Chlamydomonas reinhardtii, an Algal Model in the Nitrogen Cycle

De novo transcriptome and lipidome analysis of Desmodesmus abundans under model flue gas reveals adaptive changes after ten years of acclimation to high CO2

Microalgae's ability to mitigate flue gas is an attractive technology that can valorize gas components through biomass conversion. However, tolerance and growth must be ideal; therefore, acclimation strategies are suggested. Here, we compared the transcriptome and lipidome of Desmodesmus abundans strains acclimated to high CO2 (HCA) and low CO2 (LCA) under continuous supply of model flue gas (MFG) and incomplete culture medium (BG11-N-S). Initial growth and nitrogen consumption from MFG were superior in strain HCA, reaching maximum productivity a day before strain LCA. However, similar productivities were attained at the end of the run, probably because maximum photobioreactor capacity was reached. RNA-seq analysis during exponential growth resulted in 16,435 up-regulated and 4,219 down-regulated contigs in strain HCA compared to LCA. Most differentially expressed genes (DEGs) were related to nucleotides, amino acids, C fixation, central carbon metabolism, and proton pumps. In all pathways, a higher number of up-regulated contigs with a greater magnitude of change were observed in strain HCA. Also, cellular component GO terms of chloroplast and photosystems, N transporters, and secondary metabolic pathways of interest, such as starch and triacylglycerols (TG), exhibited this pattern. RT-qPCR confirmed N transporters expression. Lipidome analysis showed increased glycerophospholipids in strain HCA, while LCA exhibited glycerolipids. Cell structure and biomass composition also revealed strains differences. HCA possessed a thicker cell wall and presented a higher content of pigments, while LCA accumulated starch and lipids, validating transcriptome and lipidome data. Overall, results showed significant differences between strains, where characteristic features of adaptation and tolerance to high CO2 might be related to the capacity to maintain a higher flux of internal C, regulate intracellular acidification, active N transporters, and synthesis of essential macromolecules for photosynthetic growth.

Elemental and macromolecular plasticity of Chlamydomonas reinhardtii (Chlorophyta) in response to resource limitation and growth rate

With the ongoing differential disruption of the biogeochemical cycles of major elements that are essential for all life (carbon, nitrogen, and phosphorus), organisms are increasingly faced with a heterogenous supply of these elements in nature. Given that photosynthetic primary producers form the base of aquatic food webs, impacts of changed elemental supply on these organisms are particularly important. One way that phytoplankton cope with the differential availability of nutrients is through physiological changes, resulting in plasticity in macromolecular and elemental biomass composition. Here, we assessed how the green alga Chlamydomonas reinhardtii adjusts its macromolecular (e.g., carbohydrates, lipids, and proteins) and elemental (C, N, and P) biomass pools in response to changes in growth rate and the modification of resources (nutrients and light). We observed that Chlamydomonas exhibits considerable plasticity in elemental composition (e.g., molar ratios ranging from 124 to 971 for C:P, 4.5 to 25.9 for C:N, and 15.1 to 61.2 for N:P) under all tested conditions, pointing to the adaptive potential of Chlamydomonas in a changing environment. Exposure to low light modified the elemental and macromolecular composition of cells differently than limitation by nutrients. These observed differences, with potential consequences for higher trophic levels, included smaller cells, shifts in C:N and C:P ratios (due to proportionally greater N and P contents), and differential allocation of C among macromolecular pools (proportionally more lipids than carbohydrates) with different energetic value. However, substantial pools of N and P remained unaccounted for, especially at fast growth, indicating accumulation of N and P in forms we did not measure.

