NMR-Based Metabolomic Approach To Elucidate the Differential Cellular Responses during Mitigation of Arsenic(III, V) in a Green Microalga

Omics advancements towards exploring arsenic toxicity and tolerance in plants: a review

MAIN CONCLUSION

Omics approaches provide comprehensive insights into plant arsenic stress responses, setting the stage for engineering arsenic-tolerant crops. Understanding arsenic (As) toxicity in plants is crucial for environmental and agricultural sustainability, considering the implications of As in impacting soil productivity and environmental health. Although some articles already examined the detailed molecular mechanisms behind As toxicity and tolerance, a comprehensive review of recent omics advancements in studying plant responses to As exposure is needed. The present review highlights the valuable contribution of omics approaches (genomics, transcriptomics, proteomics, and metabolomics) to characterize the intricate response to As overall, which could empower As-tolerant plant development. Genomic techniques, such as QTL mapping, GWAS, RAPD, and SSH, hold the potential to provide valuable insights into the genetic diversity and expression patterns associated with the plant response to As stress, highlighting also the power of new advanced technology such as CRISPR-Cas9. Transcriptomics approaches (e.g., microarrays and RNA sequencing) revealed gene expression patterns in plants under As stress, emphasizing the role of sulfur metabolism in As tolerance. Proteomics, using 2-DE combined with MALDI-ToF MS or ESI-MS/MS, offers insights into the stress-inducible proteins and their involvement in As toxicity mitigation, while iTRAQ-based proteomics enabled an understanding of cultivar-specific responses under high As concentration. Metabolomics, with LC-MS, GC-MS, (U)HPLC, and NMR, elucidated small molecule alterations and complex metabolic activities occurring under As plant exposure. Compendium of data and evidence-related tools offers a foundation for advancing As-tolerant plant development and promoting environmental and agricultural resilience.

Industrial scale-up of flue gas bio-mitigation with chemolithotrophs in packed bed reactors: Exploring metabolite synthesis, mass transfer, and techno-economic analysis

Elevated emissions of flue gases deteriorate the quality of air, impacting both terrestrial and aquatic ecosystems through their contribution to acid rain and eutrophication. This study examines the bio-mitigation process in a packed bed reactor and its capacity to concurrently decrease the environmental consequences of industrial flue gases (CO2, NO, and SO2) and wastewater by employing mixed bacterial consortia. The highest biomass productivity achieved during the growth phase was 0.002 g L-1 h-1 in the aqueous medium and 0.006 g L-1 h-1 in the PU foam. The highest level of CO2 removal efficiency was 86.60%, while for NO and SO2, it was 77.03% and 82%, respectively. The comprehensive nutrient balance analysis revealed that the flue gas was primarily utilized for biomass assimilation. The FT-IR and GC-MS analysis detected metabolites, including carboxylic acids, esters, and fatty alcohols, that were produced during the process. The NMR study examined alterations in the concentration of metabolites within the cell, indicating metabolic pathways such as the TCA cycle, alanine, pyruvate, butanoate metabolism, and glycolysis. The mass transfer coefficient estimated for the gas-liquid-solid phase was ∼2.0 m s-1 for the flue gases. The scale-up of the reactor based on the mass transfer coefficient up to 20,000 L gives a net present value of $2,66,116.13 with a benefit-to-cost ratio of 1.47. Therefore, this study suggests that employing bacteria is a viable and energy-efficient approach to mitigate the adverse effects of flue gas on air quality. Additionally, it aids industries in minimizing waste and repurposing it for advantageous purposes, thereby diminishing their environmental footprint.

Sustainable synergistic approach to chemolithotrophs-supported bioremediation of wastewater and flue gas

Flue gas emissions are the waste gases produced during the combustion of fuel in industrial processes, which are released into the atmosphere. These identical processes also produce a significant amount of wastewater that is released into the environment. The current investigation aims to assess the viability of simultaneously mitigating flue gas emissions and remediating wastewater in a bubble column bioreactor utilizing bacterial consortia. A comparative study was done on different growth media prepared using wastewater. The highest biomass yield of 3.66 g L-1 was achieved with the highest removal efficiencies of 89.80, 77.30, and 80.77% for CO2, SO2, and NO, respectively. The study investigated pH, salinity, dissolved oxygen, and biochemical and chemical oxygen demand to assess their influence on the process. The nutrient balance validated the ability of bacteria to utilize compounds in flue gas and wastewater for biomass production. The Fourier Transform-Infrared Spectrometry (FT-IR) and Gas Chromatography-Mass Spectrometry (GC-MS) analyses detected commercial-use long-chain hydrocarbons, fatty alcohols, carboxylic acids, and esters in the biomass samples. The nuclear magnetic resonance (NMR) metabolomics detected the potential mechanism pathways followed by the bacteria for mitigation. The techno-economic assessment determined a feasible total capital investment of 245.74$ to operate the reactor for 288 h. The bioreactor's practicability was determined by mass transfer and thermodynamics assessment. Therefore, this study introduces a novel approach that utilizes bacteria and a bioreactor to mitigate flue gas and remediate wastewater.

