Nitrogen assimilation and nitrogen control in cyanobacteria

Response and acclimation of cyanobacteria to acidification: A comprehensive review

Cyanobacteria, as vital components of aquatic ecosystems, face increasing challenges due to acidification driven by various anthropogenic and natural factors. Understanding how cyanobacteria adapt and respond to acidification is crucial for predicting their ecological dynamics and potential impacts on ecosystem health. This comprehensive review synthesizes current knowledge on the acclimation mechanisms and responses of cyanobacteria to acidification stress. Detailly, ecological roles of cyanobacteria were firstly briefly concluded, followed by the effects of acidification on aquatic ecosystems and cyanobacteria. Then the review focuses on the physiological, biochemical, and molecular strategies employed by cyanobacteria to cope with acidification stress, highlighting key adaptive mechanisms and their ecological implications. Finally, a summary of strategies to enhance acid resistance in cyanobacteria and future directions was discussed. Utilizing omics data and machine learning technology to build a cyanobacterial acid regulatory network allows for predicting the impact of acidification on cyanobacteria and inferring its broader effects on ecosystems. Additionally, acquiring acid-tolerant chassis cells of cyanobacteria through innovative techniques facilitates the advancement of environmentally friendly production of acidic chemicals. By synthesizing empirical evidence and theoretical frameworks, this review aims to elucidate the complex interplay between cyanobacteria and acidification stressors, providing insights for future research directions and ecosystem management strategies.

Cyanobacterial Proteomics: Diversity and Dynamics

Cyanobacteria (oxygenic photoautrophs) comprise a diverse group holding significance both environmentally and for biotechnological applications. The utilization of proteomic techniques has significantly influenced investigations concerning cyanobacteria. Application of proteomics allows for large-scale analysis of protein expression and function within cyanobacterial systems. The cyanobacterial proteome exhibits tremendous functional, spatial, and temporal diversity regulated by multiple factors that continuously modify protein abundance, post-translational modifications, interactions, localization, and activity to meet the dynamic needs of these tiny blue greens. Modern mass spectrometry-based proteomics techniques enable system-wide examination of proteome complexity through global identification and high-throughput quantification of proteins. These powerful approaches have revolutionized our understanding of proteome dynamics and promise to provide novel insights into integrated cellular behavior at an unprecedented scale. In this Review, we present modern methods and cutting-edge technologies employed for unraveling the spatiotemporal diversity and dynamics of cyanobacterial proteomics with a specific focus on the methods used to analyze post-translational modifications (PTMs) and examples of dynamic changes in the cyanobacterial proteome investigated by proteomic approaches.

Studies on the PII-PipX-NtcA Regulatory Axis of Cyanobacteria Provide Novel Insights into the Advantages and Limitations of Two-Hybrid Systems for Protein Interactions

Yeast two-hybrid approaches, which are based on fusion proteins that must co-localise to the nucleus to reconstitute the transcriptional activity of GAL4, have greatly contributed to our understanding of the nitrogen interaction network of cyanobacteria, the main hubs of which are the trimeric PII and the monomeric PipX regulators. The bacterial two-hybrid system, based on the reconstitution in the E. coli cytoplasm of the adenylate cyclase of Bordetella pertussis, should provide a relatively faster and presumably more physiological assay for cyanobacterial proteins than the yeast system. Here, we used the bacterial two-hybrid system to gain additional insights into the cyanobacterial PipX interaction network while simultaneously assessing the advantages and limitations of the two most popular two-hybrid systems. A comprehensive mutational analysis of PipX and bacterial two-hybrid assays were performed to compare the outcomes between yeast and bacterial systems. We detected interactions that were previously recorded in the yeast two-hybrid system as negative, as well as a "false positive", the self-interaction of PipX, which is rather an indirect interaction that is dependent on PII homologues from the E. coli host, a result confirmed by Western blot analysis with relevant PipX variants. This is, to our knowledge, the first report of the molecular basis of a false positive in the bacterial two-hybrid system.

Nitrogen Forms Regulate the Response of Microcystis aeruginosa to Nanoplastics at Environmentally Relevant Nitrogen Concentrations

As essential primary producers, cyanobacteria play a major role in global carbon and nitrogen cycles. Though the influence of nanoplastics on the carbon metabolism of cyanobacteria is well-studied, little is known about how nanoplastics affect their nitrogen metabolism, especially under environmentally relevant nitrogen concentrations. Here, we show that nitrogen forms regulated growth inhibition, nitrogen consumption, and the synthesis and release of microcystin (MC) in Microcystis aeruginosa exposed to 10 μg/mL amino-modified polystyrene nanoplastics (PS-NH2) with a particle size of 50 nm under environmentally relevant nitrogen concentrations of nitrate, ammonium, and urea. We demonstrate that PS-NH2 inhibit M. aeruginosa differently in nitrate, urea, and ammonium, with inhibition rates of 51.87, 39.70, and 36.69%, respectively. It is caused through the differences in impairing cell membrane integrity, disrupting redox homeostasis, and varying nitrogen transport pathways under different nitrogen forms. M. aeruginosa respond to exposure of PS-NH2 by utilizing additional nitrogen to boost the production of amino acids, thereby enhancing the synthesis of MC, extracellular polymeric substances, and membrane phospholipids. Our results found that the threat of nanoplastics on primary producers can be regulated by the nitrogen forms in freshwater ecosystems, contributing to a better understanding of nanoplastic risks under environmentally relevant conditions.

Structure and function of the light-protective orange carotenoid protein families

Orange carotenoid proteins (OCPs) are unique photoreceptors that are critical for cyanobacterial photoprotection. Upon exposure to blue-green light, OCPs are activated from a stable orange form, OCPO, to an active red form, OCPR, which binds to phycobilisomes (PBSs) and performs photoprotective non-photochemical quenching (NPQ). OCPs can be divided into three main families: the most abundant and best studied OCP1, and two others, OCP2 and OCP3, which have different activation and quenching properties and are yet underexplored. Crystal structures have been acquired for the three OCP clades, providing a glimpse into the conformational underpinnings of their light-absorption and energy dissipation attributes. Recently, the structure of the PBS-OCPR complex has been obtained allowing for an unprecedented insight into the photoprotective action of OCPs. Here, we review the latest findings in the field that have substantially improved our understanding of how cyanobacteria protect themselves from the toxic consequences of excess light absorption. Furthermore, current research is applying the structure of OCPs to bio-inspired optogenetic tools, to function as carotenoid delivery devices, as well as engineering the NPQ mechanism of cyanobacteria to enhance their photosynthetic biomass production.

Allosteric regulation of nitrate transporter NRT via the signaling protein PII

Coordinated carbon and nitrogen metabolism is crucial for bacteria living in the fluctuating environments. Intracellular carbon and nitrogen homeostasis is maintained by a sophisticated network, in which the widespread signaling protein PII acts as a major regulatory hub. In cyanobacteria, PII was proposed to regulate the nitrate uptake by an ABC (ATP-binding cassette)-type nitrate transporter NrtABCD, in which the nucleotide-binding domain of NrtC is fused with a C-terminal regulatory domain (CRD). Here, we solved three cryoelectron microscopy structures of NrtBCD, bound to nitrate, ATP, and PII, respectively. Structural and biochemical analyses enable us to identify the key residues that form a hydrophobic and a hydrophilic cavity along the substrate translocation channel. The core structure of PII, but not the canonical T-loop, binds to NrtC and stabilizes the CRD, making it visible in the complex structure, narrows the substrate translocation channel in NrtB, and ultimately locks NrtBCD at an inhibited inward-facing conformation. Based on these results and previous reports, we propose a putative transport cycle driven by NrtABCD, which is allosterically inhibited by PII in response to the cellular level of 2-oxoglutarate. Our findings provide a distinct regulatory mechanism of ABC transporter via asymmetrically binding to a signaling protein.

Protein NirP1 regulates nitrite reductase and nitrite excretion in cyanobacteria

When the supply of inorganic carbon is limiting, photosynthetic cyanobacteria excrete nitrite, a toxic intermediate in the ammonia assimilation pathway from nitrate. It has been hypothesized that the excreted nitrite represents excess nitrogen that cannot be further assimilated due to the missing carbon, but the underlying molecular mechanisms are unclear. Here, we identified a protein that interacts with nitrite reductase, regulates nitrogen metabolism and promotes nitrite excretion. The protein, which we named NirP1, is encoded by an unannotated gene that is upregulated under low carbon conditions and controlled by transcription factor NtcA, a central regulator of nitrogen homeostasis. Ectopic overexpression of nirP1 in Synechocystis sp. PCC 6803 resulted in a chlorotic phenotype, delayed growth, severe changes in amino acid pools, and nitrite excretion. Coimmunoprecipitation experiments indicated that NirP1 interacts with nitrite reductase, a central enzyme in the assimilation of ammonia from nitrate/nitrite. Our results reveal that NirP1 is widely conserved in cyanobacteria and plays a crucial role in the coordination of C/N primary metabolism by targeting nitrite reductase.

