Nitrate assimilation in Chlamydomonas

Enhanced Marine VOC Emissions Driven by Terrestrial Nutrient Inputs and Their Impact on Urban Air Quality in Coastal Regions

Global ocean significantly contributes to atmospheric volatile organic compounds (VOCs), yet the characteristics, drivers, and impacts of marine VOC emissions on coastal air quality remain poorly understood due to limited marine-terrestrial data integration. Therefore, we conducted a study in the East China Sea─a region with high VOC emission potential─and a nearby coastal city in the Yangtze River Delta─a background receptor site. Seawater VOC emissions showed marked spatial variability, with alkenes forming an important component. Terrestrial inorganic nutrient inputs boosted marine primary productivity, elevating VOC concentrations and emissions. Interestingly, in the coastal city, severe photochemical pollution occurred when air masses originated predominantly from the sea. Although maritime air masses contained fewer VOCs, emissions from high-productivity seawater and shipping increased reactive alkene levels. Additionally, higher temperatures, stronger solar radiation, and reduced NO titration effects over the sea facilitated ozone formation. By integrating marine-terrestrial observations, this study underscores the impact of pollutant emissions from high-productivity seas on coastal air quality, particularly through secondary formation during long-range transport. The link between coastal seawater eutrophication and air photochemical pollution emphasizes the need for coordinated air and water pollution control in coastal cities. These findings may apply to other similar coastal environments worldwide.

Nitrogen removal performance and the biocenosis with microalgae consortium Nitrosifying and anammox bacteria in an upflow reactor

This study introduced an innovative pathway utilizing an algal anaerobic ammonium oxidation (ALGAMMOX) system to treat ammonium wastewater. Lake bottom sludge and anammox sludge were used to cultivate functional microorganisms and microalgae for nitrogen removal in an upflow reactor made of transparent materials. The results showed that the ALGAMMOX system achieved 87.40 % nitrogen removal when the influent NH4 +-N concentration was 100 mg-N/L. Further analysis showed that anammox bacteria Candidatus Brocadia (8.87 %) and nitrosobacteria Nitrosomonas (3.74 %) were crucial contributors, playing essential roles in nitrogen removal. The 16S rRNA gene showed that the anammox bacteria in the sludge transitioned from Candidatus Kuenenia to Candidatus Brocadia. The 18S rRNA gene revealed that Chlamydomonas, Bacillariaceae and Pinnularia were the dominant microalgae in the system at a relative abundance of 7.99 %, 3.64 % and 3.14 %, respectively. This novel approach provides a theoretical foundation for ammonium wastewater treatment.

Exploring nutrient removal mechanisms in column-type SBR with simultaneous nitrification and denitrification

A comprehensive investigation utilized a column-type sequencing batch reactor (SBR) to efficiently remove nutrients throughout various phases of its operational cycle by forming granules. This study assessed the influence and mechanisms of a simultaneous nitrification and denitrification (SND) system employing a column-type sequential batch reactor (SBR). The primary focus was on elucidating the functional groups involved in nitrogen transformation and removal within the extracellular polymeric substances (EPS). The research findings demonstrate the superior performance of the SBR process compared to the control group. It achieved an impressive SND efficiency of 69%, resulting in a remarkable 66% total nitrogen removal. Furthermore, a detailed analysis unveiled that the SBR process had a beneficial impact on the composition and properties of EPS. This impact was observed through increased EPS content and enhanced capacity to transport, convert, and retain nitrogen effectively. Additionally, after initial acclimatization, the SBR process showed its effectiveness in removing nutrients (88-98%) and COD (93%) from the generated wastewater within a hydraulic retention time (HRT) of 6 h. A statistically significant difference between the treatments for the investigated mixing ratios was found by univariate analysis of variance (ANOVA). Machine learning (CatBoost model) was employed to understand each parameter's relationship and predict the outcomes in measurable quantity. The findings of the SBR trials showed that the concentration of generated wastewater and the HRT impacted the treatment efficiency. However, the effluent may still need other physicochemical processes, such as membrane filtering, coagulation, electrocoagulation, etc., as post-treatment options, even though COD, nutrients, and turbidity have been entirely or significantly effectively removed. Overall, this work offers insightful information on the critical function of the SBR bacterial community in promoting SND.

Horizontally Acquired Nitrate Reductase Realized Kleptoplastic Photoautotrophy of Rapaza viridis

While photoautotrophic organisms utilize inorganic nitrogen as the nitrogen source, heterotrophic organisms utilize organic nitrogen and thus do not generally have an inorganic nitrogen assimilation pathway. Here, we focused on the nitrogen metabolism of Rapaza viridis, a unicellular eukaryote exhibiting kleptoplasty. Although belonging to the lineage of essentially heterotrophic flagellates, R. viridis exploits the photosynthetic products of the kleptoplasts and was therefore suspected to potentially utilize inorganic nitrogen. From the transcriptome data of R. viridis, we identified gene RvNaRL, which had sequence similarity to genes encoding nitrate reductases in plants. Phylogenetic analysis revealed that RvNaRL was acquired by a horizontal gene transfer event. To verify the function of the protein product RvNaRL, we established RNAi-mediated knock-down and CRISPR-Cas9-mediated knock-out experiments for the first time in R. viridis and applied them to this gene. The RvNaRL knock-down and knock-out cells exhibited significant growth only when ammonium was supplied. However, in contrast to the wild-type cells, no substantial growth was observed when nitrate was supplied. Such arrested growth in the absence of ammonium was attributed to impaired amino acid synthesis due to the deficiency of nitrogen supply from the nitrate assimilation pathway; this in turn resulted in the accumulation of excess photosynthetic products in the form of cytosolic polysaccharide grains, as observed. These results indicate that RvNaRL is certainly involved in nitrate assimilation by R. viridis. Thus, we inferred that R. viridis achieved its advanced kleptoplasty for photoautotrophy, owing to the acquisition of nitrate assimilation via horizontal gene transfer.

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".

Enhanced growth performance of abi5 plants under high salt and nitrate is associated with reduced nitric oxide levels

Numerous environmental stresses have a significant impact on plant growth and development. By 2050, it is anticipated that high salinity will destroy more than fifty percent of the world's agricultural land. Understanding how plants react to the excessive use of nitrogen fertilizers and salt stress is crucial for enhancing crop yield. However, the effect of excessive nitrate treatment on plant development is disputed and poorly understood; so, we evaluated the effect of excessive nitrate supply and high salinity on abi5 plant growth performance. We demonstrated that abi5 plants are tolerant to the harmful environmental conditions of excessive nitrate and salt. abi5 plants have lower amounts of endogenous nitric oxide than Arabidopsis thaliana Columbia-0 plants due to their decreased nitrate reductase activity, caused by a decrease in the transcript level of NIA2, a gene encoding nitrate reductase. Nitric oxide appeared to have a critical role in reducing the salt stress tolerance of plants, which was diminished by an excess of nitrate. Discovering regulators such as ABI5 that can modulate nitrate reductase activity and comprehending the molecular activities of these regulators are crucial for the application of gene-editing techniques. This would result in the appropriate buildup of nitric oxide to increase the production of crops subjected to a variety of environmental stresses.