Integrating physiological and multi-omics methods to elucidate heat stress tolerance for sustainable rice production

Heat stress presents unique challenges compared to other environmental stressors, as predicting crop responses and understanding the mechanisms for heat tolerance are complex tasks. The escalating impact of devastating climate changes heightens the frequency and intensity of heat stresses, posing a noteworthy threat to global agricultural productivity, especially in rice-dependent regions of the developing world. Humidity has been demonstrated to negatively affect rice yields worldwide. Plants have evolved intricate biochemical adaptations, involving intricate interactions among genes, proteins, and metabolites, to counter diverse external signals and ensure their survival. Modern-omics technologies, encompassing transcriptomics, metabolomics, and proteomics, have revolutionized our comprehension of the intricate biochemical and cellular shifts that occur in stressed agricultural plants. Integrating these multi-omics approaches offers a comprehensive view of cellular responses to heat stress and other challenges, surpassing the insights gained from multi-omics analyses. This integration becomes vital in developing heat-tolerant crop varieties, which is crucial in the face of increasingly unpredictable weather patterns. To expedite the development of heat-resistant rice varieties, aiming at sustainability in terms of food production and food security globally, this review consolidates the latest peer-reviewed research highlighting the application of multi-omics strategies.

Phycoremediation of As(III) and Cr(VI) by Desmodesmus subspicatus: Impact on growth and biomolecules (carbohydrate, protein, chlorophyll and lipid) - A dual mode investigation

Microalgae are under research focus for the simultaneous production of biomolecules (e.g., carbohydrates, proteins, pigments and lipids) and bioremediation of toxic substances from wastewater. The current study explores the capability of indigenously isolated microalgae (Desmodesmus subspicatus) for the phycoremediation of As(III) and Cr(VI). Variation of biomolecules (carbohydrate, protein, lipid and chlorophyll) was investigated during phycoremediation. D. subspicatus survived up to the toxicity level of 10 mg/L for As(III) and 0.8 mg/L for Cr(VI). A 70% decline in carbohydrate accumulation was observed at 10 mg/L of As(III). An increased content of proteins (+ 28%) and lipids (+ 32%) within the cells was observed while growing in 0.5 and 0.2 mg/L of As(III) and Cr(VI) respectively. A decrease in carbohydrate accumulation was noted with increasing Cr(VI) concentration, and the lowest (- 44%) was recorded at 0.8 mg/L Cr(VI). D. subspicatus showed an excellent maximum removal efficiency for Cr(VI) and As(III) as 77% and 90% respectively.

Deciphering Bisphenol A degradation by Coelastrella sp. M60: unravelling metabolic insights through metabolomics analysis

Microalgae, owing to their efficacy and eco-friendliness, have emerged as a promising solution for mitigating the toxicity of Bisphenol A (BPA), a hazardous environmental pollutant. This current study was focused on the degradation of BPA by Coelastrella sp. M60 at various concentrations (10-50 mg/L). Further, the metabolic profiling of Coelastrella sp. M60 was performed using GC-MS analysis, and the results were revealed that BPA exposure modulated the metabolites profile with the presence of intermediates of BPA. In addition, highest lipid (43%) and pigment content (40%) at 20 and 10 mg/L of BPA respectively exposed to Coelastrella sp. M60 was achieved and enhanced fatty acid methyl esters recovery was facilitated by Cuprous oxide nanoparticles synthesised using Spatoglossum asperum. Thus, this study persuades thepotential of Coelastrella sp. M60 for BPA degradation and suggesting new avenues to remove the emerging contaminants in polluted water bodies and targeted metabolite expression in microalgae.

Metabolic responses of Euglena gracilis under photoheterotrophic and heterotrophic conditions

The protist Euglena gracilis has various trophic modes including heterotrophy and photoheterotrophy. To investigate how cultivation mode influences metabolic regulation, the chemical composition of cellular metabolites of Euglena gracilis grown under heterotrophic and photoheterotrophic conditions was monitored from the early exponential phase to the mid-stationary phase using two different techniques, i.e, nuclear magnetic resonance (NMR) spectroscopy and high-resolution mass spectrometry (HRMS). The combined metabolomics approach allowed an in-depth understanding of the mechanism of photoheterotrophic and heterotrophic growth for biomolecule production. Heterotrophic conditions promoted the production of polar amino and oxygenated compounds such as proteins and polyphenol compounds, especially at the end of the exponential phase while photoheterotrophic cells enhanced the production of organoheterocyclic compounds, carbohydrates, and alkaloids.

Meta-metabolomic responses of river biofilms to cobalt exposure and use of dose-response model trends as an indicator of effects

The response of the meta-metabolome is rarely used to characterize the effects of contaminants on a whole community. Here, the meta-metabolomic fingerprints of biofilms were examined after 1, 3 and 7 days of exposure to five concentrations of cobalt (from background concentration to 1 × 10-5 M) in aquatic microcosms. The untargeted metabolomic data were processed using the DRomics tool to build dose-response models and to calculate benchmark-doses. This approach made it possible to use 100% of the chemical signal instead of being limited to the very few annotated metabolites (7%). These benchmark-doses were further aggregated into an empirical cumulative density function. A trend analysis of the untargeted meta-metabolomic feature dose-response curves after 7 days of exposure suggested the presence of a concentration range inducing defense responses between 1.7 × 10-9 and 2.7 × 10-6 M, and of a concentration range inducing damage responses from 2.7 × 10-6 M and above. This distinction was in good agreement with changes in the other biological parameters studied (biomass and chlorophyll content). This study demonstrated that the molecular defense and damage responses can be related to contaminant concentrations and represents a promising approach for environmental risk assessment of metals.