DNA looping mediates cooperative transcription activation

Transcription factors respond to multilevel stimuli and co-occupy promoter regions of target genes to activate RNA polymerase (RNAP) in a cooperative manner. To decipher the molecular mechanism, here we report two cryo-electron microscopy structures of Anabaena transcription activation complexes (TACs): NtcA-TAC composed of RNAP holoenzyme, promoter and a global activator NtcA, and NtcA-NtcB-TAC comprising an extra context-specific regulator, NtcB. Structural analysis showed that NtcA binding makes the promoter DNA bend by ∼50°, which facilitates RNAP to contact NtcB at the distal upstream NtcB box. The sequential binding of NtcA and NtcB induces looping back of promoter DNA towards RNAP, enabling the assembly of a fully activated TAC bound with two activators. Together with biochemical assays, we propose a 'DNA looping' mechanism of cooperative transcription activation in bacteria.

Tradeoffs between phage resistance and nitrogen fixation drive the evolution of genes essential for cyanobacterial heterocyst functionality

Harmful blooms caused by diazotrophic (nitrogen-fixing) Cyanobacteria are becoming increasingly frequent and negatively impact aquatic environments worldwide. Cyanophages (viruses infecting Cyanobacteria) can potentially regulate cyanobacterial blooms, yet Cyanobacteria can rapidly acquire mutations that provide protection against phage infection. Here, we provide novel insights into cyanophage:Cyanobacteria interactions by characterizing the resistance to phages in two species of diazotrophic Cyanobacteria: Nostoc sp. and Cylindrospermopsis raciborskii. Our results demonstrate that phage resistance is associated with a fitness tradeoff by which resistant Cyanobacteria have reduced ability to fix nitrogen and/or to survive nitrogen starvation. Furthermore, we use whole-genome sequence analysis of 58 Nostoc-resistant strains to identify several mutations associated with phage resistance, including in cell surface-related genes and regulatory genes involved in the development and function of heterocysts (cells specialized in nitrogen fixation). Finally, we employ phylogenetic analyses to show that most of these resistance genes are accessory genes whose evolution is impacted by lateral gene transfer events. Together, these results further our understanding of the interplay between diazotrophic Cyanobacteria and their phages and suggest that a tradeoff between phage resistance and nitrogen fixation affects the evolution of cell surface-related genes and of genes involved in heterocyst differentiation and nitrogen fixation.

Muscle cell proliferation using water-soluble extract from nitrogen-fixing cyanobacteria Anabaena sp. PCC 7120 for sustainable cultured meat production

Muscle cell cultivation, specifically the culture of artificial meat from livestock-derived cells in serum-free media is an emerging technology and has attracted much attention. However, till now, the high cost of production and environmental load have been significant deterrents. This study aims to provide an alternate growth-promoting substance that is free from animal derivatives and lowers nitrogen pollution. We have extracted water-soluble compounds from the filamentous nitrogen-fixing cyanobacteria Anabaena sp. PCC 7120 by the ultrasonication method. The heat-inactivated and molecular weight separation experiments were conducted to identify the bioactive compound present in the extract. Finally, the compounds soluble in water (CW) containing the water-soluble pigment protein, phycocyanin as a bioactive compound, was added as a growth supplement to cultivate muscle cells such as C2C12 muscle cells and quail muscle clone 7 (QM7) cells to analyze the effectiveness of the extract. The results indicated that CW had a positive role in muscle cell proliferation. A three-dimensional (3-D) cell-dense structure was fabricated by culturing QM7 cells using the extract. Furthermore, the nitrogen-fixing cyanobacterial extract has vast potential for cultured meat production without animal sera in the near future.

Improved lipid production and component of mycosporine-like amino acids by co-overexpression of amt1 and aroB genes in Synechocystis sp. PCC6803

Implementing homologous overexpression of the amt1 (A) and aroB (B) genes involved in ammonium transporter and the synthesis of mycosporine-like amino acids (MAAs) and aromatic amino acids, respectively, we created three engineered Synechocystis sp. PCC6803 strains, including Ox-A, Ox-B, and Ox-AB, to study the utilization of carbon and nitrogen in cyanobacteria for the production of valuable products. With respect to amt1 overexpression, the Ox-A and Ox-AB strains had a greater growth rate under (NH4)2SO4 supplemented condition. Both the higher level of intracellular accumulation of lipids in Ox-A and Ox-AB as well as the increased secretion of free fatty acids from the Ox-A strain were impacted by the late-log phase of cell growth. It is noteworthy that among all strains, the Ox-B strain undoubtedly spotted a substantial accumulation of glycogen as a consequence of aroB overexpression. Additionally, the ammonium condition drove the potent antioxidant activity in Ox strains with a late-log phase, particularly in the Ox-B and Ox-AB strains. This was probably related to the altered MAA component inside the cells. The higher proportion of P4-fraction was induced by the ammonium condition in both Ox-B and Ox-AB, while the noted increase of the P1 component was found in the Ox-A strain.

Microcystin congeners in Lake Erie follow the seasonal pattern of nitrogen availability

Cyanobacteria harmful algal blooms produce many toxic secondary metabolites called cyanotoxins. The most studied group of cyanotoxins are microcystins (MC), with over 300 congeners reported. MC-LR is the most studied congener because of its abundance and toxicity. Recent toxicology studies suggest that more hydrophobic MC congeners such as MC-LA, MC-LF, and MC-LW may be less abundant but up to seven times more toxic than MC-LR, whereas, MC-RR's toxicity is only one-fifth that of MC-LR. Hence, understanding the environmental stressors that change the MC congener profile is critical to assessing the negative impact on environmental and human health. A two-year field and experimental study investigated seasonal and spatial changes of MC congener profiles in the western basin of Lake Erie. Both studies showed that nitrogen enrichment favored the production of nitrogen-rich MC-RR (C49H75N13O12). The field study showed that nitrogen depletion favored the low-nitrogen MC-LA (C46H67N7O12). MC-LR (a medium N level, C49H75N10O12) accounted for ∼30% to 50% of the total MC concentration and was stable across nitrogen concentrations. Using the relative toxicity and concentrations of each MC congener, both LC-MS/MS and ELISA overestimated the toxicity early bloom (July) and underestimated it late bloom (September). On 24 July 2019, highly toxic MC-LW and MC-LF were detected at nearshore stations with relative toxicity exceeding drinking water standards. This study demonstrated that the less toxic, high nitrogen MC-RR dominated under nitrogen-replete conditions in the early season, whereas the more toxic, less nitrogen MC-LA dominated under nitrogen-limited conditions later in the season.

Exposure to nitrate induced growth, intestinal histology and microbiota alterations of Bufo raddei Strauch tadpoles

Nitrate (NO₃^-) is one of the ubiquitous environmental chemicals which multiplies negative impacts on aquatic life such as amphibian larvae. However, the data involving the dynamics of amphibians in response to NO₃-N are scarce. This study investigated the effects of NO₃-N on locomotor ability, growth performance, oxidative stress parameters, intestinal histology, and intestinal microbiota of Bufo raddei Strauch tadpoles. The tadpoles were chronically exposed to different concentrations of NO₃-N (10, 50, 100, and 200 mg/L) from Gosner stage 26 to 38. Our results revealed that NO₃-N exposure caused significantly reduced body weight and length, impaired locomotor activity, and severe oxidative damage to liver tissue. Moreover, the high NO₃-N (50, 100, and 200 mg/L) exposure caused irregular arrangement and indistinct cell borders of mucosal epithelial cells in the tadpoles intestine. The NO₃-N exposure significantly changed the structure of the intestinal microbiota. The phylum Cyanobacteria occupy the main niche of intestinal microbes and have a certain negative correlation with the growth and motility of tadpoles. In addition, the functional prediction revealed that NO₃-N exposure obviously downregulated the metabolism of enzyme families in tadpoles. Our comprehensive research shows the toxicity of NO₃-N exposure in B. raddei Strauch, explores the potential links between development and intestinal microbiota of tadpole, and provides a new framework for the potential health risk of nitrate in amphibians.

