induction in low CO₂ mixotrophy. Our study provides comprehensive analyses of conditions where CCM and PR were differently regulated, setting a paradigm for a detailed mechanistic probing of these responses.

Dissolved inorganic carbon uptake in Thiomicrospira crunogena XCL-2 is Δp- and ATP-sensitive and enhances RubisCO-mediated carbon fixation

The gammaproteobacterium Thiomicrospira crunogena XCL-2 is an aerobic sulfur-oxidizing hydrothermal vent chemolithoautotroph that has a CO2 concentrating mechanism (CCM), which generates intracellular dissolved inorganic carbon (DIC) concentrations much higher than extracellular, thereby providing substrate for carbon fixation at sufficient rate. This CCM presumably requires at least one active DIC transporter to generate the elevated intracellular concentrations of DIC measured in this organism. In this study, the half-saturation constant (K CO2) for purified carboxysomal RubisCO was measured (276 ± 18 µM) which was much greater than the K CO2 of whole cells (1.03 µM), highlighting the degree to which the CCM facilitates CO2 fixation under low CO2 conditions. To clarify the bioenergetics powering active DIC uptake, cells were incubated in the presence of inhibitors targeting ATP synthesis (DCCD) or proton potential (CCCP). Incubations with each of these inhibitors resulted in diminished intracellular ATP, DIC, and fixed carbon, despite an absence of an inhibitory effect on proton potential in the DCCD-incubated cells. Electron transport complexes NADH dehydrogenase and the bc 1 complex were found to be insensitive to DCCD, suggesting that ATP synthase was the primary target of DCCD. Given the correlation of DIC uptake to the intracellular ATP concentration, the ABC transporter genes were targeted by qRT-PCR, but were not upregulated under low-DIC conditions. As the T. crunogena genome does not include orthologs of any genes encoding known DIC uptake systems, these data suggest that a novel, yet to be identified, ATP- and proton potential-dependent DIC transporter is active in this bacterium. This transporter serves to facilitate growth by T. crunogena and other Thiomicrospiras in the many habitats where they are found.

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 carbonate concentration mechanism of Pyropia yezoensis (Rhodophyta): evidence from transcriptomics and biochemical data

BACKGROUND

Pyropia yezoensis (Rhodophyta) is widely cultivated in East Asia and plays important economic, ecological and research roles. Although inorganic carbon utilization of P. yezoensis has been investigated from a physiological aspect, the carbon concentration mechanism (CCM) of P. yezoensis remains unclear. To explore the CCM of P. yezoensis, especially during its different life stages, we tracked changes in the transcriptome, photosynthetic efficiency and in key enzyme activities under different inorganic carbon concentrations.

RESULTS

Photosynthetic efficiency demonstrated that sporophytes were more sensitive to low carbon (LC) than gametophytes, with increased photosynthesis rate during both life stages under high carbon (HC) compared to normal carbon (NC) conditions. The amount of starch and number of plastoglobuli in cells corresponded with the growth reaction to different inorganic carbon (Ci) concentrations. We constructed 18 cDNA libraries from 18 samples (three biological replicates per Ci treatment at two life cycles stages) and sequenced these using the Illumina platform. De novo assembly generated 182,564 unigenes, including approximately 275 unigenes related to CCM. Most genes encoding internal carbonic anhydrase (CA) and bicarbonate transporters involved in the biophysical CCM pathway were induced under LC in comparison with NC, with transcript abundance of some PyCAs in gametophytes typically higher than that in sporophytes. We identified all key genes participating in the C4 pathway and showed that their RNA abundances changed with varying Ci conditions. High decarboxylating activity of PEPCKase and low PEPCase activity were observed in P. yezoensis. Activities of other key enzymes involved in the C4-like pathway were higher under HC than under the other two conditions. Pyruvate carboxylase (PYC) showed higher carboxylation activity than PEPC under these Ci conditions. Isocitrate lyase (ICL) showed high activity, but the activity of malate synthase (MS) was very low.

CONCLUSION

We elucidated the CCM of P. yezoensis from transcriptome and enzyme activity levels. All results indicated at least two types of CCM in P. yezoensis, one involving CA and an anion exchanger (transporter), and a second, C4-like pathway belonging to the PEPCK subtype. PYC may play the main carboxylation role in this C4-like pathway, which functions in both the sporophyte and gametophyte life cycles.