Advances in Algomics technology: Application in wastewater treatment and biofuel production

Advanced sustainable bioremediation is gaining importance with rising global pollution. This review examines microalgae's potential for sustainable bioremediation and process enhancement using multi-omics approaches. Recently, microalgae-bacterial consortia have emerged for synergistic nutrient removal, allowing complex metabolite exchanges. Advanced bioremediation requires effective consortium design or pure culture based on the treatment stage and specific roles. The strain potential must be screened using modern omics approaches aligning wastewater composition. The review highlights crucial research gaps in microalgal bioremediation. It discusses multi-omics advantages for understanding microalgal fitness concerning wastewater composition and facilitating the design of microalgal consortia based on bioremediation skills. Metagenomics enables strain identification, thereby monitoring microbial dynamics during the treatment process. Transcriptomics and metabolomics encourage the algal cell response toward nutrients and pollutants in wastewater. Multi-omics role is also summarized for product enhancement to make algal treatment sustainable and fit for sustainable development goals and growing circular bioeconomy scenario.

Compound-Specific 1D 1H NMR Pulse Sequence Selection for Metabolomics Analyses

NMR-based metabolomics approaches have been used in a wide range of applications, for example, with medical, plant, and marine samples. One-dimensional (1D) ¹H NMR is routinely used to find out biomarkers in biofluids such as urine, blood plasma, and serum. To mimic biological conditions, most NMR studies have been carried out in an aqueous solution where the high intensity of the water peak is a major problem in obtaining a meaningful spectrum. Different methods have been used to suppress the water signal, including 1D Carr-Purcell-Meiboom-Gill (CPMG) presat, consisting of a T₂ filter to suppress macromolecule signals and reduce the humped curve in the spectrum. 1D nuclear Overhauser enhancement spectroscopy (NOESY) is another method for water suppression that is used routinely in plant samples with fewer macromolecules than in biofluid samples. Other common 1D ¹H NMR methods such as 1D ¹H presat and 1D ¹H ES have simple pulse sequences; their acquisition parameters can be set easily. The proton with presat has just one pulse and the presat block causes water suppression, while other 1D ¹H NMR methods including those mentioned above have more pulses. However, it is not well known in metabolomics studies because it is used only occasionally and in a few types of samples by metabolomics experts. Another effective method is excitation sculpting to suppress water. Herein, we evaluate the effect of method selection on signal intensities of commonly detected metabolites. Different classes of samples including biofluid, plant, and marine samples were investigated, and recommendations on the advantages and limitations of each method are presented.

Improvements in Bioremediation Agents and Their Modified Strains in Mediating Environmental Pollution

Environmental pollution has been a significant concern around the globe as the release of toxic pollutants is associated with carcinogenic, mutagenic, and teratogenic impacts on living organisms. Since microorganisms have the natural potential to degrade toxic metabolites into nontoxic forms, an eco-friendly approach known as bioremediation has been used to tackle toxic-induced pollution. Bioremediation has three fundamental levels, i.e., natural attenuation, bio-augmentation, and biostimulation in which the synthetic biology approach has been lately utilized to enhance the conventional bioremediation techniques. Recently, a more advanced approach of programmable nucleases such as zinc finger nucleases, tale-like effector nucleases, and clustered regularly interspaced short palindromic repeats Cas is being employed to engineer several bacterial, fungal, and algal strains for targeted mutagenesis by knocking in and out specific genes which are involved in reconstructing the metabolic pathways of native microbes. These genetically engineered microorganisms possess heavy metal resistance, greater substrate range, enhanced enzymatic activity, and binding affinity which accelerate the biodegradation of toxic pollutants to environmentally safe levels. This review provides a comprehensive understanding of how we can correlate the novel genetics-based approaches employed to produce genetically engineered microorganisms to enhance the biodegradation of hazardous pollutants, hence, developing a clean and sustainable ecosystem.

Microalgal-induced remediation of wastewaters loaded with organic and inorganic pollutants: An overview

The recent surge in industrialization has intensified the accumulation of various types of organic and inorganic pollutants due to the illegal dumping of partially and/or untreated wastewater effluents in the environment. The pollutants emitted by several industries pose serious risk to the environment, animals and human beings. Management and diminution of these hazardous organic pollutants have become an incipient research interest. Traditional physiochemical methods are energy intensive and produce secondary pollutants. So, bioremediation via microalgae has appeared to be an eco-friendly and sustainable technique to curb the adverse effects of organic and inorganic contaminants because microalgae can degrade complex organic compounds and convert them into simpler and non-toxic substances without the release of secondary pollutants. Even some of the organic pollutants can be exploited by microalgae as a source of carbon in mixotrophic cultivation. Literature survey has revealed that use of the latest modification techniques for microalgae such as immobilization (on alginate, carrageena and agar), pigment-extraction, and pretreatment (with acids) have enhaced their bioremedial potential. Moreover, microalgal components i.e., biopolymers and extracellular polymeric substances (EPS) can potentially be exploited in the biosorption of pollutants. Though bioremediation of wastewaters by microalgae is quite well-studied realm but some aspects like structural and functional responses of microalgae toward pollutant derivatives/by-products (formed during biodegradation), use of genetic engineering to improve the tolerance of microalgae against higher concentrations of polluatans, and harvesting cost reduction, and monitoring of parameters at large-scale still need more focus. This review discusses the accumulation of different types of pollutants into the environment through various sources and the mechanisms used by microalgae to degrade commonly occurring organic and inorganic pollutants.