Regulatory and metabolic adaptations in the nitrogen assimilation of marine picocyanobacteria

Prochlorococcus and Synechococcus are the two most abundant photosynthetic organisms on Earth, with a strong influence on the biogeochemical carbon and nitrogen cycles. Early reports demonstrated the streamlining of regulatory mechanisms in nitrogen metabolism and the removal of genes not strictly essential. The availability of a large series of genomes, and the utilization of latest generation molecular techniques have allowed elucidating the main mechanisms developed by marine picocyanobacteria to adapt to the environments where they thrive, with a particular interest in the strains inhabiting oligotrophic oceans. Given that nitrogen is often limited in those environments, a series of studies have explored the strategies utilized by Prochlorococcus and Synechococcus to exploit the low concentrations of nitrogen-containing molecules available in large areas of the oceans. These strategies include the reduction in the GC and the cellular protein contents; the utilization of truncated proteins; a reduced average amount of N in the proteome; the development of metabolic mechanisms to perceive and utilize nanomolar nitrate concentrations; and the reduced responsiveness of key molecular regulatory systems such as NtcA to 2-oxoglutarate. These findings are in sharp contrast with the large body of knowledge obtained in freshwater cyanobacteria. We will outline the main discoveries, stressing their relevance to the ecological success of these important microorganisms.

Simultaneous bioremediation of Disperse orange-2RL Azo dye and fatty acids production by Scenedesmus obliquus cultured under mixotrophic and heterotrophic conditions

Several types of green photosynthetic microalgae can grow through the process of heterotrophic growth in the dark with the help of a carbon source instead of the usual light energy. Heterotrophic growth overcomes important limitations in the production of valuable products from microalgae, such as the reliance on light, which complicates the process, raises costs, and lowers the yield of potentially useful products. The present study was conducted to explore the potential growth of green microalga Scenedesmus obliquus under mixotrophic and heterotrophic conditions utilizing Disperse orange 2RL Azo dye as a carbon source to produce a high lipid content and the maximum dye removal percentage. After 7 days of algal growth with dye under mixotrophic and heterotrophic conditions with varying pH levels (5, 7, 9, and 11), KNO₃ concentrations (1, 1.5, 2, and 3 g/L), and dye concentrations (20, 40, and 60 ppm); dye removal percentage, algal dry weight, and lipid content were determined. The results showed that the highest decolorization of Disperse orange 2RL Azo dye (98.14%) was attained by S. obliquus in heterotrophic medium supplemented with glucose at the optimal pH 11 when the nitrogen concentration was 1 g/L and the dye concentration was 20 ppm. FT-IR spectroscopy of the dye revealed differences in peaks position and intensity before and after algal treatment. S. obliquus has a high concentration of oleic acid, which is enhanced when it is grown with Disperse orange 2RL Azo dye, making it ideal for production of high-quality biodiesel. In general, and in the vast majority of instances, heterotrophic cultivation is substantially less expensive, easier to set up, and requires less maintenance than mixotrophic cultivation. Heterotrophic cultivation allows for large-scale applications such as separate or mixed wastewater treatment along with biofuel production.

Marine Synechococcus sp. Strain WH7803 Shows Specific Adaptative Responses to Assimilate Nanomolar Concentrations of Nitrate

Marine Synechococcus, together with Prochlorococcus, contribute to a significant proportion of the primary production on Earth. The spatial distribution of these two groups of marine picocyanobacteria depends on different factors such as nutrient availability and temperature. Some Synechococcus ecotypes thrive in mesotrophic and moderately oligotrophic waters, where they exploit both oxidized and reduced forms of nitrogen. Here, we present a comprehensive study, which includes transcriptomic and proteomic analyses of the response of Synechococcus sp. strain WH7803 to nanomolar concentrations of nitrate, compared to micromolar ammonium or nitrogen starvation. We found that Synechococcus has a specific response to a nanomolar nitrate concentration that differs from the response shown under nitrogen starvation or the presence of standard concentrations of either ammonium or nitrate. This fact suggests that the particular response to the uptake of nanomolar concentrations of nitrate could be an evolutionary advantage for marine Synechococcus against Prochlorococcus in the natural environment. IMPORTANCE Marine Synechococcus are a very abundant group of photosynthetic organisms on our planet. Previous studies have shown blooms of these organisms when nanomolar concentrations of nitrate become available. We have assessed the effect of nanomolar nitrate concentrations by studying the transcriptome and proteome of Synechococcus sp. WH7803, together with some physiological parameters. We found evidence that Synechococcus sp. strain WH7803 does sense and react to nanomolar concentrations of nitrate, suggesting the occurrence of specific adaptive mechanisms to allow their utilization. Thus, very low concentrations of nitrate in the ocean seem to be a significant nitrogen source for marine picocyanobacteria.

Sustainable citric acid production from CO2 in an engineered cyanobacterium

Citric acid is one of the most widely used organic acids in the world, with applications ranging from acidity regulation in food and beverages to metal chelation in hydrometallurgical processes. Most of its production is currently derived from fermentative processes, using plant-derived carbon feedstocks. While these are currently dominant, there is an increasing need to develop closed-loop production systems that reduce process carbon footprint. In this work, we demonstrate for the first time that an engineered marine cyanobacterium Synechococcus sp. PCC 7002 can be used as a sustainable chassis for the photosynthetic conversion of CO₂ to citric acid. Decreased citric acid cycle flux, through the use of a theophylline-responsive riboswitch, was combined with improved flux through citrate synthase and enhanced citric acid excretion, resulting in a significant improvement to citric acid production. While allowing citrate production, this strategy induces a growth defect which can be overcome by glutamate supplementation or by fine-tuning aconitase levels, resulting in an increase in production relative to WT of over 100-fold. This work represents a first step toward sustainable production of a commodity organic acid from CO₂.

The role of organic nutrients in structuring freshwater phytoplankton communities in a rapidly changing world

Carbon, nitrogen, and phosphorus are critical macroelements in freshwater systems. Historically, researchers and managers have focused on inorganic forms, based on the premise that the organic pool was not available for direct uptake by phytoplankton. We now know that phytoplankton can tap the organic nutrient pool through a number of mechanisms including direct uptake, enzymatic hydrolysis, mixotrophy, and through symbiotic relationships with microbial communities. In this review, we explore these mechanisms considering current and projected future anthropogenically-driven changes to freshwater systems. In particular, we focus on how naturally- and anthropogenically- derived organic nutrients can influence phytoplankton community structure. We also synthesize knowledge gaps regarding phytoplankton physiology and the potential challenges of nutrient management in an organically dynamic and anthropogenically modified world. Our review provides a basis for exploring these topics and suggests several avenues for future work on the relation between organic nutrients and eutrophication and their ecological implications in freshwater systems.

Can correlational analyses help determine the drivers of microcystin occurrence in freshwater ecosystems? A meta-analysis of microcystin and associated water quality parameters

Microcystin (MC) is a toxic secondary metabolite produced by select cyanobacteria that threatens aquatic and terrestrial organisms over a diverse range of freshwater systems. To assess the relationship between environmental parameters and MC, researchers frequently utilize correlational analyses. This statistical methodology has proved useful when summarizing complex water quality monitoring datasets, but the correlations between select parameters and MC have been documented to vary widely across studies and systems. Such variation within the peer-reviewed literature leaves uncertainty for resource managers when developing a MC monitoring program. The objective of this research is to determine if correlational analyses between environmental parameters and MC are helpful to resource managers desiring to understand the drivers of MC. Environmental (i.e., physical, chemical, and biological) and MC correlation data were retrieved from an estimated 2,643 waterbodies (largely from the north temperate region) and synthesized using a Fisher's z meta-analysis. Common water quality parameters, such as chlorophyll, temperature, and pH, were positively correlated with MC, while transparency was negatively correlated. Interestingly, 12 of the 15 studied nitrogen parameters, including total nitrogen, were not significantly correlated with MC. In contrast, three of the four studied phosphorus parameters, including total phosphorus, were positively related to MC. Results from this synthesis quantitatively reinforces the usefulness of commonly measured environmental parameters to monitor for conditions related to MC occurrence; however, correlational analyses by themselves are often ineffective and considering what role a parameter plays in the ecology of cyanobacterial blooms in addition to MC production is vital.

Role of key-stone microbial taxa in algae amended soil for mediating nitrogen transformation

Although the plant-growth promotion by algae have been studied comprehensively, their impacts on indigenous soil microbiome remain largely unexplored. Herein we conducted a greenhouse experiment to investigate the changes in soil properties and corresponding microbial communities (bacterial, fungal and protists) after 2-year application of algae and their dynamic variation within 60 days immediately after algae addition. In comparison with Control treatment, the impact of algae on soil properties and microbial communities was huge, especially the content of nitrate was decreased however soluble organic nitrogen (SON) was increased. The increased copies of nifH gene suggested the improved potential of nitrogen fixation in algae treated soil. By constructing multitrophic ecological network, soil microorganisms were divided into several modules, and two key-stone microbial taxa (module 1 and 2) showed strong associations with the content of nitrate and SON. With addition of algae, the abundance of most microbial taxa was decreased and increased in module 1 and module 2, respectively. Particularly, module 1 and module 2 were proved to be taxonomically and functionally comprised of different microbes. Moreover, random forest analysis and structural equation model indicated that the key-stone microbial taxa were more important factors affecting the content of nitrate and SON than algae, bacterial, fungal and protistan communities and the influence of algae on soil nitrogen cycling mostly depended on their indirect effects via module 1 and 2.