Changes in the prokaryotic diversity in response to hydrochemical variations during an acid mine drainage passive treatment

Acid mine drainage (AMD) causes major environmental problems and consequently, several treatments are proposed, favoring the passive systems because of their many advantages. The main goal of these procedures is the neutralization and removal of potentially toxic elements (PTE), yet little is known about the changes in the microbial assemblages in response to the hydrochemical variations during the treatments. Therefore, the main objective of this research was to determine the changes in the diversity and structure of the prokaryotic assemblages in a hybrid abiotic and biological (wetland) passive treatment system. The 16S rRNA gene survey showed that the AMD coming from the mine (pH 2.6) was mainly composed of acidophilic genera such as Acidithiobacillus, Leptospirillum, Ferritrophicum, and Cuniculiplasma (up to 76 % relative abundance). In the abiotic treatment, Acidiphilium was dominant in the sections with limestone filters (pH 2.2-4.8), followed by Limnobacter in the subsequent dolomite/limestone and phosphoric rock filters (pH 5.2-5.8). In these abiotic passive treatment sections, the microbial assemblage showed a limited diversity and richness. However, when the treated AMD reached the two final wetlands (pH ~6.8), the microbial diversity and richness increased, suggesting that further bioattenuation mechanisms might be occurring. Limnobacter and Novosphingobium were the main bacterial genera in the water samples of the wetland sections (Arundo donax). These changes in the composition of the microbial assemblages were highly correlated with the pH and Eh values during the treatment (p-value <0.001); however, the concentration of metal(loid)s such as Al, Cd, Fe, Mn, Ni, and Zn were also significantly related (p-value <0.05). In conclusion, the studied passive AMD treatment system enhanced the chemical quality of the treated AMD, showing high removal efficiencies for Al and Fe (> 99 %), and increasing the microbial diversity and richness in the effluent.

Advanced pathway engineering for phototrophic putrescine production

The polyamine putrescine (1,4-diaminobutane) contributes to cellular fitness in most organisms, where it is derived from the amino acids ornithine or arginine. In the chemical industry, putrescine serves as a versatile building block for polyamide synthesis. The green microalga Chlamydomonas reinhardtii accumulates relatively high putrescine amounts, which, together with recent advances in genetic engineering, enables the generation of a powerful green cell factory to promote sustainable biotechnology for base chemical production. Here, we report a systematic investigation of the native putrescine metabolism in C. reinhardtii, leading to the first CO₂ -based bio-production of putrescine, by employing modern synthetic biology and metabolic engineering strategies. A CRISPR/Cas9-based knockout of key enzymes of the polyamine biosynthesis pathway identified ornithine decarboxylase 1 (ODC1) as a gatekeeper for putrescine accumulation and demonstrated that the arginine decarboxylase (ADC) route is likely inactive and that amine oxidase 2 (AMX2) is mainly responsible for putrescine degradation in C. reinhardtii. A 4.5-fold increase in cellular putrescine levels was achieved by engineered overexpression of potent candidate ornithine decarboxylases (ODCs). We identified unexpected substrate promiscuity in two bacterial ODCs, which exhibited co-production of cadaverine and 4-aminobutanol. Final pathway engineering included overexpression of recombinant arginases for improved substrate availability as well as functional knockout of putrescine degradation, which resulted in a 10-fold increase in cellular putrescine titres and yielded 200 mg/L in phototrophic high cell density cultivations after 10 days.

A mechanistic study of the influence of nitrogen and energy availability on the NH4+ sensitivity of nitrogen assimilation in Synechococcus

In most algae, NO3- assimilation is tightly controlled and is often inhibited by the presence of NH4+. In the marine, non-colonial, non-diazotrophic cyanobacterium Synechococcus UTEX 2380, NO3- assimilation is sensitive to NH4+ only when N does not limit growth. We sequenced the genome of Synechococcus UTEX 2380, studied the genetic organization of the nitrate assimilation related (NAR) genes, and investigated expression and kinetics of the main NAR enzymes, under N or light limitation. We found that Synechococcus UTEX 2380 is a β-cyanobacterium with a full complement of N uptake and assimilation genes and NAR regulatory elements. The nitrate reductase of our strain showed biphasic kinetics, previously observed only in freshwater or soil diazotrophic Synechococcus strains. Nitrite reductase and glutamine synthetase showed little response to our growth treatments, and their activity was usually much higher than that of nitrate reductase. NH4+ insensitivity of NAR genes may be associated with the stimulation of the binding of the regulator NtcA to NAR gene promoters by the high 2-oxoglutarate concentrations produced under N limitation. NH4+ sensitivity in energy-limited cells fits with the fact that, under these conditions, the use of NH4+ rather than NO3- decreases N-assimilation cost, whereas it would exacerbate N shortage under N limitation.

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.

RNA-seq analysis reveals genes related to photosynthetic carbon partitioning and lipid production in Phaeodactylum tricornutum under alkaline conditions

Alkaline pH can induce triacylglyceride accumulation in microalgae, however its molecular mechanism remains elusive. Here, we investigated the effect of 2-[N-cyclohexylamino]-ethane-sulfonic acid (CHES) -induced intracellular alkalization on the lipid production in Phaeodactylum tricornutum. Intracellular pH was increased upon CHES treatment, displaying a high BCECF fluorescence ratio. CHES treatment significantly induced lipid accumulation but had no change in cell density and biomass. The expression of genes involved in photoreaction, carbon fixation, glycolysis, pentose phosphate pathway, amino acid catabolism, GS/GOGAT cycle, TCA cycle, triacylglyceride assembly, de novo fatty acid synthesis were up-regulated, while that in amino acid biosynthesis were down-regulated under CHES conditions. Correspondingly, the activity of phosphoribulokinase, carbonic anhydrase, pyruvate dehydrogenase and acetaldehyde dehydrogenase were enhanced by CHES treatment. Chloroplast-specific biological processes were activated by CHES treatment in P. tricornutum, which redirects the flux of carbon into lipid biosynthesis, meanwhile stimulates de novo fatty acid biosynthesis, leading to lipid accumulation under CHES conditions. These indicate an enhancement of intermediate metabolism, resulting in lipid accumulation by CHES.