Overexpression of bacteriophage T4 and T7 endolysins differentially regulate the metabolic fingerprint of host Escherichia coli

Bioactive proteins are often overexpressed in different host systems for biotechnological/biomedical applications. Endolysins are natural bactericidal proteins that cleave the bacterial peptidoglycan membrane, and have the potential to be the next-generation enzybiotics. Therefore, the present study aims to elucidate the impact of two endolysins (T4L, T7L) overexpression on metabolic fingerprint of E. coli using NMR spectroscopy. The ¹H NMR-based metabolomics analysis revealed global metabolite profiles of E. coli in response to endolysins. The study has identified nearly 75 metabolites, including organic acids, amino acids, sugars and nucleic acids. RNA Polymerase (RNAP) has been considered as reference protein for marking the specific alterations in metabolic pathways. The data suggested downregulation of central carbon metabolic pathway in both endolysins overexpression, but to a different extent. Also, the endolysin overexpression have highlighted the enhanced metabolic load and stress generation in the host cells, thus leading to the activation of osmoregulatory pathways. The overall changes in metabolic fingerprint of E. coli highlights the enhanced perturbations during the overexpression of T4L as compared to T7L. These untargeted metabolic studies shed light on the regulation of molecular pathways during the heterologous overexpression of these lytic enzymes that are lethal to the host.

Elucidating the lactic acid tolerance mechanism in vaginal clinical isolates of Candida glabrata

Incidence of vulvovaginal candidiasis are strikingly high and treatment options are limited with nearly 50% Candida glabrata cases left untreated or experience treatment failures. The vaginal microenvironment is rich in lactic acid, and the adaptation of C. glabrata to lactic acid (LA) is the main reason for clinical treatment failure. In the present study, C. glabrata and its vaginal clinical isolates were comprehensively investigated for their growth response, metabolic adaptation and altered cellular pathway to LA using different biochemical techniques, metabolic profiling and transcriptional studies. C. glabrata shown considerable variations in its topological and biochemical features without compromising growth in LA media. Chemical profiling data highlighted involvement of cell wall/membrane, ergosterol and oxidative stress related pathways in mediating adaptative response of C. glabrata towards LA. Further, one dimensional proton (1H) NMR spectroscopy based metabolic profiling revealed significant modulation in 19 metabolites of C. glabrata cells upon growth in LA. Interestingly myo-inositol, xylose, putrescine and betaine which are key metabolites for cell growth and viability were found to be differentially expressed by clinical isolates. These observations were supported by the transcriptional expression study of selected genes evidencing cell wall/membrane re-organisation, altered oxidative stress, and reprogramming of carbon metabolic pathways. Collectively, the study advances our understanding on adaptative response of C. glabrata in vaginal microenvironment to lactic acid for survival and virulence.

Molecular investigations on Candida glabrata clinical isolates for pharmacological targeting

Prevalence of drug resistant C. glabrata strains in hospitalized immune-compromised patients with invasive fungal infections has increased at an unexpected pace. This has greatly pushed researchers in identification of mutations/variations in clinical isolates for better assessment of the prevailing drug resistance trends and also for updating of antifungal therapy regime. In the present investigation, the clinical isolates of C. glabrata were comprehensively characterized at a molecular level using metabolic profiling and transcriptional expression analysis approaches in combination with biochemical, morphological and chemical profiling methods. Biochemically, significant variations in azole susceptibility, surface hydrophobicity, and oxidative stress generation were observed among the isolates as compared to wild-type. The 1H NMR profiling identified 18 differential metabolites in clinical strains compared to wild-type and were classified into five categories, that include: sugars (7), amino acids and their derivatives (7), nitrogen bases (3) and coenzymes (1). Transcriptional analysis of selective metabolic and regulatory enzymes established that the major differences were found in cell membrane stress, carbohydrate metabolism, amino acid biosynthesis, ergosterol pathway and turnover of nitrogen bases. This detailed molecular level/metabolic fingerprint study is a useful approach for differentiating pathogenic/clinical isolates to that of wild-type. This study comprehensively delineated the differential cellular pathways at a molecular level that have been re-wired by the pathogenic clinical isolates for enhanced pathogenicity and virulence traits.

Impact of Nitrate and Ammonium Concentrations on Co-Culturing of Tetradesmus obliquus IS2 with Variovorax paradoxus IS1 as Revealed by Phenotypic Responses

Mutual interactions in co-cultures of microalgae and bacteria are well known for establishing consortia and nutrient uptake in aquatic habitats, but the phenotypic changes in terms of morphological, physiological, and biochemical attributes that drive these interactions have not been clearly understood. In this novel study, we demonstrated the phenotypic response in a co-culture involving a microalga, Tetradesmus obliquus IS2, and a bacterium, Variovorax paradoxus IS1, grown with varying concentrations of two inorganic nitrogen sources. Modified Bold's basal medium was supplemented with five ratios (%) of NO₃-N:NH₄-N (100:0, 75:25, 50:50, 25:75, and 0:100), and by maintaining N:P Redfield ratio of 16:1. The observed morphological changes in microalga included an increase in granularity and a broad range of cell sizes under the influence of increased ammonium levels. Co-culturing in presence of NO₃-N alone or combination with NH₄-N up to equimolar concentrations resulted in complete nitrogen uptake, increased growth in both the microbial strains, and enhanced accumulation of carbohydrates, proteins, and lipids. Total chlorophyll content in microalga was also significantly higher when it was grown as a co-culture with NO₃-N and NH₄-N up to a ratio of 50:50. Significant upregulation in the synthesis of amino acids and sugars and downregulation of organic acids were evident with higher ammonium uptake in the co-culture, indicating the regulation of carbon and nitrogen assimilation pathways and energy synthesis. Our data suggest that the co-culture of strains IS1 and IS2 could be exploited for effluent treatment by considering the concentrations of inorganic sources, particularly ammonium, in the wastewaters.