Transcriptomic analysis dissects the regulatory strategy of toxic cyanobacterium Microcystis aeruginosa under differential nitrogen forms

The critical role of nitrogen in the global proliferation of cyanobacterial blooms is arousing increasing attention. However, the mechanism underlying the algal responses to differential nitrogen forms remains unclarified. The physiological and transcriptomic changes of Microcystis aeruginosa supplied with different nitrogen forms (nitrate and ammonium) were highlighted in this study. The results indicated that ammonium behaves better in stimulating the initial growth in N-limited cells than nitrate. However, a concomitant side effect is that cellular growth and photosynthesis decreased due to photosystem II damage induced by excess absorbed light energy under 10 mg L^-1 ammonium. By contrast, adequate nitrate supply favored more efficient photosynthesis, higher biomass yield and microcystin quotas than ammonium. Depending on the supplied nitrogen form, different transcriptomic patterns were observed in M. aeruginosa. Under nitrate, the upregulation of genes involved in Arg biosynthesis, ornithine-urea cycle and photosynthesis increased nitrogen storage and cellular growth, while genes involved in cyclic electron flow around photosystem I and CO₂-concentrating mechanism were heightened to dissipate excess energy under high ammonium. These insights provided important clues for understanding the physiological and molecular effects of available nitrogen forms on the frequent outbreaks of cyanobacteria.

Physiological, biochemical and transcriptional responses of cyanobacteria to environmentally relevant concentrations of a typical antibiotic-roxithromycin

The frequent occurrence of antibiotics in source waters may affect the formation of harmful algal blooms (HABs) dominated by the cyanobacterium Microcystis aeruginosa. However, it remains poorly understood whether dissolved algal organic matters (AOM) can be altered by the introduction of antibiotics in source waters. To resolve these discrepancies, this study investigated the physiological, biochemical, and transcriptional responses of a toxigenic strain of M. aeruginosa to the commonly-detected antibiotic roxithromycin (ROX) at environmentally relevant concentrations ranging from 30 to 8000 ng L^-1. The growth and microcystin (MC) production of M. aeruginosa was significantly stimulated by 300 and 1000 ng L^-1 ROX, whereas inhibited by 5000 and 8000 ng L^-1 ROX. This may be owing to the regulation of genes related to photosynthesis and MCs. Although the membrane of cyanobacterial cells remained intact, the release of MCs was increased significantly with the growing ROX dosages, which may cause additional challenges in drinking water treatment. The amounts of AOM were enhanced by 300 and 1000 ng L^-1 ROX, while decreased by 5000 and 8000 ng L^-1 ROX. It may be attributed to the changes of cyanobacterial cell growth and the gene expression related to carbon fixation, carbohydrate metabolism and nitrogen metabolism. To further understand the regulation of related genes in M. aeruginosa exposed to ROX, trend analysis of differentially expressed genes was performed. The results indicated that the regulation of metabolism-related genes (e.g., lipopolysaccharide biosynthesis) may be also responsible for the changes of cyanobacterial cell densities. Generally, low levels of ROX (300 and 1000 ng L^-1) could stimulated the cyanobacterial growth, MC synthesis and AOM production, which may promote the formation of HABs and reduce the source water quality. Although higher levels of ROX (5000 and 8000 ng L^-1) inhibited the formation of HABs, the threat of increasing extracellular MCs should be considered.

Cyanobacteria: Model Microorganisms and Beyond

In this review, the general background is provided on cyanobacteria, including morphology, cell membrane structure, and their photosynthesis pathway. The presence of cyanobacteria in nature, and their industrial applications are discussed, and their production of secondary metabolites are explained. Biofilm formation, as a common feature of microorganisms, is detailed and the role of cell diffusion in bacterial colonization is described. Then, the discussion is narrowed down to cyanobacterium Synechocystis, as a lab model microorganism. In this relation, the morphology of Synechocystis is discussed and its different elements are detailed. Type IV pili, the complex multi-protein apparatus for motility and cell-cell adhesion in Synechocystis is described and the underlying function of its different elements is detailed. The phototaxis behavior of the cells, in response to homogenous or directional illumination, is reported and its relation to the run and tumble statistics of the cells is emphasized. In Synechocystis suspensions, there may exist a reciprocal interaction between the cell and the carrying fluid. The effects of shear flow on the growth, doubling per day, biomass production, pigments, and lipid production of Synechocystis are reported. Reciprocally, the effects of Synechocystis presence and its motility on the rheological properties of cell suspensions are addressed. This review only takes up the general grounds of cyanobacteria and does not get into the detailed biological aspects per se. Thus, it is substantially more comprehensive in that sense than other reviews that have been published in the last two decades. It is also written not only for the researchers in the field, but for those in physics and engineering, who may find it interesting, useful, and related to their own research.

The Dark Side of Microbial Processes: Accumulation of Nitrate During Storage of Surface Water in the Dark and the Underlying Mechanism

In densely populated cities with limited land, storage of surface water in underground spaces is a potential solution to meet the rising demand of clean water. In addition, due to the imperative need of renewable solar energy and limited land resources, the deployment of floating solar photovoltaic (PV) systems over water has risen exponentially. In both scenarios, microbial communities in the water do not have access to sunlight. How the absence of sunlight influences microbial community function and the water quality is largely unknown. The objective of this study was to reveal microbial processes in surface water stored in the dark and water quality dynamics. Water from a freshwater reservoir was stored in the dark or light (control) for 6 months. Water quality was monitored at regular intervals. RNA sequencing was performed on the Illumina MiSeq platform and qPCR was used to substantiate the findings arising from the sequencing data. Our results showed that storage of surface water in the dark resulted in the accumulation of nitrate in the water. Storage in the dark promoted the decay of algal cells, increasing the amount of free nitrogen in the water. Most of the free nitrogen was eventually transformed into nitrate through microbial processes. RNA sequencing-based microbial community analyses and pure culture experiments using nitrifying bacteria Nitrosomonas europaea and Nitrobacter sp. revealed that the accumulation of nitrate in the dark was likely due to an increase in nitrification rate and a decrease in the assimilation rate of nitrate back into the biomass. IMPORTANCE Microbial communities play an essential role in maintaining a healthy aquatic ecosystem. For example, in surface water reservoirs, microorganisms produce oxygen, break down toxic contaminants and remove excess nitrogen. In densely populated cities with limited land, storing surface water in underground spaces and deploying floating solar photovoltaic (PV) systems over water are potential solutions to address water and energy sustainability challenges. In both scenarios, surface water is kept in the dark. In this work, we revealed how the absence of sunlight influences microbial community function and water quality. We showed that storage of surface water in the dark affected bacterial activities responsible for nitrogen transformation, resulting in the accumulation of nitrate in the water. Our findings highlight the importance of monitoring nitrate closely if raw surface water is to be stored in the dark and the potential need of downstream treatment to remove nitrate.

Nitrogen fixation: a poorly understood process along the freshwater-marine continuum

Although N₂ fixation is a major component of the global N cycle and has been extensively studied in open-ocean and terrestrial ecosystems, rates and ecological dynamics remain virtually unknown for the inland and coastal aquatic ecosystems (lakes, wetlands, rivers, streams, estuaries) that connect terrestrial and marine biomes. This is due to the diversity of these habitats, as well as the traditional paradigm that N₂ fixation rates were low to nonexistent, and therefore not important, in these ecosystems. We identify three major research themes to advance understanding of aquatic N₂ fixation: 1) the biological diversity of diazotrophs and variability of N₂ fixation rates, 2) the ecological stoichiometry of N₂ fixation, and 3) the upscaling of N₂ fixation rates from genes to ecosystems. Coordinating research across these areas will advance limnology and oceanography by fully integrating N₂ fixation into ecological dynamics of aquatic ecosystems from local to global scales.

