Population-level coordination of pigment response in individual cyanobacterial cells under altered nitrogen levels

In Living Color: Pigment-Based Microbial Ecology At the Mineral-Air Interface

Pigment-based color is one of the most important phenotypic traits of biofilms at the mineral-air interface (subaerial biofilms, SABs), because it reflects the physiology of the microbial community. Because color is the hallmark of all SABs, we argue that pigment-based color could convey the mechanisms that drive microbial adaptation and coexistence across different terrestrial environments and link phenotypic traits to community fitness and ecological dynamics. Within this framework, we present the most relevant microbial pigments at the mineral-air interface and discuss some of the evolutionary landscapes that necessitate pigments as adaptive strategies for resource allocation and survivability. We report several pigment features that reflect SAB communities' structure and function, as well as pigment ecology in the context of microbial life-history strategies and coexistence theory. Finally, we conclude the study of pigment-based ecology by presenting its potential application and some of the key challenges in the research.

To Die or Not to Die—Regulated Cell Death and Survival in Cyanobacteria

Regulated cell death (RCD) is central to the development, integrity, and functionality of multicellular organisms. In the last decade, evidence has accumulated that RCD is a universal phenomenon in all life domains. Cyanobacteria are of specific interest due to their importance in aquatic and terrestrial habitats and their role as primary producers in global nutrient cycling. Current knowledge on cyanobacterial RCD is based mainly on biochemical and morphological observations, often by methods directly transferred from vertebrate research and with limited understanding of the molecular genetic basis. However, the metabolism of different cyanobacteria groups relies on photosynthesis and nitrogen fixation, whereas mitochondria are the central executioner of cell death in vertebrates. Moreover, cyanobacteria chosen as biological models in RCD studies are mainly colonial or filamentous multicellular organisms. On the other hand, unicellular cyanobacteria have regulated programs of cellular survival (RCS) such as chlorosis and post-chlorosis resuscitation. The co-existence of different genetically regulated programs in cyanobacterial populations may have been a top engine in life diversification. Development of cyanobacteria-specific methods for identification and characterization of RCD and wider use of single-cell analysis combined with intelligent image-based cell sorting and metagenomics would shed more light on the underlying molecular mechanisms and help us to address the complex colonial interactions during these events. In this review, we focus on the functional implications of RCD in cyanobacterial communities.

A biochemical, physiological and molecular evaluation of how the herbicide 2, 4-dichlorophenoxyacetic acid intercedes photosynthesis and diazotrophy in the cyanobacterium Nostoc muscorum Meg 1

Among the non-target microorganisms residing in crop fields that are potentially vulnerable to herbicides are cyanobacteria. They contribute to the maintenance of soil quality and fertility and hence are considered to be an important component of soil microflora. Consequently, the present study was aimed to check the influence of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) on some major parameters of carbon (CO₂) and nitrogen (N₂) fixations of a cyanobacterium Nostoc muscorum Meg 1 isolated from a rice field in Cherrapunji, Meghalaya, India. These include various photosynthetic pigments, the oxygen-evolving complex activity of the PSII, the protein contents of RuBisCO, D1 protein, isocitrate dehydrogenase (IDH), nitrogenase and glutamine synthetase (GS) enzymes, the heterocyst percentage, nitrogenase and GS enzyme activities, and production of total proteins and carbohydrates in the cyanobacterium in a varying range of 50 to 125 ppm doses of 2,4-D. The mRNA levels of several proteins were also analyzed. Besides carotenoid concentration that enhanced at 50 ppm, all other parameters were compromised by 2,4-D in a dose-dependent manner resulting in a reduction in photosynthetic and N₂-fixing activities. The negative effect on N₂-fixation was partly due to compromised IDH activity. RT-PCR analysis further showed that these negative effects were initiated at transcription levels as mRNA contents of all enzymes studied were found compromised under 2,4-D exposure. The scanning and transmission electron microscopy further revealed herbicide induced adverse changes in the morphology and ultrastructure of the organism. The significance of the work lies in its detailed analysis of the effect of 2,4-D at biochemical, physiological, and molecular levels.