Multi-Fold Enhancement of Tocopherol Yields Employing High CO2 Supplementation and Nitrate Limitation in Native Isolate Monoraphidium sp

Tocopherols are the highly active form of the antioxidant molecules involved in scavenging of free radicals and protect the cell membranes from reactive oxygen species (ROS). In the present study, we focused on employing carbon supplementation with varying nitrate concentrations to enhance the total tocopherol yields in the native isolate Monoraphidium sp. CABeR41. The total tocopherol productivity of NRHC (Nitrate replete + 3% CO2) supplemented was (306.14 µg·L−1 d−1) which was nearly 2.5-fold higher compared to NRVLC (Nitrate replete + 0.03% CO2) (60.35 µg·L−1 d−1). The best tocopherol productivities were obtained in the NLHC (Nitrate limited + 3% CO2) supplemented cells (734.38 µg·L−1 d−1) accompanied by a significant increase in cell biomass (2.65-fold) and total lipids (6.25-fold). Further, global metabolomics using gas chromatography-mass spectrometry (GC-MS) was done in the defined conditions to elucidate the molecular mechanism during tocopherol accumulation. In the present study, the Monoraphidium sp. responded to nitrogen limitation by increase in nitrogen assimilation, with significant upregulation in gamma-Aminobutyric acid (GABA). Moreover, the tricarboxylic acid (TCA) cycle upregulation depicted increased availability of carbon skeletons and reducing power, which is leading to increased biomass yields along with the other biocommodities. In conclusion, our study depicts valorization of carbon dioxide as a cost-effective alternative for the enhancement of biomass along with tocopherols and other concomitant products like lipids and carotenoids in the indigenous strain Monoraphidium sp., as an industrial potential strain with relevance in nutraceuticals and pharmaceuticals.

Cytotoxicity and 1H NMR metabolomics analyses of microalgal extracts for synergistic application with Tamoxifen on breast cancer cells with reduced toxicity against Vero cells

This study evaluated the cytotoxic activity of Tamoxifen (TMX), an anti-estrogen drug, with microalgal crude extracts (MCEs) in single and synergistic application (TMX-MCEs) on MCF-7 and 4T1 breast cancer cells, and non-cancerous Vero cells. The MCEs of Nannochloropsis oculata, Tetraselmis suecica and Chlorella sp. from five different solvents (methanol, MET; ethanol, ETH; water, W; chloroform, CHL; and hexane, HEX) were developed. The TMX-MCEs-ETH and W at the 1:2 and 1:3 ratios, attained IC50 of 15.84-29.51 μg/mL against MCF-7; 13.8-31.62 μg/mL against 4T1; and 24.54-85.11 μg/mL against Vero cells. Higher late apoptosis was exhibited against MCF-7 by the TMX-N. oculata-ETH (41.15 %); and by the TMX-T. suecica-ETH (65.69 %) against 4T1 cells. The TMX-T. suecica-ETH also showed higher ADP/ATP ratios, but comparable Caspase activities to control. For Vero cells, overall apoptotic effects were lowered with synergistic application, and only early apoptosis was higher with TMX-T. suecica-ETH but at lower levels (29.84 %). The MCEs-W showed the presence of alanine, oleic acid, linoleic acid, lactic acid, and fumaric acid. Based on Principal Component Analysis (PCA), the spectral signals for polar solvents such as MET and ETH, were found in the same cluster, while the non-polar solvent CHL was with HEX, suggesting similar chemical profiles clustered for the same polarity. The CHL and HEX were more effective with N. oculata and T. suecica which were of the marine origin, while the ETH and MET were more effective with Chlorella sp., which was of the freshwater origin. The synergistic application of microalgal bioactive compounds with TMX can maintain the cytotoxicity against breast cancer cells whilst reducing the toxicity against non-cancerous Vero cells. These findings will benefit the biopharmaceutical, and functional and healthy food industries.

Physiological and Multi-Omics Approaches for Explaining Drought Stress Tolerance and Supporting Sustainable Production of Rice

Drought differs from other natural disasters in several respects, largely because of the complexity of a crop's response to it and also because we have the least understanding of a crop's inductive mechanism for addressing drought tolerance among all abiotic stressors. Overall, the growth and productivity of crops at a global level is now thought to be an issue that is more severe and arises more frequently due to climatic change-induced drought stress. Among the major crops, rice is a frontline staple cereal crop of the developing world and is critical to sustaining populations on a daily basis. Worldwide, studies have reported a reduction in rice productivity over the years as a consequence of drought. Plants are evolutionarily primed to withstand a substantial number of environmental cues by undergoing a wide range of changes at the molecular level, involving gene, protein and metabolite interactions to protect the growing plant. Currently, an in-depth, precise and systemic understanding of fundamental biological and cellular mechanisms activated by crop plants during stress is accomplished by an umbrella of -omics technologies, such as transcriptomics, metabolomics and proteomics. This combination of multi-omics approaches provides a comprehensive understanding of cellular dynamics during drought or other stress conditions in comparison to a single -omics approach. Thus a greater need to utilize information (big-omics data) from various molecular pathways to develop drought-resilient crop varieties for cultivation in ever-changing climatic conditions. This review article is focused on assembling current peer-reviewed published knowledge on the use of multi-omics approaches toward expediting the development of drought-tolerant rice plants for sustainable rice production and realizing global food security.