Cross-Activation of Two Nitrogenase Gene Clusters by CnfR1 or CnfR2 in the Cyanobacterium Anabaena variabilis

In Anabaena variabilis, the nif1 genes, which are activated by CnfR1, produce a Mo-nitrogenase that is expressed only in heterocysts. Similarly, the nif2 genes, which are activated by CnfR2, make a Mo-nitrogenase that is expressed only in anaerobic vegetative cells. However, CnfR1, when it was expressed in anaerobic vegetative cells under the control of the cnfR2 promoter or from the Co²⁺-inducible coaT promoter, activated the expression of both nifB1 and nifB2. Activation of nifB2, but not nifB1, by CnfR1 required NtcA. Thus, expression of the nif1 system requires no heterocyst-specific factor other than CnfR1. In contrast, CnfR2, when it was expressed in heterocysts under the control of the cnfR1 promoter or from the coaT promoter, did not activate the expression of nifB1 or nifB2. Thus, activation of the nif2 system in anaerobic vegetative cells by CnfR2 requires additional factors absent in heterocysts. CnfR2 made from the coaT promoter activated nifB2 expression in anaerobic vegetative cells grown with fixed nitrogen; however, oxygen inhibited CnfR2 activation of nifB2 expression. In contrast, activation of nifB1 and nifB2 by CnfR1 was unaffected by oxygen. CnfR1, which does not activate the nifB2 promoter in heterocysts, activated the expression of the entire nif2 gene cluster from a nifB2::nifB1::nifB2 hybrid promoter in heterocysts, producing functional Nif2 nitrogenase in heterocysts. However, activity was poor compared to the normal Nif1 nitrogenase. Expression of the nif2 cluster in anaerobic vegetative cells of Nostoc sp. PCC 7120, a strain lacking the nif2 nitrogenase, resulted in expression of the nif2 genes but weak nitrogenase activity.

IMPORTANCE Cyanobacterial nitrogen fixation is important in the global nitrogen cycle, in oceanic productivity, and in many plant and fungal symbioses. While the proteins that mediate nitrogen fixation have been well characterized, the regulation of this complex and expensive process is poorly understood in cyanobacteria. Using a genetic approach, we have characterized unique and overlapping functions for two homologous transcriptional activators CnfR1 and CnfR2 that activate two distinct nitrogenases in a single organism. We found that CnfR1 is promiscuous in its ability to activate both nitrogenase systems, whereas CnfR2 depends on additional cellular factors; thus, it activates only one nitrogenase system.

Numerical simulation of microcystin distribution in Liangxi River, downstream of Taihu Lake

Microcystins (MCs), the algal toxins produced by cyanobacteria, raised a worldwide concern in recent decades. Limited monitoring stations for MCs make it hard to map the MC spatial distribution in certain areas. To tackle such problems, we selected Liangxi River as our research area and developed an integrated model to get spatial continuous MC data without too many sampling sites, which integrates a hydro-environment model and an artificial neural network algorithm (ANN). The ANN algorithm can estimate concentration MCs via environmental factors. In this paper, we selected chl-a, TN, TP, NO 2 - , NO 3 - , NH₃ -N, and PO 4 3 - as stressors. The ANN model we established showed good performances both in train (R²  = 0.8407) and test set (R²  = 0.7543). In the hydro-environment model, by inputting river geometry and model boundary data, the spatial continuous water quality data could be simulated. The water quality data returned from the hydro-environmental model were used as input variables of the well-trained ANN model; the continuous MC data were derived. To evaluate this model on geo-mapping the MC distribution in Liangxi River, we compared the performance of this model and spatial interpolation on the test set, it turns out the integrated model showed a better performance. © 2020 Water Environment Federation PRACTITIONER POINTS: The cost of microcystin (MC) detection is too high for routine monitoring. We integrated regression method and hydro-environment model to predict MCs. Results derived from spatial interpolation are not robust in unmonitored area. The new integration model can minimize the drawback of spatial interpolation.

A system-oriented strategy to enhance electron production of Synechocystis sp. PCC6803 in bio-photovoltaic devices: experimental and modeling insights

Bio-photovoltaic devices (BPVs) harness photosynthetic organisms to produce bioelectricity in an eco-friendly way. However, their low energy efficiency is still a challenge. A comprehension of metabolic constraints can result in finding strategies for efficiency enhancement. This study presents a systemic approach based on metabolic modeling to design a regulatory defined medium, reducing the intracellular constraints in bioelectricity generation of Synechocystis sp. PCC6803 through the cellular metabolism alteration. The approach identified key reactions that played a critical role in improving electricity generation in Synechocystis sp. PCC6803 by comparing multiple optimal solutions of minimal and maximal NADH generation using two criteria. Regulatory compounds, which controlled the enzyme activity of the key reactions, were obtained from the BRENDA database. The selected compounds were subsequently added to the culture media, and their effect on bioelectricity generation was experimentally assessed. The power density curves for different culture media showed the BPV fed by Synechocystis sp. PCC6803 suspension in BG-11 supplemented with NH₄Cl achieved the maximum power density of 148.27 mW m^-2. This produced power density was more than 40.5-fold of what was obtained for the BPV fed with cyanobacterial suspension in BG-11. The effect of the activators on BPV performance was also evaluated by comparing their overpotential, maximum produced power density, and biofilm morphology under different conditions. These findings demonstrated the crucial role of cellular metabolism in improving bioelectricity generation in BPVs.

Regulatory mechanisms of lipid biosynthesis in microalgae

Microalgal lipids are highly promising feedstocks for biofuel production. Microalgal lipids, especially triacylglycerol, and practical applications of these compounds have received increasing attention in recent years. For the commercial use of microalgal lipids to be feasible, many fundamental biological questions must be addressed based on detailed studies of algal biology, including how lipid biosynthesis occurs and is regulated. Here, we review the current understanding of microalgal lipid biosynthesis, with a focus on the underlying regulatory mechanisms. We also present possible solutions for overcoming various obstacles to understanding the basic biology of microalgal lipid biosynthesis and the practical application of microalgae-based lipids. This review will provide a theoretical reference for both algal researchers and decision makers regarding the future directions of microalgal research, particularly pertaining to microalgal-based lipid biosynthesis.

Calm on the surface, dynamic on the inside. Molecular homeostasis of Anabaena sp. PCC 7120 nitrogen metabolism

Nitrogen sources are all converted into ammonium/ia as a first step of assimilation. It is reasonable to expect that molecular components involved in the transport of ammonium/ia across biological membranes connect with the regulation of both nitrogen and central metabolism. We applied both genetic (i.e., Δamt mutation) and environmental treatments to a target biological system, the cyanobacterium Anabaena sp PCC 7120. The aim was to both perturb nitrogen metabolism and induce multiple inner nitrogen states, respectively, followed by targeted quantification of key proteins, metabolites and enzyme activities. The absence of AMT transporters triggered a substantial whole-system response, affecting enzyme activities and quantity of proteins and metabolites, spanning nitrogen and carbon metabolisms. Moreover, the Δamt strain displayed a molecular fingerprint indicating nitrogen deficiency even under nitrogen replete conditions. Contrasting with such dynamic adaptations was the striking near-complete lack of an externally measurable altered phenotype. We conclude that this species evolved a highly robust and adaptable molecular network to maintain homeostasis, resulting in substantial internal but minimal external perturbations. This analysis provides evidence for a potential role of AMT transporters in the regulatory/signalling network of nitrogen metabolism and the existence of a novel fourth regulatory mechanism controlling glutamine synthetase activity.

Rapid Changes in the Phytoplankton Community of a Subtropical, Shallow, Hypereutrophic Lake During the Rainy Season

Lake Cajititlán is a small, shallow, subtropical lake located in an endorheic basin in western Mexico. It is characterized by a strong seasonality of climate with pronounced wet and dry seasons and has been classified as a hypereutrophic lake. This eutrophication was driven by improperly treated sewage discharges from four municipal wastewater treatment plants (WWTPs) and by excessive agricultural activities, including the overuse of fertilizers that reach the lake through surface runoff during the rainy season. This nutrient rich runoff has caused algal blooms, which have led to anoxic or hypoxic conditions, resulting in large-scale fish deaths that have occurred during or immediately after the rainy season. This study investigated the changes in the phytoplankton community in Lake Cajititlán during the rainy season and the association between these changes and the physicochemical water quality and environmental parameters measured in the lake’s basin. Planktothrix and Cylindrospermopsis were the dominant genera of the cyanobacterial community, while the Chlorophyceae, Chrysophyceae, and Trebouxiophyceae classes dominated the microalgae community. However, the results showed a significant temporal shift in the phytoplankton communities in Lake Cajititlán induced by the rainy season. The findings of this study suggest that significant climatic variations cause high seasonal surface runoff and rapid changes in the water quality (Chlorophyll-a, DO, NH₄⁺, and NO₃^–) and in variations in the composition of the phytoplankton community. Finally, an alternation between phosphorus and nitrogen limitation was observed in Lake Cajititlán during the rainy season, clearly correlating to the presence of Planktothrix when the lake was limited by phosphorus and to the presence of Cylindrospermopsis when the lake was limited by nitrogen. The evidence presented in this study supports the idea that the death of fish in Lake Cajititlán could be mainly caused by anoxia, caused by rapid changes in water quality during the rainy season. Based on our review of the literature, this is the first study on the phytoplankton community in a subtropical lake during the rainy season using high throughput 16S rRNA and 18S rRNA amplicon sequencing.