Pigment analysis based on a line-scanning fluorescence hyperspectral imaging microscope combined with multivariate curve resolution

A rapid and cost-effective system is vital for the detection of harmful algae that causes environmental problems in terms of water quality. The approach for algae detection was to capture images based on hyperspectral fluorescence imaging microscope by detecting specific fluorescence signatures. With the high degree of overlapping spectra of algae, the distribution of pigment in the region of interest was unknown according to a previous report. We propose an optimization method of multivariate curve resolution (MCR) to improve the performance of pigment analysis. The reconstruction image described location and concentration of the microalgae pigments. This result indicated the cyanobacterial pigment distribution and mapped the relative pigment content. In conclusion, with the advantage of acquiring two-dimensional images across a range of spectra, HSI conjoining spectral features with spatial information efficiently estimated specific features of harmful microalgae in MCR models.

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.

A Novel Mode of Photoprotection Mediated by a Cysteine Residue in the Chlorophyll Protein IsiA

Oxygenic photosynthetic organisms have evolved a multitude of mechanisms for protection against high-light stress. IsiA, a chlorophyll a-binding cyanobacterial protein, serves as an accessory antenna complex for photosystem I. Intriguingly, IsiA can also function as an independent pigment protein complex in the thylakoid membrane and facilitate the dissipation of excess energy, providing photoprotection. The molecular basis of the IsiA-mediated excitation quenching mechanism remains poorly understood. In this study, we demonstrate that IsiA uses a novel cysteine-mediated process to quench excitation energy. The single cysteine in IsiA in the cyanobacterium Synechocystis sp. strain PCC 6803 was converted to a valine. Ultrafast fluorescence spectroscopic analysis showed that this single change abolishes the excitation energy quenching ability of IsiA, thus providing direct evidence of the crucial role of this cysteine residue in energy dissipation from excited chlorophylls. Under stress conditions, the mutant cells exhibited enhanced light sensitivity, indicating that the cysteine-mediated quenching process is critically important for photoprotection.

Primary role of increasing urea-N concentration in a novel Microcystis densa bloom: Evidence from ten years of field investigations and laboratory experiments

A novel Microcystis bloom caused by Microcystis densa has occurred in a typical subtropical reservoir every spring and summer since 2012, and it has caused several ecological and economic losses. To determine the environmental factors that influence the growth and physiological characteristics of M. densa, we investigated the variations in physicochemical factors and M. densa cell density from 2007 to 2017. The results showed that the urea-N concentration increased significantly (from 0.02 ± 0.00-0.20 ± 0.01 mg N l^-1), whereas other factors did not vary significantly. NO₃^--N and urea-N concentrations were higher than the NH₄⁺-N concentration during the M. densa bloom. The nitrogen composition changed, and urea-N and NO₃^--N became a major nitrogen sources in the reservoir. Water temperature and increased urea-N concentrations were the primary factors that influenced variations in M. densa cell density (45.5%, p < 0.05). Laboratory experiments demonstrated that M. densa cultured with urea-N exhibited a higher maximum cell density (9.8 ± 0.5 × 10⁸ cells l^-1), more cellular pigments for photosynthesis (chlorophyll a and phycocyanin) and photoprotection (carotenoid), and more proteins than those cultured with NH₄⁺-N and NO₃^--N. These results suggested that M. densa cultured with urea-N exhibited preferable growth and physiological conditions. Moreover, M. densa exhibited an increased maximum specific uptake rate (0.93 pg N cell^-1 h^-1) and reduced half-saturation constant (0.03 mg N l^-1) for urea-N compared with NH₄⁺-N and NO₃^--N, suggesting that M. densa preferred urea-N as its major nitrogen source. These results collectively indicated that the increasing urea-N concentration was beneficial for the growth and physiological conditions of M. densa. This study provided ten years of field data and detailed physiological information supporting the critical effect of urea-N on the growth of a novel bloom species M. densa. These findings helped to reveal the mechanism of M. densa bloom formation from the perspective of dissolved organic nitrogen.