RWP-RK domain-containing transcription factors in the Viridiplantae: biology and phylogenetic relationships

The RWP-RK protein family is a group of transcription factors containing the RWP-RK DNA-binding domain. This domain is an ancient motif that emerged before the establishment of the Viridiplantae-the green plants, consisting of green algae and land plants. The domain is mostly absent in other kingdoms but widely distributed in Viridiplantae. In green algae, a liverwort, and several angiosperms, RWP-RK proteins play essential roles in nitrogen responses and sexual reproduction-associated processes, which are seemingly unrelated phenomena but possibly interdependent in autotrophs. Consistent with related but diversified roles of the RWP-RK proteins in these organisms, the RWP-RK protein family appears to have expanded intensively, but independently, in the algal and land plant lineages. Thus, bryophyte RWP-RK proteins occupy a unique position in the evolutionary process of establishing the RWP-RK protein family. In this review, we summarize current knowledge of the RWP-RK protein family in the Viridiplantae, and discuss the significance of bryophyte RWP-RK proteins in clarifying the relationship between diversification in the RWP-RK protein family and procurement of sophisticated mechanisms for adaptation to the terrestrial environment.

Transcriptome Profiling in the Marine Red Alga Neopyropia yezoensis Under Light/Dark Cycle

Many organisms are subjected to a daily cycle of light and darkness, which significantly influences metabolic and physiological processes. In the present study, Neopyropia yezoensis, one of the major cultivated seaweeds used in "nori," was harvested in the morning and evening during light/dark treatments to investigate daily changes in gene expression using RNA-sequencing. A high abundance of transcripts in the morning includes the genes associated with carbon-nitrogen assimilations, polyunsaturated fatty acid, and starch synthesis. In contrast, the upregulation of a subset of the genes associated with the pentose phosphate pathway, cell cycle, and DNA replication at evening is necessary for the tight control of light-sensitive processes, such as DNA replication. Additionally, a high abundance of transcripts at dusk encoding asparaginase and glutamate dehydrogenase imply that regulation of asparagine catabolism and tricarboxylic acid cycle possibly contributes to supply nitrogen and carbon, respectively, for growth during the dark. In addition, genes encoding cryptochrome/photolyase family and histone modification proteins were identified as potential key players for regulating diurnal rhythmic genes.

Optimal Nitrate Supplementation in Phaeodactylum tricornutum Culture Medium Increases Biomass and Fucoxanthin Production

Phaeodactylum tricornutum is a model diatom with numerous potential applications in the industry, including the production of high-value carotenoid pigments such as fucoxanthin. This compound is a potent antioxidant currently extracted mainly from brown macroalgae. Fucoxanthin exhibits several biological properties with well-known beneficial effects in the treatment and prevention of lifestyle-related diseases. P. tricornutum offers a valuable alternative to macroalgae for fucoxanthin production as it has a specific productivity that is 10-fold higher as compared with macroalgae. However, production processes still need to be optimised to become a cost-effective alternative. In this work, we investigated the optimal supplementation of nitrate in a cultivation medium that is currently used for P. tricornutum and how this nitrate concentration affects cell growth and fucoxanthin production. It has previously been shown that the addition of sodium nitrate increases productivity, but optimal conditions were not accurately determined. In this report, we observed that the continuous increase in nitrate concentration did not lead to an increase in biomass and fucoxanthin content, but there was rather a window of optimal values of nitrate that led to maximum growth and pigment production. These results are discussed considering both the scale up for industrial production and the profitability of the process, as well as the implications in the cell’s metabolism and effects in fucoxanthin production.

Phylogenomic and Microsynteny Analysis Provides Evidence of Genome Arrangements of High-Affinity Nitrate Transporter Gene Families of Plants

Nitrate transporter 2 (NRT2) and NRT3 or nitrate-assimilation-related 2 (NAR2) proteins families form a two-component, high-affinity nitrate transport system, which is essential for the acquisition of nitrate from soils with low N availability. An extensive phylogenomic analysis across land plants for these families has not been performed. In this study, we performed a microsynteny and orthology analysis on the NRT2 and NRT3 genes families across 132 plants (Sensu lato) to decipher their evolutionary history. We identified significant differences in the number of sequences per taxonomic group and different genomic contexts within the NRT2 family that might have contributed to N acquisition by the plants. We hypothesized that the greater losses of NRT2 sequences correlate with specialized ecological adaptations, such as aquatic, epiphytic, and carnivory lifestyles. We also detected expansion on the NRT2 family in specific lineages that could be a source of key innovations for colonizing contrasting niches in N availability. Microsyntenic analysis on NRT3 family showed a deep conservation on land plants, suggesting a high evolutionary constraint to preserve their function. Our study provides novel information that could be used as guide for functional characterization of these gene families across plant lineages.

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.

The potential of foodwaste leachate as a phycoremediation substrate for microalgal CO2 fixation and biodiesel production

Foodwaste leachate (FWL) is often generated during foodwaste treatment processes. Owing to its high nutrient content, FWL has high potential for phycoremediation, a microalgal technology application for water treatment while acting as CO₂ fixation tank. Additionally, the end product of microalgal from phycoremediation can be potentially used for biodiesel production. Therefore, the phycoremediation has drawn a lot of attention in recent decades. This study evaluates the performance of microalgal foodwaste leachate treatment and the potential of utilizing FWL as medium for microalgal biodiesel production. Two microalgal species, Dunaliella tertiolecta and Cyanobacterium aponinum, were selected. For each species, two experimental levels of diluted FWL were used: 5 and 10% FWL. The partial inhibition growth model indicates that some inhibit factors such as ammonia; total suspended solids and oil and grease (O&G) content suppress the microalgal growth. Most of the nutrient such as nitrogen and phosphorus (> 80%) can be removed in the last day of phycoremediation by D. tertiolecta. C. aponinum also show considerable removal rate on total nitrogen ammonia and nitrate (> 60%). Biomass (0.4-0.5 g/L/day) of D. tertiolecta and C. aponinum can be produced though cultivated in diluted FWL. The bio-CO₂ fixation rates of the two species were 610.7 and 578.3 mg/L/day of D. tertiolecta and C. aponinum. The strains contain high content of saturated fatty acid such as C₁₆ and C₁₈ making them having potential for producing good quality biodiesel.

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.