Effects of environmental microplastic exposure on Chlorella sp. biofilm characteristics and its interaction with nitric oxide signaling

Microalgal biofilm is promising in simultaneous pollutants removal, CO2 fixation, and biomass resource transformation when wastewater is used as culturing medium. Nitric oxide (NO) often accumulates in microalgal cells under wastewater treatment relevant abiotic stresses such as nitrogen deficiency, heavy metals, and antibiotics. However, the influence of emerging contaminants such as microplastics (MPs) on microalgal intracellular NO is still unknown. Moreover, the investigated MPs concentrations among existing studies were mostly several magnitudes higher than in real wastewaters, which could offer limited guidance for the effects of MPs on microalgae at environment-relevant concentrations. Therefore, this study investigated three commonly observed MPs in wastewater at environment-relevant concentrations (10-10,000 μg/L) and explored their impacts on attached Chlorella sp. growth characteristics, nutrients removal, and anti-oxidative responses (including intracellular NO content). The nitrogen source NO3--N at 49 mg/L being 20 % of the nitrogen strength in classic BG-11 medium was selected for MPs exposure experiments because of least intracellular NO accumulation, so that disturbance of intracellular NO by nitrogen availability could be avoided. Under such condition, 10 μg/L polyethylene (PE) MPs displayed most significant microalgal growth inhibition comparing with polyvinyl chloride (PVC) and polyamide (PA) MPs, showing extraordinarily low chlorophyll a/b ratios, and highest superoxide dismutase (SOD) activity and intracellular NO content after 12 days of MPs exposure. PVC MPs exposed cultures displayed highest malonaldehyde (MDA) content because of the toxic characteristics of organochlorines, and most significant correlations of intracellular NO content with conventional anti-oxidative parameters of SOD, CAT (catalase), and MDA. MPs accelerated phosphorus removal, and the type rather than concentration of MPs displayed higher influences, following the trend of PE > PA > PVC. This study expanded the knowledge of microalgal biofilm under environment-relevant concentrations of MPs, and innovatively discovered the significance of intracellular NO as a more sensitive indicator than conventional anti-oxidative parameters under MPs exposure.

Microalgal-bacterial biofilms for wastewater treatment: Operations, performances, mechanisms, and uncertainties

Microalgal-bacterial biofilms have been increasingly considered of great potential in wastewater treatment due to the advantages of microalgal-bacterial synergistic pollutants removal/recovery, CO2 sequestration, and cost-effective biomass-water separation. However, such advantages may vary widely among different types of microalgal-bacterial biofilms, as the biofilms could be formed on different shapes and structures of attachment substratum, generating "false hope" for certain systems in large-scale wastewater treatment if the operating conditions and pollutants removal properties are evaluated based on the general term "microalgal-bacterial biofilm". This study, therefore, classified microalgal-bacterial biofilms into biofilms formed on 2D substratum, biofilms formed on 3D substratum, and biofilms formed without substratum (i.e. microalgal-bacterial granular sludge, MBGS). Biofilms formed on 2D substratum display higher microalgae fractions and nutrients removal efficiencies, while the adopted long hydraulic retention times were unacceptable for large-scale wastewater treatment. MBGS are featured with much lower microalgae fractions, most efficient pollutants removal, and acceptable retention times for realistic application, yet the feasibility of using natural sunlight should be further explored. 3D substratum systems display wide variations in operating conditions and pollutants removal properties because of diversified substratum shapes and structures. 2D and 3D substratum biofilms share more common in eukaryotic and prokaryotic microbial community structures, while MGBS biofilms are more enriched with microorganisms favoring EPS production, biofilm formation, and denitrification. The specific roles of stratified extracellular polymeric substances (EPS) in nutrients adsorption and condensation still require in-depth exploration. Nutrients removal uncertainties caused by microalgal-bacterial synergy decoupling under insufficient illumination, limited microbial community control, and possible greenhouse gas emission exacerbation arising from microalgal N2O generation were also indicated. This review is helpful for revealing the true potential of applying various microalgal-bacterial biofilms in large-scale wastewater treatment, and will provoke some insights on the challenges to the ideal state of synergistic pollutants reclamation and carbon neutrality via microalgal-bacterial interactions.