Isolation and purification of glycoglycerolipids to induce apoptosis in breast cancer cells

Monogalactosyldiacylglycerol (MGDG) is the most abundant type of glycoglycerolipid found in the plant cell membrane and mostly in the chloroplast thylakoid membrane. The amphiphilic nature of MGDG is attractive in pharmaceutical fields for interaction with other biological molecules and hence exerting therapeutic anti-cancer, anti-viral, and anti-inflammatory activities. In this study, we investigated the therapeutic efficacy of cyanobacteria derived MGDG to inhibit breast cancer cell growth. MGDG was extracted from a cyanobacteria Synechocystis sp. PCC 6803 followed by a subsequent fractionation by column chromatographic technique. The purity and molecular structure of MGDG were analyzed by nuclear magnetic resonance (NMR) spectroscopy analysis. The presence of MGDG in the extracted fraction was further confirmed and quantified by high-performance liquid chromatography (HPLC). The anti-proliferation activity of the extracted MGDG molecule was tested against BT-474 and MDA-MB-231 breast cancer cell lines. The in vitro study showed that MGDG extracted from Synechocystis sp. PCC 6803 induced apoptosis in (70 ± 8) % of BT-474 (p < 0.001) and (58 ± 5) % of MDA-MB-231 cells (p < 0.001) using ~ 60 and 200 ng/ml of concentrations, respectively. The half-maximal inhibitory concentration, IC₅₀ of MGDG extracted from Synechocystis sp. PCC 6803 were (27.2 ± 7.6) and (150 ± 70) ng/ml in BT-474 and MDA-MB-231 cell lines, respectively. Quantification of caspase-3/7 activity using flow cytometry showed (3.0 ± 0.4) and (2.1 ± 0.04)-fold (p < 0.001) higher protein expressions in the MGDG treated BT-474 and MDA-MB-231 cells, respectively than untreated controls conferring to the caspase-dependent apoptosis. The MGDG did not show any significant cytotoxic side effects in human dermal fibroblasts cells. A commercially available MGDG control did not induce any apoptotic cell death in cancer cells substantiating the potential of the MGDG extracted from Synechocystis sp. PCC 6803 for the treatment of breast cancer cells through the apoptosis-mediated pathway.

Cellular localization of tolyporphins, unusual tetrapyrroles, in a microbial photosynthetic community determined using hyperspectral confocal fluorescence microscopy

The cyanobacterial culture HT-58-2, composed of a filamentous cyanobacterium and accompanying community bacteria, produces chlorophyll a as well as the tetrapyrrole macrocycles known as tolyporphins. Almost all known tolyporphins (A-M except K) contain a dioxobacteriochlorin chromophore and exhibit an absorption spectrum somewhat similar to that of chlorophyll a. Here, hyperspectral confocal fluorescence microscopy was employed to noninvasively probe the locale of tolyporphins within live cells under various growth conditions (media, illumination, culture age). Cultures grown in nitrate-depleted media (BG-11₀ vs. nitrate-rich, BG-11) are known to increase the production of tolyporphins by orders of magnitude (rivaling that of chlorophyll a) over a period of 30-45 days. Multivariate curve resolution (MCR) was applied to an image set containing images from each condition to obtain pure component spectra of the endogenous pigments. The relative abundances of these components were then calculated for individual pixels in each image in the entire set, and 3D-volume renderings were obtained. At 30 days in media with or without nitrate, the chlorophyll a and phycobilisomes (combined phycocyanin and phycobilin components) co-localize in the filament outer cytoplasmic region. Tolyporphins localize in a distinct peripheral pattern in cells grown in BG-11₀ versus a diffuse pattern (mimicking the chlorophyll a localization) upon growth in BG-11. In BG-11₀, distinct puncta of tolyporphins were commonly found at the septa between cells and at the end of filaments. This work quantifies the relative abundance and envelope localization of tolyporphins in single cells, and illustrates the ability to identify novel tetrapyrroles in the presence of chlorophyll a in a photosynthetic microorganism within a non-axenic culture.

Proteomic Insights into Phycobilisome Degradation, A Selective and Tightly Controlled Process in The Fast-Growing Cyanobacterium Synechococcus elongatus UTEX 2973