Swine digestate treatment by prior nitrogen-starved Chlorella vulgaris: The effect of over-compensation strategy on microalgal biomass production and nutrient removal

Anaerobic digester effluent containing high levels of ammonia poses a threat to the environment. To hinder this issue, a modern and promising treatment method incorporates both microalgae and their bioconversion potential. When culturing Chlorella vulgaris at a 1:7 digestate supernatant dilution ratio, biomass concentration was 1.33 g L^-1 and 66% of ammonia nitrogen was removed. Furthermore, a prior nitrogen-starved seed method, namely over-compensation strategy, was applied to improve both biomass production and nutrient removal. By using nitrogen-starved seeds after a 48 h nitrogen-free stimulation, biomass yield increased by 1.7-times to 2.56 g L^-1. Simultaneously, ammonia nitrogen and total phosphorus removal efficiencies reached 99% and 97% respectively. The enhanced production corresponds to higher chlorophyll fluorescence in the middle and late stages of the culture. In addition, the bioproduct contained 39% carbohydrates, and the proportion of polyunsaturated fatty acids in lipids was 66%. These findings demonstrated that the over-compensation strategy contributed to greater nitrogen removal and high-value bioproduct production in the microalgae-digestate treatment system.

High cell density cultivation enables efficient and sustainable recombinant polyamine production in the microalga Chlamydomonas reinhardtii

Modern chemical industry calls for new resource-efficient and sustainable value chains for production of key base chemicals such as polyamines. The green microalga Chlamydomonas reinhardtii offers great potential as an innovative green-cell factory by combining fast and inexpensive, phototrophic growth with mature genetic engineering. Here, overexpression of recombinant lysine decarboxylases in C. reinhardtii enabled the robust accumulation of the non-native polyamine cadaverine, which serves as building block for bio-polyamides. The issue of low cell densities, limiting most microalgal cultivation processes was resolved by systematically optimizing cultivation parameters. A new, easy-to-apply and fully phototrophic medium enables high cell density cultivations of C. reinhardtii with a 6-fold increase in biomass and cell count (20 g/L biomass dry weight, ~2·10⁸ cells/mL). Application of high cell density cultivations in established photobioreactors resulted in a 10-fold increase of cadaverine yields, with up to 0.24 g/L after 9 days and maximal productivity of 0.1 g/L/d.

Phosphate or nitrate imbalance induces stronger molecular responses than combined nutrient deprivation in roots and leaves of chickpea plants

The negative effects of phosphate (Pi) and/or nitrate (NO₃^- ) fertilizers on the environment have raised an urgent need to develop crop varieties with higher Pi and/or nitrogen use efficiencies for cultivation in low-fertility soils. Achieving this goal depends upon research that focuses on the identification of genes involved in plant responses to Pi and/or NO₃^- starvation. Although plant responses to individual deficiency in either Pi (-Pi/+NO₃^- ) or NO₃^- (+Pi/-NO₃^- ) have been separately studied, our understanding of plant responses to combined Pi and NO₃^- deficiency (-Pi/-NO₃^- ) is still very limited. Using RNA-sequencing approach, transcriptome changes in the roots and leaves of chickpea cultivated under -Pi/+NO₃^- , +Pi/-NO₃^- or -Pi/-NO₃^- conditions were investigated in a comparative manner. -Pi/-NO₃^- treatment displayed lesser effect on expression changes of genes related to Pi or NO₃^- transport, signalling networks, lipid remodelling, nitrogen and Pi scavenging/remobilization/recycling, carbon metabolism and hormone metabolism than -Pi/+NO₃^- or +Pi/-NO₃^- treatments. Therefore, the plant response to -Pi/-NO₃^- is not simply an additive result of plant responses to -Pi/+NO₃^- and +Pi/-NO₃^- treatments. Our results indicate that nutrient imbalance is a stronger stimulus for molecular reprogramming than an overall deficiency.

A marine Chlamydomonas sp. emerging as an algal model

The freshwater microalga Chlamydomonas reinhardtii, which lives in wet soil, has served for decades as a model for numerous biological processes, and many tools have been introduced for this organism. Here, we have established a stable nuclear transformation for its marine counterpart, Chlamydomonas sp. SAG25.89, by fusing specific cis-acting elements from its Actin gene with the gene providing hygromycin resistance and using an elaborated electroporation protocol. Like C. reinhardtii, Chlamydomonas sp. has a high GC content, allowing reporter genes and selection markers to be applicable in both organisms. Chlamydomonas sp. grows purely photoautotrophically and requires ammonia as a nitrogen source because its nuclear genome lacks some of the genes required for nitrogen metabolism. Interestingly, it can grow well under both low and very high salinities (up to 50 g · L^-1 ) rendering it as a model for osmotolerance. We further show that Chlamydomonas sp. grows well from 15 to 28°C, but halts its growth at 32°C. The genome of Chlamydomonas sp. contains some gene homologs the expression of which is regulated according to the ambient temperatures and/or confer thermal acclimation in C. reinhardtii. Thus, knowledge of temperature acclimation can now be compared to the marine species. Furthermore, Chlamydomonas sp. can serve as a model for studying marine microbial interactions and for comparing mechanisms in freshwater and marine environments. Chlamydomonas sp. was previously shown to be immobilized rapidly by a cyclic lipopeptide secreted from the antagonistic bacterium Pseudomonas protegens PF-5, which deflagellates C. reinhardtii.

Nitrate-N-mediated toxicological responses of Scenedesmus acutus and Daphnia pulex to cadmium, arsenic and their binary mixture (Cd/Asmix) at environmentally relevant concentrations

Several biomarkers used for ecological risk assessment have been established for single contaminant toxicity, many of which are less predictive of the influence of media and/or dietary nutrients on toxicity outcomes of contaminant mixtures. In this study, we investigate toxicological responses and life traits of Scenedesmus acutus and Daphnia pulex to heavy metals (cadmium-Cd, arsenic-As, binary mixture-Cd/As_mix) in media and diets with varied nutrient (nitrate-N) conditions (low-LN, median-MN, optimum-COMBO). Results showed that nitrate-N-mediated metal inhibitory effects on growth and productivity of primary producer (S. acutus) were significantly interactive (p < 0.05; effect size, ƞ²≤56 %). Cadmium toxicities (Cd-IC₅₀s) in S. acutus were 1.2×, 5.3×, and 4.3× As-IC₅₀s in LN, MN and COMBO media, respectively, while mixture (Cd/As_mix) toxicities were synergistic in MN medium and partial additivity in COMBO and LN media. Nitrate-N and metal exposure effects on S. acutus nutrient stoichiometry, metal uptake and bioaccumulation were significantly interactive (p < 0.05, ƞ²≤100 %). Moreover, survival of primary consumer (D. pulex) was significantly impaired by single and mixed dietary-metal exposures with greater effect under LN condition coupled with significant interactive effects on reproductive capacity (p < 0.05, ƞ²≤21.2 %) but not on swimming activity. We recommend that nitrate-N-mediated metal exposure effects/toxicity in bioindicator species should be considered during ecological risk assessments.