Advances in "Omics" Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

Food safety has emerged as a high-urgency matter for sustainable agricultural production. Toxic metal contamination of soil and water significantly affects agricultural productivity, which is further aggravated by extreme anthropogenic activities and modern agricultural practices, leaving food safety and human health at risk. In addition to reducing crop production, increased metals/metalloids toxicity also disturbs plants' demand and supply equilibrium. Counterbalancing toxic metals/metalloids toxicity demands a better understanding of the complex mechanisms at physiological, biochemical, molecular, cellular, and plant level that may result in increased crop productivity. Consequently, plants have established different internal defense mechanisms to cope with the adverse effects of toxic metals/metalloids. Nevertheless, these internal defense mechanisms are not adequate to overwhelm the metals/metalloids toxicity. Plants produce several secondary messengers to trigger cell signaling, activating the numerous transcriptional responses correlated with plant defense. Therefore, the recent advances in omics approaches such as genomics, transcriptomics, proteomics, metabolomics, ionomics, miRNAomics, and phenomics have enabled the characterization of molecular regulators associated with toxic metal tolerance, which can be deployed for developing toxic metal tolerant plants. This review highlights various response strategies adopted by plants to tolerate toxic metals/metalloids toxicity, including physiological, biochemical, and molecular responses. A seven-(omics)-based design is summarized with scientific clues to reveal the stress-responsive genes, proteins, metabolites, miRNAs, trace elements, stress-inducible phenotypes, and metabolic pathways that could potentially help plants to cope up with metals/metalloids toxicity in the face of fluctuating environmental conditions. Finally, some bottlenecks and future directions have also been highlighted, which could enable sustainable agricultural production.

Metabolomics-based engineering for biofuel and bio-based chemical production in microalgae and cyanobacteria: A review

Metabolomics, an essential tool in modern synthetic biology based on the design-build-test-learn platform, is useful for obtaining a detailed understanding of cellular metabolic mechanisms through comprehensive analyses of the metabolite pool size and its dynamic changes. Metabolomics is critical to the design of a rational metabolic engineering strategy by determining the rate-limiting reaction and assimilated carbon distribution in a biosynthetic pathway of interest. Microalgae and cyanobacteria are promising photosynthetic producers of biofuels and bio-based chemicals, with high potential for developing a bioeconomic society through bio-based carbon neutral manufacturing. Metabolomics technologies optimized for photosynthetic organisms have been developed and utilized in various microalgal and cyanobacterial species. This review provides a concise overview of recent achievements in photosynthetic metabolomics, emphasizing the importance of microalgal and cyanobacterial cell factories that satisfy industrial requirements.

Unraveling metabolic alterations in Chlorella vulgaris cultivated on renewable sugars using time resolved multi-omics

The inherent metabolic versatility of Chlorella vulgaris that enables it to metabolize both inorganic and organic carbon under various trophic modes of cultivation makes it a promising candidate for industrial applications. To shed light on the metabolic flexibility of this microalga, time resolved proteomic and metabolomic studies were conducted in three distinct trophic modes (autotrophic, heterotrophic, mixotrophic) at two growth stages (end of linear growth at 6 days and during nutrient deprivation at 10 days). Sweet sorghum bagasse (SSB) hydrolysate was supplied to the cultivation medium as a renewable source of organic carbon mainly in the form of glucose. Integrated multi-omics data showed improved nitrogen assimilation, re-allocation, and recycling and increased levels of photosystem II (PS II) proteins indicating effective cellular quenching of excess electrons during mixotrophy. As external addition of organic carbon (glucose) to the cultivation medium decreases the cell's dependence on photosynthesis, an upregulation in the mitochondrial electron transport chain was recorded that led to increased cellular energy generation and hence higher growth rates under mixotrophy. Moreover, upregulation of the lipid-packaging proteins caleosin and 14_3_3 domain-containing protein resulted in maximum expression during mixotrophy suggesting a strong correlation between lipid synthesis, stabilization, and assembly. Overall, cells cultivated under mixotrophy showed better nutrient stress tolerance and redox balancing leading to higher biomass and lipid production. The study offers a panoramic view of the microalga's metabolic flexibility and contributes to a deeper understanding of the altered biochemical pathways that can be exploited to enhance algal productivity and commercial potential.