Algal or bacterial community: Who can be an effective indicator of the impact of reclaimed water recharge in an urban river

Reclaimed water has been widely utilized for water resource replenishment, yet little is known regarding its impacts on various microorganisms in the receiving water. To address this knowledge gap, we systematically investigated the responses of bacteria and algae to the recharge of reclaimed water by using the high-throughput sequencing technology in the urban Chaobai River. After the inputs of reclaimed water, lower contents of NO2--N, NH4+-N, and TP were observed in the downstream section compared to that of upstream without reclaimed water, indicating that reclaimed water could improve the water quality of the receiving water. Correspondingly, both bacterial and algal communities showed the decreased network complexity in the downstream section, but many common freshwater bacteria and typical bloom-forming algae were dominant in the downstream, potentially suggesting that algae were more sensitive to the local environmental conditions. More importantly, although nitrogen and phosphorus served as the paramount factors in shaping both bacterial and algal communities, environmental selection contributed more to algal rather than bacterial community, and simultaneously algal variations could further affect bacterial dynamics in the urban river. Overall, these findings revealed distinct characteristics of bacteria and algae in responding to the reclaimed water recharge, highlighting the superiority of algae in indicating environmental changes, especially in monitoring and regulating the replenishment of reclaimed water in urban rivers.

N-Acetyl-L-glutamate Kinase of Chlamydomonas reinhardtii: In Vivo Regulation by PII Protein and Beyond

N-Acetyl-L-glutamate kinase (NAGK) catalyzes the rate-limiting step in the ornithine/arginine biosynthesis pathway in eukaryotic and bacterial oxygenic phototrophs. NAGK is the most highly conserved target of the PII signal transduction protein in Cyanobacteria and Archaeplastida (red algae and Chlorophyta). However, there is still much to be learned about how NAGK is regulated in vivo. The use of unicellular green alga Chlamydomonas reinhardtii as a model system has already been instrumental in identifying several key regulation mechanisms that control nitrogen (N) metabolism. With a combination of molecular-genetic and biochemical approaches, we show the existence of the complex CrNAGK control at the transcriptional level, which is dependent on N source and N availability. In growing cells, CrNAGK requires CrPII to properly sense the feedback inhibitor arginine. Moreover, we provide primary evidence that CrPII is only partly responsible for regulating CrNAGK activity to adapt to changing nutritional conditions. Collectively, our results suggest that in vivo CrNAGK is tuned at the transcriptional and post-translational levels, and CrPII and additional as yet unknown factor(s) are integral parts of this regulation.

Chlamydomonas reinhardtii-A Reference Microorganism for Eukaryotic Molybdenum Metabolism

Molybdenum (Mo) is vital for the activity of a small but essential group of enzymes called molybdoenzymes. So far, specifically five molybdoenzymes have been discovered in eukaryotes: nitrate reductase, sulfite oxidase, xanthine dehydrogenase, aldehyde oxidase, and mARC. In order to become biologically active, Mo must be chelated to a pterin, forming the so-called Mo cofactor (Moco). Deficiency or mutation in any of the genes involved in Moco biosynthesis results in the simultaneous loss of activity of all molybdoenzymes, fully or partially preventing the normal development of the affected organism. To prevent this, the different mechanisms involved in Mo homeostasis must be finely regulated. Chlamydomonas reinhardtii is a unicellular, photosynthetic, eukaryotic microalga that has produced fundamental advances in key steps of Mo homeostasis over the last 30 years, which have been extrapolated to higher organisms, both plants and animals. These advances include the identification of the first two molybdate transporters in eukaryotes (MOT1 and MOT2), the characterization of key genes in Moco biosynthesis, the identification of the first enzyme that protects and transfers Moco (MCP1), the first characterization of mARC in plants, and the discovery of the crucial role of the nitrate reductase-mARC complex in plant nitric oxide production. This review aims to provide a comprehensive summary of the progress achieved in using C. reinhardtii as a model organism in Mo homeostasis and to propose how this microalga can continue improving with the advancements in this field in the future.