The Cryptic Plastid of Euglena longa Defines a New Type of Nonphotosynthetic Plastid Organelle

Most secondary nonphotosynthetic eukaryotes have retained residual plastids whose physiological role is often still unknown. One such example is Euglena longa, a close nonphotosynthetic relative of Euglena gracilis harboring a plastid organelle of enigmatic function. By mining transcriptome data from E. longa, we finally provide an overview of metabolic processes localized to its elusive plastid. The organelle plays no role in the biosynthesis of isoprenoid precursors and fatty acids and has a very limited repertoire of pathways concerning nitrogen-containing metabolites. In contrast, the synthesis of phospholipids and glycolipids has been preserved, curiously with the last step of sulfoquinovosyldiacylglycerol synthesis being catalyzed by the SqdX form of an enzyme so far known only from bacteria. Notably, we show that the E. longa plastid synthesizes tocopherols and a phylloquinone derivative, the first such report for nonphotosynthetic plastids studied so far. The most striking attribute of the organelle could be the presence of a linearized Calvin-Benson (CB) pathway, including RuBisCO yet lacking the gluconeogenetic part of the standard cycle, together with ferredoxin-NADP⁺ reductase (FNR) and the ferredoxin/thioredoxin system. We hypothesize that the ferredoxin/thioredoxin system activates the linear CB pathway in response to the redox status of the E. longa cell and speculate on the role of the pathway in keeping the redox balance of the cell. Altogether, the E. longa plastid defines a new class of relic plastids that is drastically different from the best-studied organelle of this category, the apicoplast.IMPORTANCE Colorless plastids incapable of photosynthesis evolved in many plant and algal groups, but what functions they perform is still unknown in many cases. Here, we study the elusive plastid of Euglena longa, a nonphotosynthetic cousin of the familiar green flagellate Euglena gracilis We document an unprecedented combination of metabolic functions that the E. longa plastid exhibits in comparison with previously characterized nonphotosynthetic plastids. For example, and truly surprisingly, it has retained the synthesis of tocopherols (vitamin E) and a phylloquinone (vitamin K) derivative. In addition, we offer a possible solution of the long-standing conundrum of the presence of the CO₂-fixing enzyme RuBisCO in E. longa Our work provides a detailed account on a unique variant of relic plastids, the first among nonphotosynthetic plastids that evolved by secondary endosymbiosis from a green algal ancestor, and suggests that it has persisted for reasons not previously considered in relation to nonphotosynthetic plastids.

Chlamydomonas reinhardtii, an Algal Model in the Nitrogen Cycle

Nitrogen (N) is an essential constituent of all living organisms and the main limiting macronutrient. Even when dinitrogen gas is the most abundant form of N, it can only be used by fixing bacteria but is inaccessible to most organisms, algae among them. Algae preferentially use ammonium (NH₄⁺) and nitrate (NO₃⁻) for growth, and the reactions for their conversion into amino acids (N assimilation) constitute an important part of the nitrogen cycle by primary producers. Recently, it was claimed that algae are also involved in denitrification, because of the production of nitric oxide (NO), a signal molecule, which is also a substrate of NO reductases to produce nitrous oxide (N₂O), a potent greenhouse gas. This review is focused on the microalga Chlamydomonas reinhardtii as an algal model and its participation in different reactions of the N cycle. Emphasis will be paid to new actors, such as putative genes involved in NO and N₂O production and their occurrence in other algae genomes. Furthermore, algae/bacteria mutualism will be considered in terms of expanding the N cycle to ammonification and N fixation, which are based on the exchange of carbon and nitrogen between the two organisms.

Hypolimnetic assimilation of ammonium by the nuisance alga Gonyostomum semen

Gonyostomum semen is a bloom-forming freshwater raphidophyte that is currently on the increase, which concerns water managers and ecologists alike. Much indicates that the recent success of G. semen is linked to its diel vertical migration (DVM), which helps to overcome the spatial separation of optimal light conditions for photosynthesis at the surface of a lake and the high concentration of phosphate in the hypolimnion. I here present data from a field study conducted in Lake Lundebyvannet (Norway) in 2017-2019 that are consistent with the idea that the DVM of G. semen also allows for a hypolimnetic uptake of ammonium. As expected, microbial mineralization of organic matter in a low-oxygen environment led to an accumulation of ammonium in the hypolimnion as long as G. semen was absent. In contrast, a decreasing or constantly lower concentration of hypolimnetic ammonium was found in presence of a migrating G. semen population. In summer of 2019, a short break in the DVM of G. semen coincided with a rapid accumulation of hypolimnetic ammonium, which was equally rapidly decimated when G. semen resumed its DVM. Taken together, these data support the idea that G. semen can exploit the hypolimnetic pool of ammonium, which may be one reason for the recent success of the species and its significant impact on the structure of the aquatic food web.

Dur3 and nrt2 genes in the bloom-forming dinoflagellate Prorocentrum minimum: Transcriptional responses to available nitrogen sources

The increasing inflow of nitrogen (N) substrates into marine nearshore ecosystems induces proliferation of harmful algal blooms (HABs) of dinoflagellates, such as potentially toxic invasive species Prorocentrum minimum. In this study, we estimated the influence of NO3-, NH4+ and urea on transcription levels and urea transporter dur3 and nitrate transporter nrt2 genes expression in these dinoflagellates. We identified dur3 and nrt2 genes sequences in unannotated transcriptomes of P. minimum and other dinoflagellates presented in MMETSP database. Phylogenetic analysis showed that these genes of dinoflagellates clustered to the distinct clade demonstrating evolutionary relationship with the other known dur3 and nrt2 genes of microalgae. The evaluation of expression levels of dur3 and nrt2 genes by RT-qPCR revealed their sensitivity to input of the studied N sources. Dur3 expression levels were downregulated after the supplementation of additional N sources and were 1.7-2.6-fold lower than in the nitrate-grown culture. Nrt2 expression levels decreased 1.9-fold in the presence of NH4+. We estimated total RNA and DNA synthesis rates by the analysis of incorporation of 3H-thymidine and 3H-uridine in batch and continuous cultures. Addition of N compounds did not affect the DNA synthesis rates. Transcription levels increased up to 12.5-fold after the N supplementation in urea-limited treatments. Investigation of various nitrogen sources as biomarkers of dinoflagellate proliferation due to their differentiated impact on expression of dur3 and nrt2 genes and transcription rates in P. minimum cells allowed concluding about high potential of the studied parameters for future modeling of HABs under global N pollution.