Impact of pyrene (polycyclic aromatic hydrocarbons) pollutant on metabolites and lipid induction in microalgae Chlorella sorokiniana (UUIND6) to produce renewable biodiesel

Pyrene (polycyclic aromatic hydrocarbon), an anthropogenic organic pollutant prevalent in various ecological units, receives more attention for bioremediation and energy transformation using microalgae. In this study, we have used pyrene pollutant (50-500 ppm) to evaluate the half-maximal inhibitory concentrations (IC₅₀) of Chlorella sorokiniana and the impact on metabolites as well as the induction of lipid biosynthesis to produce renewable biodiesel. Pyrene concentration at 230 ppm (IC₅₀) caused half-maximum inhibition for the 96 h incubation. The harvest in the stationary stage (day 16) for C. sorokiniana revealed a biomass generation of 449 ± 7 mg L^-1 and 444 ± 8 mg L^-1 dcw in the control medium and pyrene IC₅₀ medium, respectively. An insignificant decline in biomass generation (1.2%) was observed due to the stress effect of the pyrene IC₅₀ medium on metabolic biosynthesis. Although contrary to biomass generation, IC₅₀ of pyrene assisted to induce lipid biosynthesis in C. sorokiniana. The improvement in lipid biosynthesis was observed as ~24% higher in pyrene IC₅₀ compared to the control medium. The chemical composition of the microalgae biomass, metabolites, and lipids was examined using FTIR spectra. The extracted lipid was transesterified to produce biodiesel via methanolic-H₂SO₄ catalysis. The renewable biodiesel obtained was evaluated using FTIR and ¹H NMR spectra. The transformation efficiency of the lipid of C. sorokiniana in biodiesel was calculated as ~81%. This research offers the incentive in lipid biosynthesis in microalgae cells using pyrene for the production of renewable and sustainable ecological biofuels along with bioremediation of pyrene.

Interactions with Arsenic: Mechanisms of Toxicity and Cellular Resistance in Eukaryotic Microorganisms

Arsenic (As) is quite an abundant metalloid, with ancient origin and ubiquitous distribution, which represents a severe environmental risk and a global problem for public health. Microbial exposure to As compounds in the environment has happened since the beginning of time. Selective pressure has induced the evolution of various genetic systems conferring useful capacities in many microorganisms to detoxify and even use arsenic, as an energy source. This review summarizes the microbial impact of the As biogeochemical cycle. Moreover, the poorly known adverse effects of this element on eukaryotic microbes, as well as the As uptake and detoxification mechanisms developed by yeast and protists, are discussed. Finally, an outlook of As microbial remediation makes evident the knowledge gaps and the necessity of new approaches to mitigate this environmental challenge.

Metabolomic Profiling Revealed Diversion of Cytidinediphosphate-Diacylglycerol and Glycerol Pathway towards Denovo Triacylglycerol Synthesis in Rhodosporidium toruloides

Oleaginous yeast Rhodosporidium toruloides has great biotechnological potential and scientific interest, yet the molecular rationale of its cellular behavior to carbon and nitrogen ratios with concurrent lipid agglomeration remains elusive. Here, metabolomics adaptations of the R. toruloides in response to varying glucose and nitrogen concentrations have been investigated. In preliminary screening we found that 5% glucose (w/v) was optimal for further analysis in Rhodosporidium toruloides 3641. Hereafter, the effect of complementation to increase lipid agglomeration was evaluated with different nitrogen sources and their concentration. The results obtained illustrated that the biomass (13 g/L) and lipid (9.1 g/L) production were maximum on 5% (w/v) glucose and 0.12% (NH₄)₂SO₄. Furthermore, to shed lights on lipid accumulation induced by nitrogen-limitation, we performed metabolomic analysis of the oleaginous yeast R. toruloides 3641. Significant changes were observed in metabolite concentrations by qualitative metabolomics through gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS), which were mapped onto the governing metabolic pathways. Notable finding in this strain concerns glycerol and CDP-DAG metabolism wherein reduced production of glycerol and phospholipids induced a bypass leading to enhanced de-novo triacylglyceride synthesis. Collectively, our findings help in understanding the central carbon metabolism of R. toruloides which may assist in developing rationale metabolic models and engineering efforts in this organism.

Elucidating the bioremediation mechanism of Scenedesmus sp. IITRIND2 under cadmium stress

Cadmium (Cd) is a non-biodegradable pollutant that has become a global threat due to its bioaccumulation and biomagnification in higher trophic levels of the food chain. Green technologies such as phycoremediation is an emerging approach and possess edge over conventional methods to remediate Cd from the environment. The present investigation elucidates the adaptive mechanism of a freshwater microalga, Scenedesmus sp. IITRIND2 under Cd stress. The microalga showed excellent tolerance to Cd stress with IC₅₀ value of ~32 ppm. The microalga showed phenomenal removal efficiency (~80%) when exposed to 25 ppm of Cd. Such a high uptake of Cd by the cells was accompanied with increased total lipid content (~33% of dry cell weight). Additionally, the elevated level of ROS, lipid peroxidation, glycine-betaine, and antioxidant enzymes evidenced the activation of efficient antioxidant machinery for alleviating the Cd stress. Further, analysis of the fatty acid methyl ester (FAME) presented a steady increase in saturated and polyunsaturated fatty acids with biodiesel properties complying the American and European fuel standards. The study proposes an integrated approach for bioremediation of toxic Cd using hyper-tolerant microalgal strains along with biodiesel production from the generated algal biomass.

Heavy metal detoxification mechanisms by microalgae: Insights from transcriptomics analysis

Heavy metal pollution in ecosystem is a global threat. The associated toxicity and carcinogenic nature of heavy metals/metalloids such as mercury, cadmium, lead, and arsenic are imposing a severe risk to both ecological diversity and human lives. Harnessing the adaptive feature of microalgae for remediating toxic heavy metal has reached a milestone in past few decades. Transcriptomics analyses have provided mechanistic insights to map the dynamics of cellular events under heavy metal stress, thus deciphering the strategic responses of microalgae. Here, the present review comprehensively addresses the elicited molecular responses of microalgae to detoxify the heavy metal stress. The review highlights the intricate role of biochemical components and signaling networks mediating stress responsive transitions of microalgae at physiological level. Furthermore, the differential gene expression signifying the transporters involved in uptake, distribution/sequestration, and efflux of heavy metal has also been reviewed. In a nutshell, this study provided a comprehensive understanding of the molecular mechanisms adopted by microalgae at transcriptome level to nullify the oxidative stress while detoxifying the heavy metals.