Site-specific gene knock-in and bacterial phytase gene expression in Chlamydomonas reinhardtii via Cas9 RNP-mediated HDR

In the present study, we applied the HDR (homology-directed DNA repair) CRISPR-Cas9-mediated knock-in system to accurately insert an optimized foreign bacterial phytase gene at a specific site of the nitrate reductase (NR) gene (exon 2) to achieve homologous recombination with the stability of the transgene and reduce insertion site effects or gene silencing. To this end, we successfully knocked-in the targeted NR gene of Chlamydomonas reinhardtii using the bacterial phytase gene cassette through direct delivery of the CRISPR/Cas9 system as the ribonucleoprotein (RNP) complex consisting of Cas9 protein and the specific single guide RNAs (sgRNAs). The NR insertion site editing was confirmed by PCR and sequencing of the transgene positive clones. Moreover, 24 clones with correct editing were obtained, where the phytase gene cassette was located in exon 2 of the NR gene, and the editing efficiency was determined to be 14.81%. Additionally, site-specific gene expression was analyzed and confirmed using RT-qPCR. Cultivation of the positive knocked-in colonies on the selective media during 10 generations indicated the stability of the correct editing without gene silencing or negative insertion site effects. Our results demonstrated that CRISPR-Cas9-mediated knock-in could be applied for nuclear expression of the heterologous gene of interest, and also confirmed its efficacy as an effective tool for site-specific gene knock-in, avoiding nuclear positional effects and gene silencing in C. reinhardtii. These findings could also provide a new perspective on the advantageous application of RNP-CRISPR/Cas9 gene-editing to accelerate the commercial production of complex recombinant proteins in the food-grade organism "C. reinhardtii".

The long overlooked microalgal nitrous oxide emission: Characteristics, mechanisms, and influencing factors in microalgae-based wastewater treatment scenarios

Microalgae-based wastewater treatment is particularly advantageous in simultaneous CO₂ sequestration and nutrients recovery, and has received increasing recognition and attention in the global context of synergistic pollutants and carbon reduction. However, the fact that microalgae themselves can generate the potent greenhouse gas nitrous oxide (N₂O) has been long overlooked, most previous research mainly regarded microalgae as labile organic carbon source or oxygenic approach that interfere bacterial nitrification-denitrification and the concomitant N₂O production. This study, therefore, summarized the amount and rate of N₂O emission in microalgae-based systems, interpreted in-depth the multiple pathways that lead to NO formation as the key precursor of N₂O, and the pathways that transform NO into N₂O. Reduction of nitrite could take place in either the cytoplasm or the mitochondria to form NO by a series of enzymes, while the NO could be enzymatically reduced to N₂O at the chloroplasts or the mitochondria respectively under light and dark conditions. The influences of abiotic factors on microalgal N₂O emission were analyzed, including nitrogen types and concentrations that directly affect the nitrogen transformation routes, illumination and oxygen conditions that regulate the enzymatic activities related to N₂O generation, and other factors that indirectly interfere N₂O emission via NO regulation. The uncertainty of microalgae-based N₂O emission in wastewater treatment scenarios were emphasized, which would be particularly impacted by the complex competition between microalgae and ammonia oxidizing bacteria or nitrite oxidizing bacteria over ammonium or inorganic carbon source. Future studies should put more efforts in improving the compatibility of N₂O emission results expressions, and adopting consistent NO detection methods for N₂O emission prediction. This review will provide much valuable information on the characteristics and mechanisms of microalgal N₂O emission, and arouse more attention to the non-negligible N₂O emission that may impair overall greenhouse gas reduction efficiency in microalgae-based wastewater treatment systems.