Algal photosynthesis converts nitric oxide into nitrous oxide

Nitrous oxide (N₂O), the third most important greenhouse gas in the atmosphere, is produced in great quantities by microalgae, but molecular mechanisms remain elusive. Here we show that the green microalga Chlamydomonas reinhardtii produces N₂O in the light by a reduction of NO driven by photosynthesis and catalyzed by flavodiiron proteins, the dark N₂O production being catalyzed by a cytochrome p450. Both mechanisms of N₂O production are present in chlorophytes, but absent from diatoms. Our study provides an unprecedented mechanistic understanding of N₂O production by microalgae, allowing a better assessment of N₂O-producing hot spots in aquatic environments.

Nitrous oxide (N₂O), a potent greenhouse gas in the atmosphere, is produced mostly from aquatic ecosystems, to which algae substantially contribute. However, mechanisms of N₂O production by photosynthetic organisms are poorly described. Here we show that the green microalga Chlamydomonas reinhardtii reduces NO into N₂O using the photosynthetic electron transport. Through the study of C. reinhardtii mutants deficient in flavodiiron proteins (FLVs) or in a cytochrome p450 (CYP55), we show that FLVs contribute to NO reduction in the light, while CYP55 operates in the dark. Both pathways are active when NO is produced in vivo during the reduction of nitrites and participate in NO homeostasis. Furthermore, NO reduction by both pathways is restricted to chlorophytes, organisms particularly abundant in ocean N₂O-producing hot spots. Our results provide a mechanistic understanding of N₂O production in eukaryotic phototrophs and represent an important step toward a comprehensive assessment of greenhouse gas emission by aquatic ecosystems.

Role of Nitrate Reductase in NO Production in Photosynthetic Eukaryotes

Nitric oxide is a gaseous secondary messenger that is critical for proper cell signaling and plant survival when exposed to stress. Nitric oxide (NO) synthesis in plants, under standard phototrophic oxygenic conditions, has long been a very controversial issue. A few algal strains contain NO synthase (NOS), which appears to be absent in all other algae and land plants. The experimental data have led to the hypothesis that molybdoenzyme nitrate reductase (NR) is the main enzyme responsible for NO production in most plants. Recently, NR was found to be a necessary partner in a dual system that also includes another molybdoenzyme, which was renamed NO-forming nitrite reductase (NOFNiR). This enzyme produces NO independently of the molybdenum center of NR and depends on the NR electron transport chain from NAD(P)H to heme. Under the circumstances in which NR is not present or active, the existence of another NO-forming system that is similar to the NOS system would account for NO production and NO effects. PII protein, which senses and integrates the signals of the C–N balance in the cell, likely has an important role in organizing cell responses. Here, we critically analyze these topics.

Role of nutrient concentrations and water movement on diatom's productivity in culture

Microalgal growth maximization is becoming a duty for enhancing the biotechnological fate of these photosynthetic microorganisms. This study, based on an extensive set of data, aims to revisit diatom’s cultivation in laboratory with the objective to increase growth rate and biomass production. We investigated the growth ability and resource requirements of the coastal diatom Skeletonema marinoi Sarno & Zingone grown in laboratory in the conventional f/2 medium with aeration and in two modified conditions: (i) the same medium with water movement inside and (ii) an enriched medium with the same water movement. Results revealed that, by doubling the concentration of phosphate, silicate, microelements and vitamins, growth rate was successfully enhanced, preventing phosphate or silicate limitation in the f/2 culture medium. Yet, irrespective of the media (f/2 or enriched one), water movement induced an increase of growth efficiency compared to aeration, affecting nutrients’ requirement and consumption by diatoms. This study is an important step for enhancing diatom biomass production, reducing its cost, as required in the blue biotechnology context.

Dual positive and negative control of Chlamydomonas PII signal transduction protein expression by nitrate/nitrite and NO via the components of nitric oxide cycle

BACKGROUND

The PII proteins constitute a large superfamily, present in all domains of life. Until now, PII proteins research in Chloroplastida (green algae and land plants) has mainly focused on post-translation regulation of these signal transductors. Emerging evidence suggests that PII level is tightly controlled with regard to the nitrogen source and the physiological state of cells.

RESULT

Here we identify that a balance of positive (nitrate and nitrite) and negative (nitric oxide) signals regulates Chlamydomonas GLB1. We found that PII expression is downregulated by ammonium through a nitric oxide (NO)-dependent mechanism. We show that nitrate reductase (NR) and its partner, truncated hemoglobin 1 (THB1), participate in a signaling pathway for dual control of GLB1 expression. Moreover, NO dependent guanilate cyclase appeared to be involved in the negative control of GLB1 transcription.

CONCLUSION

This study has revealed the existence of the complex GLB1 control at transcription level, which is dependent on nitrogen source. Importantly, we found that GLB1 gene expression pattern is very similar to that observed for nitrate assimilation genes, suggesting interconnecting/coordinating PII-dependent and nitrate assimilation pathways.

The biosynthesis of nitrous oxide in the green alga Chlamydomonas reinhardtii

Over the last decades, several studies have reported emissions of nitrous oxide (N₂ O) from microalgal cultures and aquatic ecosystems characterized by a high level of algal activity (e.g. eutrophic lakes). As N₂ O is a potent greenhouse gas and an ozone-depleting pollutant, these findings suggest that large-scale cultivation of microalgae (and possibly, natural eutrophic ecosystems) could have a significant environmental impact. Using the model unicellular microalga Chlamydomonas reinhardtii, this study was conducted to investigate the molecular basis of microalgal N₂ O synthesis. We report that C. reinhardtii supplied with nitrite (NO₂^- ) under aerobic conditions can reduce NO₂^- into nitric oxide (NO) using either a mitochondrial cytochrome c oxidase (COX) or a dual enzymatic system of nitrate reductase (NR) and amidoxime-reducing component, and that NO is subsequently reduced into N₂ O by the enzyme NO reductase (NOR). Based on experimental evidence and published literature, we hypothesize that when nitrate (NO₃^- ) is the main Nitrogen source and the intracellular concentration of NO₂^- is low (i.e. under physiological conditions), microalgal N₂ O synthesis involves the reduction of NO₃^- to NO₂^- by NR followed by the reduction of NO₂^- to NO by the dual system involving NR. This microalgal N₂ O pathway has broad implications for environmental science and algal biology because the pathway of NO₃^- assimilation is conserved among microalgae, and because its regulation may involve NO.