Revisiting carbon, nitrogen, and phosphorus metabolisms in microalgae for wastewater treatment

Threats posed to humans - including environmental pollution, water scarcity, food shortages, and resource crises drive a new concept to think about wastewater and its treatment. Wastewater is not only a waste but also a source of energy, renewable and/or non-renewable resources, including water itself. The nutrient in wastewater should not only be removed but also need to be upcycled. Microalgae based wastewater treatment has attracted considerable interests because algae have the potential to efficiently redirect nutrients from wastewater to the accumulated algal biomass. Additionally, microalgae are commercialized in human consumption and animal feed owing to their high content of essential amino and fatty acids, vitamins, and pigments. The whole process establishes a circular economy, totally relying on the ability of microalgae to uptake and store nutrients in wastewater, such as carbon (C), nitrogen (N), and phosphorus (P). It makes the study of the mechanisms underlying the uptake and storage of nutrients in microalgae of great interest. This review specifically aims to summarize C, N, and P metabolisms in microalgae for a better understanding of the microalgae-based wastewater treatment from the nutrient uptake pathway, and examine the key physiological factors or the operating conditions related to nutrient metabolisms that may affect the treatment efficiency. At last, I discuss the potential approaches to enhance the overall treatment performance by adjusting the critical parameters for C, N, and P metabolisms.

PhotoModPlus: A web server for photosynthetic protein prediction from genome neighborhood features

A new web server called PhotoModPlus is presented as a platform for predicting photosynthetic proteins via genome neighborhood networks (GNN) and genome neighborhood-based machine learning. GNN enables users to visualize the overview of the conserved neighboring genes from multiple photosynthetic prokaryotic genomes and provides functional guidance on the query input. In the platform, we also present a new machine learning model utilizing genome neighborhood features for predicting photosynthesis-specific functions based on 24 prokaryotic photosynthesis-related GO terms, namely PhotoModGO. The new model performed better than the sequence-based approaches with an F1 measure of 0.872, based on nested five-fold cross-validation. Finally, we demonstrated the applications of the webserver and the new model in the identification of novel photosynthetic proteins. The server is user-friendly, compatible with all devices, and available at bicep.kmutt.ac.th/photomod.

Biological stoichiometry and growth dynamics of a diazotrophic cyanobacteria in nitrogen sufficient and deficient conditions

The role of nitrogen (N) fixation in determining the frequency, magnitude, and extent of harmful algal blooms (HABs) has not been well studied. Dolichospermum is a common HAB species that is diazotrophic (capable of N fixation) and thus growth is often considered never to be limited by low combined N sources. However, N fixation is energetically expensive and its cost during bloom formation has not been quantified. Additionally, it is unknown how acclimation to differing nutrient ratios affects growth and cellular carbon (C):N stoichiometry. Here, we test the hypotheses that diazotrophic cyanobacteria are homeostatic for N because of their ability to fix atmospheric N₂ and that previous acclimation to low N environments will result in more fixed N and lower C:N stoichiometry. Briefly, cultures that varied in resource N:phosphorus (P) ranging from 0.01 to 100 (atom), were seeded with Dolichospermum which were previously acclimated to low and high N:P conditions and then sampled temporally for growth and C:N stoichiometry. We found that Dolichospermum was not homeostatic for N and displayed classic signs of N limitation and elevated C:N stoichiometry, highlighting the necessary growth trade-off within cells when expending energy to fix N. Acclimation to N limited conditions caused differences in both C:N and fixed N at various time points in the experiment. These results highlight the importance of environmentally available N to a diazotrophic bloom, as well as how previous growth conditions can influence population growth during blooms experiencing variable N:P.

Nitrogen form, concentration, and micronutrient availability affect microcystin production in cyanobacterial blooms

Harmful algal blooms (HABs) are increasing in magnitude, frequency, and duration caused by anthropogenic factors such as eutrophication and altered climatic regimes. While the concentrations and ratios of nitrogen (N) and phosphorus are correlated with bloom biomass and cyanotoxin production, there is less known about how N forms and micronutrients (MN) interact to regulate HABs and cyanotoxin production. Here, we used two separate approaches to examine how N and MN supply affects cyanobacteria biomass and cyanotoxin production. First, we used a Microcystis laboratory culture to examine how N and MN concentration and N form affected the biomass, particulate N, and microcystin-LR concentration and cell quotas. Then, we monitored the N, iron, molybdenum, and total microcystin concentrations from a hypereutrophic reservoir. From this hypereutrophic reservoir, we performed a community HAB bioassay to examine how N and MN addition affected the biomass, particulate N, and microcystin concentration. Microcystis laboratory cultures grown in high urea and MN conditions produced more biomass, particulate N, and had similar C:N stoichiometry, but lower microcystin-LR concentrations and cell quotas when compared to high nitrate and MN conditions. Our community HAB bioassay revealed no interactions between N concentration and MN addition caused by non-limiting MN background concentrations. Biomass, particulate N, and microcystin concentration increased with N addition. The community HAB amended with MN resulted in greater microcystin-LA concentration compared to non-MN amended community HABs. Our results highlight the complexity of how abiotic variables control biomass and cyanotoxin production in both laboratory cultures of Microcystis and community HABs.

Effects of chronic nitrate exposure on the intestinal morphology, immune status, barrier function, and microbiota of juvenile turbot (Scophthalmus maximus)

Coming along with high water reuse in sustainable and intensive recirculating aquaculture systems (RASs), the waste products of fish in rearing water is continuously accumulated. Nitrate, the final product of biological nitrification processes, which may cause aquatic toxicity to fish in different degrees when exposed for a long time. Therefore, the present study was conducted to evaluate the impact of chronic nitrate exposure on intestinal morphology, immune status, barrier function, and microbiota of juvenile turbot. For that, groups of juvenile turbot were exposed to 0 (control check, CK), 50 (low nitrate, L), 200 (medium nitrate, M), and 400 (high nitrate, H) mg L^-1 nitrate-N in small-sized recirculating aquaculture systems. After the 60-day experiment period, we found that exposure to a high concentration of nitrate-N caused obvious pathological damages to the intestine; for instance, atrophy of intestinal microvilli and necrosis in the lamina propria. Quantitative real-time PCR analysis revealed a significant downregulation of the barrier forming tight junction genes like occludin, claudin-like etc. under H treatment (P < 0.05). Intestinal MUC-2 expression also decreased significantly in the nitrate treatment groups compared to that in the control (P < 0.05). Additionally, the expression of HSP70 and HSP90 heat-shock proteins, toll-like receptor-3 (TLR-3), interleukin-1β (IL-1β), and tumor necrosis factor-α (TNF-α) significantly increased (P < 0.05), whereas that of transforming growth factor-β (TGF-β), lysozyme (LYS), and insulin-like growth factor-I (IGF-I) significantly decreased with H treatment (P < 0.05). The results also revealed that intestinal microbial community was changed following nitrate exposure and could alter the α-diversity and β-diversity. Specifically, the proportion of intrinsic flora decreased, whereas that of the potential pathogens significantly increased with M and H treatments (P < 0.05). In conclusion, chronic nitrate exposure could weaken the barrier function and disturb the composition of intestinal microbiota in marine teleosts, thereby harming their health condition.

Understanding the Differences in the Growth and Toxin Production of Anatoxin-Producing Cuspidothrix issatschenkoi Cultured with Inorganic and Organic N Sources from a New Perspective: Carbon/Nitrogen Metabolic Balance

Cyanotoxins are the underlying cause of the threat that globally pervasive Cyanobacteria Harmful algal blooms (CyanoHABs) pose to humans. Major attention has been focused on the cyanobacterial hepatotoxin microcystins (MCs); however, there is a dearth of studies on cyanobacterial neurotoxin anatoxins. In this study, we explored how an anatoxin-producing Cuspidothrix issatschenkoi strain responded to culture with inorganic and organic nitrogen sources in terms of growth and anatoxins production. The results of our study revealed that ʟ- alanine could greatly boost cell growth, and was associated with the highest cell productivity, while urea significantly stimulated anatoxin production with the maximum anatoxin yield reaching 25.86 μg/mg dry weight, which was 1.56-fold higher than that in the control group (BG11). To further understand whether the carbon/nitrogen balance in C. issatschenkoi would affect anatoxin production, we explored growth and toxin production in response to different carbon/nitrogen ratios (C/N). Anatoxin production was mildly promoted when the C/N ratio was within low range, and significantly inhibited when the C/N ratio was within high range, showing approximately a three-fold difference. Furthermore, the transcriptional profile revealed that anaC gene expression was significantly up-regulated over 2–24 h when the C/N ratio was increased, and was significantly down-regulated after 96 h. Overall, our results further enriched the evidence that urea can stimulate cyanotoxin production, and ʟ-alanine could boost C. issatschenkoi proliferation, thus providing information for better management of aquatic systems. Moreover, by focusing on the intracellular C/N metabolic balance, this study explained the anatoxin production dynamics in C. issatschenkoi in response to different N sources.