Nitrate reductase enzymes in alga Chattonella subsalsa are regulated by environmental cues at the translational and post-translational levels

Nitrate reductase (NR) catalyzes the rate-limiting step in nitrate assimilation. Plant and algal NRs have a highly conserved domain architecture but differ in regulation. In plants, NR activity is regulated by reversible phosphorylation and subsequent binding of 14-3-3 proteins at a conserved serine residue. Algal NRs typically lack 14-3-3 binding motifs, which have only recently been identified in a few algal species. Previous research indicates that the alga, Chattonella subsalsa, possesses a novel NR, NR2-2/2HbN (NR2), which incorporates a 2/2 hemoglobin domain. A second NR (NR3) in C. subsalsa lacks the cytochrome b5 (heme-Fe) domain but includes a putative binding motif for 14-3-3 proteins. The expression of NR2 and NR3 genes indicates that NR2 transcript abundance was regulated by light, nitrogen source, and temperature, while NR3 transcript levels were only regulated by light. Here, we measured total NR activity in C. subsalsa and the potential for regulation of NR activity by putative 14-3-3 binding proteins. Results indicate that NR activity in C. subsalsa was regulated by light, nitrogen source, and temperature at the translational level. NR activity was also regulated by endogenous rhythm and temperature at the post-translational level, supporting the hypothesis that NR3 is regulated by 14-3-3 binding proteins. Together with a previous report describing the regulation of NR gene expression in C. subsalsa, results suggest that C. subsalsa responds to environmental conditions by differential regulation of NRs at transcriptional, translational, and post-translational levels. This flexibility may provide a competitive advantage for this species in the environment. To date, this is the first report which provides evidence for the potential post-translational regulation of NR by 14-3-3 proteins in algal species and suggests that regulatory mechanisms for NR activity may be shared between plants and some algal species.

Nitrous Oxide Emissions from Nitrite Are Highly Dependent on Nitrate Reductase in the Microalga Chlamydomonas reinhardtii

Nitrous oxide (N₂O) is a powerful greenhouse gas and an ozone-depleting compound whose synthesis and release have traditionally been ascribed to bacteria and fungi. Although plants and microalgae have been proposed as N₂O producers in recent decades, the proteins involved in this process have been only recently unveiled. In the green microalga Chlamydomonas reinhardtii, flavodiiron proteins (FLVs) and cytochrome P450 (CYP55) are two nitric oxide (NO) reductases responsible for N₂O synthesis in the chloroplast and mitochondria, respectively. However, the molecular mechanisms feeding these NO reductases are unknown. In this work, we use cavity ring-down spectroscopy to monitor N₂O and CO₂ in cultures of nitrite reductase mutants, which cannot grow on nitrate or nitrite and exhibit enhanced N₂O emissions. We show that these mutants constitute a very useful tool to study the rates and kinetics of N₂O release under different conditions and the metabolism of this greenhouse gas. Our results indicate that N₂O production, which was higher in the light than in the dark, requires nitrate reductase as the major provider of NO as substrate. Finally, we show that the presence of nitrate reductase impacts CO₂ emissions in both light and dark conditions, and we discuss the role of NO in the balance between CO₂ fixation and release.

Algae biofertilisers promote sustainable food production and a circular nutrient economy - An integrated empirical-modelling study

Agriculture has radically changed the global nitrogen (N) cycle and is heavily dependent on synthetic N-fertiliser. However, the N-use efficiency of synthetic fertilisers is often only 50% with N-losses from crop systems polluting the biosphere, hydrosphere and atmosphere. To address the large carbon and energy footprint of N-fertiliser synthesis and curb N-pollution, new technologies are required to deliver enhanced energy efficiency, decarbonisation and a circular nutrient economy. Algae fertilisers (AF) are an alternative to synthetic N-fertiliser (SF). Here microalgae were used as biofertiliser for spinach production. AF production was evaluated using life-cycle analyses. Over 4 weeks, AF released 63.5% of N as bioavailable ammonium and nitrate, and 25% of phosphorous (P) as phosphate to the growth substrate; SF released 100% N and 20% P. To maximise crop N-use and minimise N-leaching, we explored AF and SF dose-response-curves with spinach in glasshouse conditions. AF-grown spinach produced 36% less biomass than SF-grown plants due to AF's slower and linear N-release; SF exhibited 5-times higher N-leaching than AF. Optimised AF:SF blends yielded greater synchrony between N-release and crop-uptake, boosting crop yields and minimising N-loss. Additional benefits of AF included greener leaves, lower leaf nitrate concentration, and higher microbial diversity and water holding capacity of the growth substrate. An integrated techno-economic and life-cycle-analysis of scaled-up microalgae systems (+/- wastewater) normalised to the application dose showed that replacing the most effective SF-dose with AF lowered the annual carbon footprint of fertiliser production from 3.644 kg CO₂ m^-2 (C-producing) to -6.039 kg CO₂ m^-2 (C-assimilation). N-loss from growth substrate was lowered by 54%. Embodied energy for AF:SF blends could be reduced by 29% when cultivating microalgae on wastewater. Conclusions: (i) microalgae offer a sustainable alternative to synthetic N-fertiliser for spinach production and potentially other crop systems, (ii) microalgae biofertilisers support the circular-nutrient-economy and several UN-Sustainable-Development-Goals.