Nitrate concentration-shift cultivation to enhance protein content of heterotrophic microalga Chlorella vulgaris: Over-compensation strategy

Protein production from microalgae requires both high cell density during cultivation and high protein content in cells. Heterotrophic microalgae can achieve high cell density, and yet are confronted with the problem of low protein content. Based on over-compensation strategy, a new concentration-shift method was proposed to cultivate heterotrophic Chlorella vulgaris, aiming to increase protein content. With a prior starvation period, microalgae utilized more nitrate and accumulated more proteins compared to one-stage cultivation. Considering the convenience of operation, nitrate-added culture was adopted for producing heterotrophic microalgae, rather than sterile centrifugal culture. Operating parameters including nitrate concentration in N-deficient medium, N-starved time and nitrate concentration in N-rich medium were optimized, which were 0.18gl^-1, 38h and 2.45gl^-1, respectively. Under the optimized conditions, protein content in heterotrophic Chlorella reached 44.3%. Furthermore, the heterotrophic microalga was suggested to be a potential single-cell protein source according to the amino acid composition.

How Chlamydomonas handles nitrate and the nitric oxide cycle

The green alga Chlamydomonas is a valuable model system capable of assimilating different forms of nitrogen (N). Nitrate (NO3-) has a relevant role in plant-like organisms, first as a nitrogen source for growth and second as a signalling molecule. Several modules are necessary for Chlamydomonas to handle nitrate, including transporters, nitrate reductase (NR), nitrite reductase (NiR), GS/GOGAT enzymes for ammonium assimilation, and regulatory protein(s). Transporters provide a first step for influx/efflux, homeostasis, and sensing of nitrate; and NIT2 is the key transcription factor (RWP-RK) for mediating the nitrate-dependent activation of a number of genes. Here, we review how NR participates in the cycle NO3- →NO2- →NO →NO3-. NR uses the partner protein amidoxime-reducing component/nitric oxide-forming nitrite reductase (ARC/NOFNiR) for the conversion of nitrite (NO2-) into nitric oxide (NO). It also uses the truncated haemoglobin THB1 in the conversion of nitric oxide to nitrate. Nitric oxide is a negative signal for nitrate assimilation; it inhibits the activity and expression of high-affinity nitrate/nitrite transporters and NR. During this cycle, the positive signal of nitrate is transformed into the negative signal of nitric oxide, which can then be converted back into nitrate. Thus, NR is back in the spotlight as a strategic regulator of the nitric oxide cycle and the nitrate assimilation pathway.

Post-translational regulation of nitrogen transporters in plants and microorganisms

For microorganisms and plants, nitrate and ammonium are the main nitrogen sources and they are also important signaling molecules controlling several aspects of metabolism and development. Over the past decade, numerous studies revealed that nitrogen transporters are strongly regulated at the transcriptional level. However, more and more reports are now showing that nitrate and ammonium transporters are also subjected to post-translational regulations in response to nitrogen availability. Phosphorylation is so far the most well studied post-translational modification for these transporters and it affects both the regulation of nitrogen uptake and nitrogen sensing. For example, in Arabidopsis thaliana, phosphorylation was shown to activate the sensing function of the root nitrate transporter NRT1.1 and to switch the transport affinity. Also, for ammonium transporters, a phosphorylation-dependent activation/inactivation mechanism was elucidated in recent years in both plants and microorganisms. However, despite the fact that these regulatory mechanisms are starting to be thoroughly described, the signaling pathways involved and their action on nitrogen transporters remain largely unknown. In this review, we highlight the inorganic nitrogen transporters regulated at the post-translational level and we compare the known mechanisms in plants and microorganisms. We then discuss how these mechanisms could contribute to the regulation of nitrogen uptake and/or nitrogen sensing.

Gene Expression and Silencing Studies in Phytophthora infestans Reveal Infection-Specific Nutrient Transporters and a Role for the Nitrate Reductase Pathway in Plant Pathogenesis

To help learn how phytopathogens feed from their hosts, genes for nutrient transporters from the hemibiotrophic potato and tomato pest Phytophthora infestans were annotated. This identified 453 genes from 19 families. Comparisons with a necrotrophic oomycete, Pythium ultimum var. ultimum, and a hemibiotrophic fungus, Magnaporthe oryzae, revealed diversity in the size of some families although a similar fraction of genes encoded transporters. RNA-seq of infected potato tubers, tomato leaves, and several artificial media revealed that 56 and 207 transporters from P. infestans were significantly up- or down-regulated, respectively, during early infection timepoints of leaves or tubers versus media. About 17 were up-regulated >4-fold in both leaves and tubers compared to media and expressed primarily in the biotrophic stage. The transcription pattern of many genes was host-organ specific. For example, the mRNA level of a nitrate transporter (NRT) was about 100-fold higher during mid-infection in leaves, which are nitrate-rich, than in tubers and three types of artificial media, which are nitrate-poor. The NRT gene is physically linked with genes encoding nitrate reductase (NR) and nitrite reductase (NiR), which mobilize nitrate into ammonium and amino acids. All three genes were coregulated. For example, the three genes were expressed primarily at mid-stage infection timepoints in both potato and tomato leaves, but showed little expression in potato tubers. Transformants down-regulated for all three genes were generated by DNA-directed RNAi, with silencing spreading from the NR target to the flanking NRT and NiR genes. The silenced strains were nonpathogenic on leaves but colonized tubers. We propose that the nitrate assimilation genes play roles both in obtaining nitrogen for amino acid biosynthesis and protecting P. infestans from natural or fertilization-induced nitrate and nitrite toxicity.

Little is known of how plant pathogens adapt to different growth conditions and host tissues. To understand the interaction between the filamentous eukaryotic microbe Phytophthora infestans and its potato and tomato hosts, we mined the genome for genes encoding proteins involved in nutrient uptake and measured their expression in leaves, tubers, and three artificial media. We observed dynamic changes between the growth conditions, and identified transporters expressed mainly in the biotrophic stage, leaves, tubers, or artificial media. When we blocked the expression of a nitrate transporter and two other genes involved in assimilating nitrate, we observed that those genes were required for successful colonization of nitrate-rich leaves but not nitrate-poor tissues, and that nitrate had become toxic to the silenced strains. We therefore hypothesize that the nitrate assimilation pathway may help the pathogen use inorganic nitrogen for nutrition and/or detoxify nitrate when its levels may become damaging.

A dual system formed by the ARC and NR molybdoenzymes mediates nitrite-dependent NO production in Chlamydomonas

Nitric oxide (NO) is a relevant signal molecule involved in many plant processes. However, the mechanisms and proteins responsible for its synthesis are scarcely known. In most photosynthetic organisms NO synthases have not been identified, and Nitrate Reductase (NR) has been proposed as the main enzymatic NO source, a process that in vitro is also catalysed by other molybdoenzymes. By studying transcriptional regulation, enzyme approaches, activity assays with in vitro purified proteins and in vivo and in vitro NO determinations, we have addressed the role of NR and Amidoxime Reducing Component (ARC) in the NO synthesis process. N\R and ARC were intimately related both at transcriptional and activity level. Thus, arc mutants showed high NIA1 (NR gene) expression and NR activity. Conversely, mutants without active NR displayed an increased ARC expression in nitrite medium. Our results with nia1 and arc mutants and with purified enzymes support that ARC catalyses the NO production from nitrite taking electrons from NR and not from Cytb5-1/Cytb5-Reductase, the component partners previously described for ARC (proposed as NOFNiR, Nitric Oxide-Forming Nitrite Reductase). This NR-ARC dual system would be able to produce NO in the presence of nitrate, condition under which NR is unable to do it.