Nitrogen Flow in Diazotrophic Cyanobacterium Aphanizomenon flos-aquae Is Altered by Cyanophage Infection

Viruses can significantly influence cyanobacteria population dynamics and activity, and through this the biogeochemical cycling of major nutrients. However, surprisingly little attention has been given to understand how viral infections alter the ability of diazotrophic cyanobacteria for atmospheric nitrogen fixation and its release to the environment. This study addressed the importance of cyanophages for net ¹⁵N₂ assimilation rate, expression of nitrogenase reductase gene (nifH) and changes in nitrogen enrichment (¹⁵N/¹⁴N) in the diazotrophic cyanobacterium Aphanizomenon flos-aquae during infection by the cyanophage vB_AphaS-CL131. We found that while the growth of A. flos-aquae was inhibited by cyanophage addition (decreased from 0.02 h^–1 to 0.002 h^–1), there were no significant differences in nitrogen fixation rates (control: 22.7 × 10^–7 nmol N heterocyte^–1; infected: 23.9 × 10^–7 nmol N heterocyte^–1) and nifH expression level (control: 0.6–1.6 transcripts heterocyte^–1; infected: 0.7–1.1 transcripts heterocyte^–1) between the infected and control A. flos-aquae cultures. This implies that cyanophage genome replication and progeny production within the vegetative cells does not interfere with the N₂ fixation reactions in the heterocytes of these cyanobacteria. However, higher ¹⁵N enrichment at the poles of heterocytes of the infected A. flos-aquae, revealed by NanoSIMS analysis indicates the accumulation of fixed nitrogen in response to cyanophage addition. This suggests reduced nitrogen transport to vegetative cells and the alterations in the flow of fixed nitrogen within the filaments. In addition, we found that cyanophage lysis resulted in a substantial release of ammonium into culture medium. Cyanophage infection seems to substantially redirect N flow from cyanobacterial biomass to the production of N storage compounds and N release.

Multiscale drivers of phytoplankton communities in north-temperate lakes

Multiple factors operating across different spatial and temporal scales affect β-diversity, the variation in community composition among sites. Disentangling the relative influence of co-occurring ecological drivers over broad biogeographic gradients and time is critical to developing mechanistic understanding of community responses to natural environmental heterogeneity as well as predicting the effects of anthropogenic change. We partitioned taxonomic β-diversity in phytoplankton communities across 75 north-temperate lakes and reservoirs in Alberta, Canada, using data-driven, spatially constrained null models to differentiate between spatially structured, spatially independent, and spuriously correlated associations with a suite of biologically relevant environmental variables. Phytoplankton β-diversity was largely independent of space, indicating spatial processes (e.g., dispersal limitation) likely play a minor role in structuring communities at the regional scale. Our analysis also identified seasonal differences in the importance of environmental factors, suggesting a general shift toward greater relevance of local, in-lake (e.g., nutrients and Secchi depth) over regional, atmospheric and catchment-level (e.g., monthly solar radiation and grassland coverage) drivers as the open-water growing season progressed. Several local and regional variables explained taxonomic variation jointly, reflecting climatic and land-use linkages (e.g., air temperature and water column stability or pastureland and nutrient enrichment) that underscore the importance of understanding how phytoplankton communities integrate, and may serve as sentinels of, broader anthropogenic changes. We also discovered similar community composition in natural and constructed water bodies, demonstrating rapid filtering of regional species to match local environmental conditions in reservoirs comparable to those in natural habitats. Finally, certain factors related to human footprint (e.g., cropland development) explained the composition of bloom-forming and/or toxic cyanobacteria more than the overall phytoplankton community, suggesting their heightened importance to integrated watershed management.

Nitrogen flux into metabolites and microcystins changes in response to different nitrogen sources in Microcystis aeruginosa NIES-843

The over-enrichment of nitrogen (N) in the environment has contributed to severe and recurring harmful cyanobacterial blooms, especially by the non-N₂ -fixing Microcystis spp. N chemical speciation influences cyanobacterial growth, persistence and the production of the hepatotoxin microcystin, but the physiological mechanisms to explain these observations remain unresolved. Stable-labelled isotopes and metabolomics were employed to address the influence of nitrate, ammonium, and urea on cellular physiology and production of microcystins in Microcystis aeruginosa NIES-843. Global metabolic changes were driven by both N speciation and diel cycling. Tracing ¹⁵ N-labelled nitrate, ammonium, and urea through the metabolome revealed N uptake, regardless of species, was linked to C assimilation. The production of amino acids, like arginine, and other N-rich compounds corresponded with greater turnover of microcystins in cells grown on urea compared to nitrate and ammonium. However, ¹⁵ N was incorporated into microcystins from all N sources. The differences in N flux were attributed to the energetic efficiency of growth on each N source. While N in general plays an important role in sustaining biomass, these data show that N-speciation induces physiological changes that culminate in differences in global metabolism, cellular microcystin quotas and congener composition.

Phytoplankton transcriptomic and physiological responses to fixed nitrogen in the California current system

Marine phytoplankton are responsible for approximately half of photosynthesis on Earth. However, their ability to drive ocean productivity depends on critical nutrients, especially bioavailable nitrogen (N) which is scarce over vast areas of the ocean. Phytoplankton differ in their preferences for N substrates as well as uptake efficiencies and minimal N requirements relative to other critical nutrients, including iron (Fe) and phosphorus. In this study, we used the MicroTOOLs high-resolution environmental microarray to examine transcriptomic responses of phytoplankton communities in the California Current System (CCS) transition zone to added urea, ammonium, nitrate, and also Fe in the late summer when N depletion is common. Transcript level changes of photosynthetic, carbon fixation, and nutrient stress genes indicated relief of N limitation in many strains of Prochlorococcus, Synechococcus, and eukaryotic phytoplankton. The transcriptomic responses helped explain shifts in physiological and growth responses observed later. All three phytoplankton groups had increased transcript levels of photosynthesis and/or carbon fixation genes in response to all N substrates. However, only Prochlorococcus had decreased transcript levels of N stress genes and grew substantially, specifically after urea and ammonium additions, suggesting that Prochlorococcus outcompeted other community members in these treatments. Diatom transcript levels of carbon fixation genes increased in response to Fe but not to Fe with N which might have favored phytoplankton that were co-limited by N and Fe. Moreover, transcription patterns of closely related strains indicated variability in N utilization, including nitrate utilization by some high-light adapted Prochlorococcus. Finally, up-regulation of urea transporter genes by both Prochlorococcus and Synechococcus in response to filtered deep water suggested a regulatory mechanism other than classic control via the global N regulator NtcA. This study indicated that co-existing phytoplankton strains experience distinct nutrient stresses in the transition zone of the CCS, an understudied region where oligotrophic and coastal communities naturally mix.

Characterizing glucose, illumination, and nitrogen-deprivation phenotypes of Synechocystis PCC6803 with Raman spectroscopy

Background

Synechocystis sp. PCC6803 is a model cyanobacterium that has been studied widely and is considered for metabolic engineering applications. Here, Raman spectroscopy and Raman chemometrics (Rametrix™) were used to (i) study broad phenotypic changes in response to growth conditions, (ii) identify phenotypic changes associated with its circadian rhythm, and (iii) correlate individual Raman bands with biomolecules and verify these with more accepted analytical methods.

Methods

Synechocystis cultures were grown under various conditions, exploring dependencies on light and/or external carbon and nitrogen sources. The Rametrix™ LITE Toolbox for MATLAB® was used to process Raman spectra and perform principal component analysis (PCA) and discriminant analysis of principal components (DAPC). The Rametrix™ PRO Toolbox was used to validate these models through leave-one-out routines that classified a Raman spectrum when growth conditions were withheld from the model. Performance was measured by classification accuracy, sensitivity, and specificity. Raman spectra were also subjected to statistical tests (ANOVA and pairwise comparisons) to identify statistically relevant changes in Synechocystis phenotypes. Finally, experimental methods, including widely used analytical and spectroscopic assays were used to quantify the levels of glycogen, fatty acids, amino acids, and chlorophyll a for correlations with Raman data.

Results

PCA and DAPC models produced distinct clustering of Raman spectra, representing multiple Synechocystis phenotypes, based on (i) growth in the presence of 5 mM glucose, (ii) illumination (dark, light/dark [12 h/12 h], and continuous light at 20 µE), (iii) nitrogen deprivation (0–100% NaNO₃ of native BG-11 medium in continuous light), and (iv) throughout a 24 h light/dark (12 h/12 h) circadian rhythm growth cycle. Rametrix™ PRO was successful in identifying glucose-induced phenotypes with 95.3% accuracy, 93.4% sensitivity, and 96.9% specificity. Prediction accuracy was above random chance values for all other studies. Circadian rhythm analysis showed a return to the initial phenotype after 24 hours for cultures grown in light/dark (12 h/12 h) cycles; this did not occur for cultures grown in the dark. Finally, correlation coefficients (R > 0.7) were found for glycogen, all amino acids, and chlorophyll a when comparing specific Raman bands to other experimental results.