Realization process of microalgal biorefinery: The optional approach toward carbon net-zero emission

Increasing carbon dioxide (CO2) emission has already become a dire threat to the human race and Earth's ecology. Microalgae are recommended to be engineered as CO2 fixers in biorefinery, which play crucial roles in responding climate change and accelerating the transition to a sustainable future. This review sorted through each segment of microalgal biorefinery to explore the potential for its practical implementation and commercialization, offering valuable insights into research trends and identifies challenges that needed to be addressed in the development process. Firstly, the known mechanisms of microalgal photosynthetic CO2 fixation and the approaches for strain improvement were summarized. The significance of process regulation for strengthening fixation efficiency and augmenting competitiveness was emphasized, with a specific focus on CO2 and light optimization strategies. Thereafter, the massive potential of microalgal refineries for various bioresource production was discussed in detail, and the integration with contaminant reclamation was mentioned for economic and ecological benefits. Subsequently, economic and environmental impacts of microalgal biorefinery were evaluated via life cycle assessment (LCA) and techno-economic analysis (TEA) to lit up commercial feasibility. Finally, the current obstacles and future perspectives were discussed objectively to offer an impartial reference for future researchers and investors.

A membrane-bound cAMP receptor protein, SyCRP1 mediates inorganic carbon response in Synechocystis sp. PCC 6803

The availability of inorganic carbon (C_i) as the source for photosynthesis is fluctuating in aquatic environments. Despite the involvement of transcriptional regulators CmpR and NdhR in regulating genes encoding C_i transporters at limiting CO₂, the C_i-sensing mechanism is largely unknown among cyanobacteria. Here we report that a cAMP-dependent transcription factor SyCRP1 mediates C_i response in Synechocystis. The mutant ∆sycrp1 exhibited a slow-growth phenotype and reduced maximum rate of bicarbonate-dependent photosynthetic electron transport (V_max) compared to wild-type at the scarcity of CO₂. The number of carboxysomes was decreased significantly in the ∆sycrp1 at low CO₂ consistent with its reduced V_max. The DNA microarray analysis revealed the upregulation of genes encoding C_i transporters in ∆sycrp1. The membrane-localized SyCRP1 was released into the cytosol in wild-type cells shifted from low to high CO₂ or upon cAMP treatment. Soluble His-tagged SyCRP1 was shown to target DNA-binding sites upstream of the C_i-regulated genes sbtA and ccmK3. In addition, cAMP enhanced the binding of SyCRP1 to its target sites. Our data collectively suggest that the C_i is sensed through the second messenger cAMP releasing membrane-bound SyCRP1 into cytoplasm under sufficient CO₂ conditions. Hence, SyCRP1 is a possible regulator of carbon concentrating mechanism, and such a regulation might be mediated via sensing C_i levels through cAMP in Synechocystis.

Co-option of immune and digestive cellular machinery to support photosymbiosis in amoebocytes of the upside-down jellyfish Cassiopea xamachana

The upside-down jellyfish, Cassiopea spp., host their algal symbionts inside a subset of amoebocytes, phagocytic cells that also play innate immune functions akin to macrophages from vertebrate animals. Amoebocyte precursors phagocytose algae from the jellyfish gut and store them inside intracellular compartments called symbiosomes. Subsequently, the precursors migrate to the mesoglea, differentiate into symbiotic amoebocytes, and roam throughout the jellyfish body where the algae remain photosynthetically active and supply the jellyfish host with a significant portion of their organic carbon needs. Here, we show that the amoebocyte symbiosome membrane contains V-H+-ATPase (VHA), the proton pump that acidifies phagosomes and lysosomes in all eukaryotes. Many symbiotic amoebocytes also abundantly express a carbonic anhydrase (CA), an enzyme that reversibly hydrates CO2 into H+ and HCO3-. Moreover, we found that the symbiosome lumen is pronouncedly acidic and that pharmacological inhibition of VHA or CA activities significantly decreases photosynthetic oxygen production in live jellyfish. These results point to a carbon concentrating mechanism (CCM) that co-opts VHA and CA from the phago-lysosomal machinery that ubiquitously mediates food digestion and innate immune responses. Analogous VHA-dependent CCMs have been previously described in reef-building corals, anemones, and giant clams; however, these other two cnidarians host their dinoflagellate algae inside gastrodermal cells -not in amoebocytes- and the clam hosts theirs within the gut lumen. Thus, our study identifies an example of convergent evolution at the cellular level that might broadly apply to invertebrate-microbe photosymbioses while also providing evolutionary links with intra- and extracellular food digestion and the immune system.