Assessment of Nitrate Removal Capacity of Two Selected Eukaryotic Green Microalgae

Eutrophication is a leading problem in water bodies all around the world in which nitrate is one of the major contributors. The present study was conducted to study the effects of various concentrations of nitrate on two eukaryotic green microalgae, Chlamydomonas sp. MACC-216 and Chlorella sp. MACC-360. For this purpose, both microalgae were grown in a modified tris-acetate-phosphate medium (TAP-M) with three different concentrations of sodium nitrate, i.e., 5 mM (TAP-M5), 10 mM (TAP-M10) and 15 mM (TAP-M15), for 6 days and it was observed that both microalgae were able to remove nitrate completely from the TAP-M5 medium. Total amount of pigments decreased with the increasing concentration of nitrate, whereas protein and carbohydrate contents remained unaffected. High nitrate concentration (15 mM) led to an increase in lipids in Chlamydomonas sp. MACC-216, but not in Chlorella sp. MACC-360. Furthermore, Chlamydomonas sp. MACC-216 and Chlorella sp. MACC-360 were cultivated for 6 days in synthetic wastewater (SWW) with varying concentrations of nitrate where both microalgae grew well and showed an adequate nitrate removal capacity.

Special Issue Editorial: Plant Nitrogen Assimilation and Metabolism

Nitrogen is an important macronutrient for plant growth and development. Research has long been carried out to elucidate the mechanisms involved in nitrogen uptake, assimilation, and utilization in plants. However, despite recent advances, many of these mechanisms still are not fully understood. In this special issue, several research articles and two reviews, all of them aiming to elucidate some specific aspects of nitrogen (N) metabolism, are presented. Together, the articles in this issue provide a state-of-the-art perspective on important questions related to nitrogen metabolism in photosynthetic organisms, highlighting the fundamental importance of research in this field.

Control of distal lysine coordination in a monomeric hemoglobin: A role for heme peripheral interactions

THB1 is a monomeric truncated hemoglobin (TrHb) found in the cytoplasm of the green alga Chlamydomonas reinhardtii. The canonical heme coordination scheme in hemoglobins is a proximal histidine ligand and an open distal site. In THB1, the latter site is occupied by Lys53, which is likely to facilitate Fe(II)/Fe(III) redox cycling but hinders dioxygen binding, two features inherent to the NO dioxygenase activity of the protein. TrHb surveys show that a lysine at a position aligning with Lys53 is an insufficient determinant of coordination, and in this study, we sought to identify factors controlling lysine affinity for the heme iron. We solved the "Lys-off" X-ray structure of THB1, represented by the cyanide adduct of the Fe(III) protein, and hypothesized that interactions that differ between the known "Lys-on" structure and the Lys-off structure participate in the control of Lys53 affinity for the heme iron. We applied an experimental approach (site-directed mutagenesis, heme modification, pH titrations in the Fe(III) and Fe(II) states) and a computational approach (MD simulations in the Fe(II) state) to assess the role of heme propionate-protein interactions, distal helix capping, and the composition of the distal pocket. All THB1 modifications resulted in a weakening of lysine affinity and affected the coupling between Lys53 proton binding and heme redox potential. The results supported the importance of specific heme peripheral interactions for the pH stability of iron coordination and the ability of the protein to undergo redox reactions.