Dual gradients of light intensity and nutrient concentration for full-factorial mapping of photosynthetic productivity

Optimizing bioproduct generation from microalgae is complicated by the myriad of coupled parameters affecting photosynthetic productivity. Quantifying the effect of multiple coupled parameters in full-factorial fashion requires a prohibitively high number of experiments. We present a simple hydrogel-based platform for the rapid, full-factorial mapping of light and nutrient availability on the growth and lipid accumulation of microalgae. We accomplish this without microfabrication using thin sheets of cell-laden hydrogels. By immobilizing the algae in a hydrogel matrix we are able to take full advantage of the continuous spatial chemical gradient produced by a diffusion-based gradient generator while eliminating the need for chambers. We map the effect of light intensities between 0 μmol m(-2) s(-1) and 130 μmol m(-2) s(-1) (∼28 W m(-2)) coupled with ammonium concentrations between 0 mM and 7 mM on Chlamydomonas reinhardtii. Our data set, verified with bulk experiments, clarifies the role of ammonium availability on the photosynthetic productivity Chlamydomonas reinhardtii, demonstrating the dependence of ammonium inhibition on light intensity. Specifically, a sharp optimal growth peak emerges at approximately 2 mM only for light intensities between 80 and 100 μmol m(-2) s(-1)- suggesting that ammonium inhibition is insignificant at lower light intensities. We speculate that this phenomenon is due to the regulation of the high affinity ammonium transport system in Chlamydomonas reinhardtii as well as free ammonia toxicity. The complexity of this photosynthetic biological response highlights the importance of full-factorial data sets as enabled here.

Cloning of chrysanthemum high-affinity nitrate transporter family (CmNRT2) and characterization of CmNRT2.1

The family of NITRATE TRANSPORTER 2 (NRT2) proteins belongs to the high affinity transport system (HATS) proteins which acts at low nitrate concentrations. The relevant gene content of the chrysanthemum genome was explored here by isolating the full length sequences of six distinct CmNRT2 genes. One of these (CmNRT2.1) was investigated at the functional level. Its transcription level was inducible by low concentrations of both nitrate and ammonium. A yeast two hybrid assay showed that CmNRT2.1 interacts with CmNAR2, while a BiFC assay demonstrated that the interaction occurs at the plasma membrane. Arabidopsis thaliana plants heterologously expressing CmNRT2.1 displayed an enhanced rate of labeled nitrogen uptake, suggesting that CmNRT2.1 represents a high affinity root nitrate transporter.

The Involvement of hybrid cluster protein 4, HCP4, in Anaerobic Metabolism in Chlamydomonas reinhardtii

The unicellular green algae Chlamydomonas reinhardtii has long been studied for its unique fermentation pathways and has been evaluated as a candidate organism for biofuel production. Fermentation in C. reinhardtii is facilitated by a network of three predominant pathways producing four major byproducts: formate, ethanol, acetate and hydrogen. Previous microarray studies identified many genes as being highly up-regulated during anaerobiosis. For example, hybrid cluster protein 4 (HCP4) was found to be one of the most highly up-regulated genes under anoxic conditions. Hybrid cluster proteins have long been studied for their unique spectroscopic properties, yet their biological functions remain largely unclear. To probe its role during anaerobiosis, HCP4 was silenced using artificial microRNAs (ami-hcp4) followed by extensive phenotypic analyses of cells grown under anoxic conditions. Both the expression of key fermentative enzymes and their respective metabolites were significantly altered in ami-hcp4, with nitrogen uptake from the media also being significantly different than wild-type cells. The results strongly suggest a role for HCP4 in regulating key fermentative and nitrogen utilization pathways.

Understanding nitrate assimilation and its regulation in microalgae

Nitrate assimilation is a key process for nitrogen (N) acquisition in green microalgae. Among Chlorophyte algae, Chlamydomonas reinhardtii has resulted to be a good model system to unravel important facts of this process, and has provided important insights for agriculturally relevant plants. In this work, the recent findings on nitrate transport, nitrate reduction and the regulation of nitrate assimilation are presented in this and several other algae. Latest data have shown nitric oxide (NO) as an important signal molecule in the transcriptional and posttranslational regulation of nitrate reductase and inorganic N transport. Participation of regulatory genes and proteins in positive and negative signaling of the pathway and the mechanisms involved in the regulation of nitrate assimilation, as well as those involved in Molybdenum cofactor synthesis required to nitrate assimilation, are critically reviewed.

High-affinity nitrate/nitrite transporter genes (Nrt2) in Tisochrysis lutea: identification and expression analyses reveal some interesting specificities of Haptophyta microalgae

Microalgae have a diversity of industrial applications such as feed, food ingredients, depuration processes and energy. However, microalgal production costs could be substantially improved by controlling nutrient intake. Accordingly, a better understanding of microalgal nitrogen metabolism is essential. Using in silico analysis from transcriptomic data concerning the microalgae Tisochrysis lutea, four genes encoding putative high-affinity nitrate/nitrite transporters (TlNrt2) were identified. Unlike most of the land plants and microalgae, cloning of genomic sequences and their alignment with complementary DNA (cDNA) sequences did not reveal the presence of introns in all TlNrt2 genes. The deduced TlNRT2 protein sequences showed similarities to NRT2 proteins of other phyla such as land plants and green algae. However, some interesting specificities only known among Haptophyta were also revealed, especially an additional sequence of 100 amino acids forming an atypical extracellular loop located between transmembrane domains 9 and 10 and the function of which remains to be elucidated. Analyses of individual TlNrt2 gene expression with different nitrogen sources and concentrations were performed. TlNrt2.1 and TlNrt2.3 were strongly induced by low NO3 (-) concentration and repressed by NH4 (+) substrate and were classified as inducible genes. TlNrt2.2 was characterized by a constitutive pattern whatever the substrate. Finally, TlNrt2.4 displayed an atypical response that was not reported earlier in literature. Interestingly, expression of TlNrt2.4 was rather related to internal nitrogen quota level than external nitrogen concentration. This first study on nitrogen metabolism of T. lutea opens avenues for future investigations on the function of these genes and their implication for industrial applications.