Evolutionary diversification of C2 photosynthesis in the grass genus Homolepis (Arthropogoninae)

BACKGROUND AND AIMS

To better understand C4 evolution in monocots, we characterized C3-C4 intermediate phenotypes in the grass genus Homolepis (subtribe Arthropogoninae).

METHODS

Carbon isotope ratio (δ13C), leaf gas exchange, mesophyll (M) and bundle sheath (BS) tissue characteristics, organelle size and numbers in M and BS tissue, and tissue distribution of the P-subunit of glycine decarboxylase (GLDP) were determined for five Homolepis species and the C4 grass Mesosetum loliiforme from a phylogenetic sister clade. We generated a transcriptome-based phylogeny for Homolepis and Mesosetum species to interpret physiological and anatomical patterns in an evolutionary context, and to test for hybridization.

KEY RESULTS

Homolepis contains two C3 species (H. glutinosa, H. villaricensis), one species with a weaker form of C2 termed sub-C2 (H. isocalycia), and two C2 species (H. longispicula, H. aturensis). Homolepis longispicula and H. aturensis express over 85 % of leaf glycine in centripetal mitochondria within the BS, and have increased fractions of leaf chloroplasts, mitochondria and peroxisomes within the BS relative to H. glutinosa. Analysis of leaf gas exchange, cell ultrastructure and transcript expression show M. loliiforme is a C4 plant of the NADP-malic enzyme subtype. Homolepis comprises two sister clades, one containing H. glutinosa and H. villaricensis and the second H. longispicula and H. aturensis. Homolepis isocalycia is of hybrid origin, its parents being H. aturensis and a common ancestor of the C3  Homolepis clade and H. longispicula.

CONCLUSIONS

Photosynthetic activation of BS tissue in the sub-C2 and C2 species of Homolepis is similar to patterns observed in C3-C4 intermediate eudicots, indicating common evolutionary pathways from C3 to C4 photosynthesis in these disparate clades. Hybridization can diversify the C3-C4 intermediate character state and should be considered in reconstructing putative ancestral states using phylogenetic analyses.

Different preferences for inorganic carbon influence CO2 flux under Cyanobacteria or Chlorophyta dominance days

Algae play critical roles in the carbon dioxide (CO2) exchange between the water bodies and the atmosphere. However, the effects of prokaryotic and eukaryotic algae on carbon utilization, CO2 flux, and the underlying mechanisms remain poorly understood. Therefore, this study investigated the differences in carbon preferences and CO2 fluxes under different algal dominance days. Our research revealed that dissolved inorganic carbon (DIC) concentration fluctuations had a limited effect on the relative abundance of algae. However, shifts in dominant algal phyla induced changes in DIC, with Cyanobacteria preferring HCO3- and Chlorophyta preferring CO2. Analysis of the water chemistry balance indicated that the growth of Chlorophyta had a 15.59 times greater effect on CO2 sinks compared with that of Cyanobacteria. During the Cyanobacteria dominance days, the lower DIC concentration did not result in a reduction in CO2 emissions. However, increases in the dissolved organic carbon concentration provided a favorable environment for Cyanobacteria, which promoted CO2 emissions. The CCM model indicated that the growth of Chlorophyta resulted in CO2 uptake rates at least 3.57 times higher and CO2 leakage rates up to 0.97 times lower compared to Cyanobacteria, accelerating CO2 transport into the cell. Overall, CO2 sink was stronger on Chlorophyta dominance days than on Cyanobacteria dominance days. This study emphasized the influence of algal phyla on CO2 fluxes, revealing the significant CO2 sink associated with Chlorophyta. Further research should investigate how to manipulate environmental factors to favor Chlorophyta growth and effectively reduce CO2 emissions.