Differential Drawdown of Ammonium, Nitrate, and Urea by Freshwater Chlorophytes and Cyanobacteria1

The chemical form of nitrogen (N) is deemed to be decisive in shaping the composition of the primary producer community. Recently, there has been a shift in the dominant form of N delivered to agricultural landscapes. Urea-based fertilizers are a mainstay in modern agriculture, and their ubiquitous use has increased the likelihood of urea export to nearby freshwaters. The shift to urea fertilizers has coincided with the recent expansion of cyanobacteria harmful algal blooms (cyanoHABs). This study investigated N drawdown patterns between two major freshwater phytoplankton groups-chlorophytes and cyanobacteria. Experiments were designed to understand if different patterns of N drawdown occurred among taxa and the potential synergistic effects of multiple N substrates. Nitrate (NO₃^- ), ammonium (NH₄⁺ ), and urea were supplied in a series of paired combinations, and N concentrations were monitored to track N drawdowns. We did not find significant differences between phytoplankton classes when supplied with a single N substrate. However, we found that when N substrates were supplied in combination, significant differences in N drawdown patterns were observed. Urea was consumed more rapidly among cyanobacteria, being drawn down at significantly higher rates relative to inorganic N substrates. In contrast, inorganic N substrates were drawn down more rapidly among chlorophytes relative to urea. Our findings support the emerging urea-cyanoHAB link and the potential importance of urea in freshwater eutrophication. As society becomes increasingly dependent on urea for agricultural crops, the need to understand how urea influences phytoplankton community composition may be instrumental in predicting bloom dynamics.

Crystal structure of Alr1298, a pentapeptide repeat protein from the cyanobacterium Nostoc sp. PCC 7120, determined at 2.1 Å resolution

Nostoc sp. PCC 7120 are filamentous cyanobacteria capable of both oxygenic photosynthesis and nitrogen fixation, with the latter taking place in specialized cells known as heterocysts that terminally differentiate from vegetative cells under conditions of nitrogen starvation. Cyanobacteria have existed on earth for more than 2 billion years and are thought to be responsible for oxygenation of the earth's atmosphere. Filamentous cyanobacteria such as Nostoc sp. PCC 7120 may also represent the oldest multicellular organisms on earth that undergo cell differentiation. Pentapeptide repeat proteins (PRPs), which occur most abundantly in cyanobacteria, adopt a right-handed quadrilateral β-helical structure, also referred to as a repeat five residue (Rfr) fold, with four-consecutive pentapeptide repeats constituting a single coil in the β-helical structure. PRPs are predicted to exist in all compartments within cyanobacteria including the thylakoid and cell-wall membranes as well as the cytoplasm and thylakoid periplasmic space. Despite their intriguing structure and importance to understanding ancient cyanobacteria, the biochemical function of PRPs in cyanobacteria remains largely unknown. Here we report the crystal structure of Alr1298, a PRP from Nostoc sp. PCC 7120 predicted to reside in the cytoplasm. The structure displays the typical right-handed quadrilateral β-helical structure and includes a four-α-helix cluster capping the N-terminus and a single α-helix capping the C-terminus. A gene cluster analysis indicated that Alr1298 may belong to an operon linked to cell proliferation and/or thylakoid biogenesis. Elevated alr1298 gene expression following nitrogen starvation indicates that Alr1298 may play a role in response to nitrogen starvation and/or heterocyst differentiation.

Transcriptomic survey on the microcystins production and growth of Microcystis aeruginosa under nitrogen starvation

Cyanobacteria are a vital component of freshwater phytoplankton, and many species are recognized for their ability to produce toxins and harmful algal blooms (HABs). Nitrogen is an essential element of all the complex macromolecules in algal cells. However, the underlying molecular mechanism of the changes in transcriptomic patterns and physiological responses in response to N starvation is poorly understood. The transcriptomes were generated via RNA-sequencing (RNA-Seq) technology to study the major metabolic pathway under N starvation. The results shed light on the mechanism of toxin production and physiological adaptations in Microcystis aeruginosa (M. aeruginosa). The cell density gradually increased during the first two days then declined over time and was finally stable at (15.50 ± 0.5) × 10⁵ cell mL^-1 after 6 days. The chlorophyll-a content and phycocyanin content of M. aeruginosa increased during the first two days and subsequently decreased markedly over time under N starvation. The variable to maximum chlorophyll fluorescence ratio (F_v/F_m ratio) decreased with time under N starvation. Most photosynthesis genes have similarity decreasing trends with growth physiological changes. The microcystins (MCs) levels generally increased first, reaching a peak value with 1.35 pg cell^-1 on the fifth day, and then remained roughly constant. The genes involved in N metabolism-related gene expression were upregulated to maintain normal biological activity, while the genes involved in photosynthesis-related gene expression were downregulated to save energy. All genes encoding algae toxin synthesis were upregulated under N starvation. The observed expression patterns demonstrate that all MCs genes respond similarly to MCs production within the cell. Our results indicate the response mechanism of M. aeruginosa under N starvation and provide a comprehensive understanding of N-controlling cyanobacteria and MCs synthesis.

Plasticity of Cyanobacterial Thylakoid Microdomains Under Variable Light Conditions

Photosynthetic light reactions proceed in thylakoid membranes (TMs) due to the activity of pigment-protein complexes. These complexes are heterogeneously organized into granal/stromal thylakoids (in plants) or into recently identified cyanobacterial microdomains (MDs). MDs are characterized by specific ratios of photosystem I (PSI), photosystem II (PSII), and phycobilisomes (PBS) and they are visible as sub-micrometer sized areas with different fluorescence ratios. In this report, the process of long-term plasticity in cyanobacterial thylakoid MDs has been explored under variable growth light conditions using Synechocystis sp. PCC6803 expressing YFP tagged PSI. TM organization into MDs has been observed for all categorized shapes of cells independently of their stage in cell cycle. The heterogeneous PSI, PSII, and PBS thylakoid areas were also identified under two types of growth conditions: at continuous light (CL) and at light-dark (L-D) cycle. The acclimation from CL to L-D cycle changed spatial distribution of photosystems, in particular PSI became more evenly distributed in thylakoids under L-D cycle. The process of the spatial PSI (and partially also PSII) redistribution required 1 week and was accompanied by temporal appearance of PBS decoupling probably caused by the re-organization of photosystems. The overall acclimation we observed was defined as TM plasticity as it resembles higher plants grana/stroma reorganization at variable growth light conditions. In addition, we observed large cell to cell variability in the actual MDs organization. It leads us to suggest that the plasticity, and cell to cell variability in MDs could be a manifestation of phenotypic heterogeneity, a recently broadly discussed phenomenon for prokaryotes.

A Bayesian risk assessment framework for microcystin violations of drinking water and recreational standards in the Bay of Quinte, Lake Ontario, Canada

Freshwater ecosystems can experience harmful algal blooms, which negatively impact recreational uses, aesthetics, taste, and odor in drinking water. Cyanobacterial toxins can have dire repercussions on aquatic wildlife and human health, and the most ubiquitous worldwide are the hepatotoxic compounds known as microcystins. The factors that influence the occurrence and magnitude of cyanobacteria blooms and toxin production vary in space and time and remain poorly understood. It is within this context that we present a suite of statistical models, parameterized with Bayesian inference techniques, to link the retrospective analysis of important environmental factors with the probability of exceedance of threshold microcystin levels. Our modelling framework is applied to the Bay of Quinte, Lake Ontario, Canada; a system with a long history of eutrophication problems. Collectively, 16.1% of the samples of the system collected during the study period (2003-2016) exceeded the drinking water guideline of 1.5 μgL^-1, while approximately 3% of recorded values exceeded the recommended recreational threshold of 20 μgL^-1. Using a segmented regression model with a stochastic breakpoint of microcystin concentrations estimated at 0.54 μg L^-1, we demonstrate that the environmental conditions associated with increased probability of exceedance of the drinking water standard are chlorophyll a concentration ≥7 μg L^-1, water temperature ≥20 °C, ammonium concentration ≤40 μgL^-1, total phosphorus concentration ≥25 μg L^-1, and wind speed ≤37 km h^-1. Considering the multitude of factors that can influence the ambient levels of toxins, our study argues that the adoption of probabilistic water quality criteria offers a pragmatic approach to accommodate the associated uncertainty by permitting a realistic frequency of violations. In this context, we present a framework to evaluate the confidence of compliance with probabilistic standards that stipulate less than 10% violations of microcystin threshold ambient levels.