Phycobilisomes (PBSs) are large (3-5 megadalton) pigment-protein complexes in cyanobacteria that associate with thylakoid membranes and harvest light primarily for photosystem II. PBSs consist of highly ordered assemblies of pigmented phycobiliproteins (PBPs) and linker proteins that can account for up to half of the soluble protein in cells. Cyanobacteria adjust to changing environmental conditions by modulating PBS size and number. In response to nutrient depletion such as nitrogen (N) deprivation, PBSs are degraded in an extensive, tightly controlled, and reversible process. In Synechococcus elongatus UTEX 2973, a fast-growing cyanobacterium with a doubling time of two hours, the process of PBS degradation is very rapid, with 80% of PBSs per cell degraded in six hours under optimal light and CO₂ conditions. Proteomic analysis during PBS degradation and re-synthesis revealed multiple proteoforms of PBPs with partially degraded phycocyanobilin (PCB) pigments. NblA, a small proteolysis adaptor essential for PBS degradation, was characterized and validated with targeted mass spectrometry. NblA levels rose from essentially 0 to 25,000 copies per cell within 30 min of N depletion, and correlated with the rate of decrease in phycocyanin (PC). Implications of this correlation on the overall mechanism of PBS degradation during N deprivation are discussed.

Internalization and accumulation of model lignin breakdown products in bacteria and fungi

BACKGROUND

Valorization of lignin has the potential to significantly improve the economics of lignocellulosic biorefineries. However, its complex structure makes conversion to useful products elusive. One promising approach is depolymerization of lignin and subsequent bioconversion of breakdown products into value-added compounds. Optimizing transport of these depolymerization products into one or more organism(s) for biological conversion is important to maximize carbon utilization and minimize toxicity. Current methods assess internalization of depolymerization products indirectly-for example, growth on, or toxicity of, a substrate. Furthermore, no method has been shown to provide visualization of depolymerization products in individual cells.

RESULTS

We applied mass spectrometry to provide direct measurements of relative internalized concentrations of several lignin depolymerization compounds and single-cell microscopy methods to visualize cell-to-cell differences in internalized amounts of two lignin depolymerization compounds. We characterized internalization of 4-hydroxybenzoic acid, vanillic acid, p-coumaric acid, syringic acid, and the model dimer guaiacylglycerol-beta-guaiacyl ether (GGE) in the lignolytic organisms Phanerochaete chrysosporium and Enterobacter lignolyticus and in the non-lignolytic but genetically tractable organisms Saccharomyces cerevisiae and Escherichia coli. The results show varying degrees of internalization in all organisms for all the tested compounds, including the model dimer, GGE. Phanerochaete chrysosporium internalizes all compounds in non-lignolytic and lignolytic conditions at comparable levels, indicating that the transporters for these compounds are not specific to the lignolytic secondary metabolic system. Single-cell microscopy shows that internalization of vanillic acid and 4-hydroxybenzoic acid analogs varies greatly among individual fungal and bacterial cells in a given population. Glucose starvation and chemical inhibition of ATP hydrolysis during internalization significantly reduced the internalized amount of vanillic acid in bacteria.

CONCLUSIONS

Mass spectrometry and single-cell microscopy methods were developed to establish a toolset for providing direct measurement and visualization of relative internal concentrations of mono- and di-aryl compounds in microbes. Utilizing these methods, we observed broad variation in intracellular concentration between organisms and within populations and this may have important consequences for the efficiency and productivity of an industrial process for bioconversion. Subsequent application of this toolset will be useful in identifying and characterizing specific transporters for lignin-derived mono- and di-aryl compounds.

Photosynthetic physiological performance and proteomic profiling of the oleaginous algae Scenedesmus acuminatus reveal the mechanism of lipid accumulation under low and high nitrogen supplies

In this study, we presented cellular morphological changes, time-resolved biochemical composition, photosynthetic performance and proteomic profiling to capture the photosynthetic physiological response of Scenedesmus acuminatus under low nitrogen (3.6 mM NaNO₃, N^-) and high nitrogen supplies (18.0 mM NaNO₃, N⁺). S. acuminatus cells showed extensive lipid accumulation (53.7% of dry weight) and were enriched in long-chain fatty acids (C16 & C18) under low nitrogen supply. The activity of PSII and photosynthetic rate decreases, whereas non-photochemical quenching and dark respiration rates were increased in the N^- group. In addition, the results indicated a redistribution of light excitation energy between PSII and PSI in S. acuminatus exists before lipid accumulation. The iTRAQ results showed that, under high nitrogen supply, protein abundance of the chlorophyll biosynthesis, the Calvin cycle and ribosomal proteins decreased in S. acuminatus. In contrast, proteins associated with the photosynthetic machinery, except for F-type ATPase, were increased in the N⁺ group (N⁺, 3 vs. 9 days and 3 days, N⁺ vs. N^-). Under low nitrogen supply, proteins involved in central carbon metabolism, fatty acid synthesis and branched-chain amino acid metabolism were increased, whereas the abundance of proteins of the photosynthetic machinery had decreased, with exception of PSI (N^-, 3 vs. 9 days and 9 days, N⁺ vs. N^-). Collectively, the current study has provided a basis for the metabolic engineering of S. acuminatus for biofuel production.

Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria

Dissolved organic matter (DOM) plays a central role in the microbial ecology and biogeochemistry of aquatic environments, yet little is known about how the mechanism of DOM release from its ultimate source, primary producer biomass, affects the molecular composition of the inputs to the dissolved pool. Here we used a model marine phytoplankton, the picocyanobacterium Synechococcus WH7803, to compare the composition of DOM released by three mechanisms: exudation, mechanical cell lysis and infection by the lytic phage S-SM1. A broad, untargeted analytical approach reveals the complexity of this freshly sourced DOM, and comparative analysis between DOM produced by the different mechanisms suggests that exudation and viral lysis are sources of unsaturated, oxygen-rich and possibly novel biomolecules. Furthermore, viral lysis of WH7803 by S-SM1 releases abundant peptides derived from specific proteolysis of the major light-harvesting protein phycoerythrin, raising the possibility that phage infection of these abundant cyanobacteria could be a significant source of high molecular weight dissolved organic nitrogen compounds.

Phycocyanin Production by Aphanothece microscopica Nägeli in Synthetic Medium Supplemented with Sugarcane Vinasse

This study focused on the evaluation of mixotrophic and heterotrophic production of phycocyanin by A. microscopica, analysis of kinetic parameters, the effect of freezing and thawing on phycocyanin yield, and nutrient removal during heterotrophic growth. During mixotrophic growth, maximum phycocyanin yield (1.50 mg_phycocyanin g^-1_biomass) was obtained after 12 h, while the heterotrophic cultivation yielded 1.39 mg_phycocyanin g^-1_biomass. The mixotrophic cultivation of A. microscopica showed maximum specific growth rate of 0.025 h^-1, against 0.010 h^-1 for the photoautotrophic cultivation, and 0.08 h^-1 in heterotrophic conditions. The mixotrophic cultivation had a specific rate of phycocyanin production of 9.86 mg_phycocyanin mg_biomass^-1 h^-1, while the photoautotrophic had 2.81 mg_phycocyanin mg_biomass^-1 h^-1, and the heterotrophic, 49.18 mg_phycocyanin mg_biomass^-1 h^-1. Carbon and nitrogen contents present in sugarcane vinasse were decreased in 16.69 and 15.97%, respectively, after 6 h of heterotrophic growth. Thus, it was shown that the mixotrophic production of phycocyanin by Aphanothece microscopica Nägeli in BG11 medium supplemented with vinasse is feasible.

Chlorosis as a Developmental Program in Cyanobacteria: The Proteomic Fundament for Survival and Awakening

Cyanobacteria that do not fix atmospheric nitrogen gas survive prolonged periods of nitrogen starvation in a chlorotic, dormant state where cell growth and metabolism are arrested. Upon nutrient availability, these dormant cells return to vegetative growth within 2-3 days. This resuscitation process is highly orchestrated and relies on the stepwise reinstallation and activation of essential cellular structures and functions. We have been investigating the transition to chlorosis and the return to vegetative growth as a simple model of a cellular developmental process and a fundamental survival strategy in biology. In the present study, we used quantitative proteomics and phosphoproteomics to describe the proteomic landscape of a dormant cyanobacterium and its dynamics during the transition to vegetative growth. We identified intriguing alterations in the set of ribosomal proteins, in RuBisCO components, in the abundance of central regulators and predicted metabolic enzymes. We found O-phosphorylation as an abundant protein modification in the chlorotic state, specifically of metabolic enzymes and proteins involved in photosynthesis. Nondegraded phycobiliproteins were hyperphosphorylated in the chlorotic state. We provide evidence that hyperphosphorylation of the terminal rod linker CpcD increases the lifespan of phycobiliproteins during chlorosis.