Bacteria, Fungi and Microalgae for the Bioremediation of Marine Sediments Contaminated by Petroleum Hydrocarbons in the Omics Era

Petroleum hydrocarbons (PHCs) are one of the most widespread and heterogeneous organic contaminants affecting marine ecosystems. The contamination of marine sediments or coastal areas by PHCs represents a major threat for the ecosystem and human health, calling for urgent, effective, and sustainable remediation solutions. Aside from some physical and chemical treatments that have been established over the years for marine sediment reclamation, bioremediation approaches based on the use of microorganisms are gaining increasing attention for their eco-compatibility, and lower costs. In this work, we review current knowledge concerning the bioremediation of PHCs in marine systems, presenting a synthesis of the most effective microbial taxa (i.e., bacteria, fungi, and microalgae) identified so far for hydrocarbon removal. We also discuss the challenges offered by innovative molecular approaches for the design of effective reclamation strategies based on these three microbial components of marine sediments contaminated by hydrocarbons.

Acid-adapted microalgae exhibit phenotypic changes for their survival in acid mine drainage samples

Phenotypic plasticity or genetic adaptation in an organism provides phenotypic changes when exposed to the extreme environmental conditions. The resultant physiological and metabolic changes greatly enhance the organism's potential for its survival in such harsh environments. In the present novel approach, we tested the hypothesis whether acid-adapted microalgae, initially isolated from non-acidophilic environments, can survive and grow in acid-mine-drainage (AMD) samples. Two acid-adapted microalgal strains, Desmodesmus sp. MAS1 and Heterochlorella sp. MAS3, were tested individually or in combination (co-culture) for phenotypic changes during their growth in samples collected from AMD. The acid-adapted microalgae in AMD exhibited a two-fold increase in growth when compared with those grown at pH 3.5 in BBM up to 48 h and then declined. Furthermore, oxidative stress triggered several alterations such as increased cell size, granularity, and enhanced lipid accumulation in AMD-grown microalgae. Especially, the apparent limitation of phosphate in AMD inhibited the uptake of copper and iron in the cultures. Interestingly, growth of the acid-adapted microalgae in AMD downregulated amino acid metabolic pathways as a survival mechanism. This study demonstrates for the first time that acid-adapted microalgae can survive under extreme environmental conditions as exist in AMD by effecting significant phenotypic changes.

Arsenate-Induced Changes in Bacterial Metabolite and Lipid Pools during Phosphate Stress

Agrobacterium tumefaciens GW4 is a heterotrophic arsenite-oxidizing bacterium with a high resistance to arsenic toxicity. It is now a model organism for studying the processes of arsenic detoxification and utilization. Previously, we demonstrated that under low-phosphate conditions, arsenate [As(V)] could enhance bacterial growth and be incorporated into biomolecules, including lipids. While the basic microbial As(V) resistance mechanisms have been characterized, global metabolic responses under low phosphate remain largely unknown. In the present work, the impacts of As(V) and low phosphate on intracellular metabolite and lipid profiles of GW4 were quantified using liquid chromatography-mass spectroscopy (LC-MS) in combination with transcriptional assays and the analysis of intracellular ATP and NADH levels. Metabolite profiling revealed that oxidative stress response pathways were altered and suggested an increase in DNA repair. Changes in metabolite levels in the tricarboxylic acid (TCA) cycle along with increased ATP are consistent with As(V)-enhanced growth of A. tumefaciens GW4. Lipidomics analysis revealed that most glycerophospholipids decreased in abundance when As(V) was available. However, several glycerolipid classes increased, an outcome that is consistent with maximizing growth via a phosphate-sparing phenotype. Differentially regulated lipids included phosphotidylcholine and lysophospholipids, which have not been previously reported in A. tumefaciens The metabolites and lipids identified in this study deepen our understanding of the interplay between phosphate and arsenate on chemical and metabolic levels.IMPORTANCE Arsenic is widespread in the environment and is one of the most ubiquitous environmental pollutants. Parodoxically, the growth of certain bacteria is enhanced by arsenic when phosphate is limited. Arsenate and phosphate are chemically similar, and this behavior is believed to represent a phosphate-sparing phenotype in which arsenate is used in place of phosphate in certain biomolecules. The research presented here uses a global approach to track metabolic changes in an environmentally relevant bacterium during exposure to arsenate when phosphate is low. Our findings are relevant for understanding the environmental fate of arsenic as well as how human-associated microbiomes respond to this common toxin.

High-throughput proteomics and metabolomic studies guide re-engineering of metabolic pathways in eukaryotic microalgae: A review

Eukaryotic microalgae are a rich source of commercially important metabolites including lipids, pigments, sugars, amino acids and enzymes. However, their inherent genetic potential is usually not enough to support high level production of metabolites of interest. In order to move on from the traditional approach of improving product yields by modification of the cultivation conditions, understanding the metabolic pathways leading to the synthesis of the bioproducts of interest is crucial. Identification of new targets for strain engineering has been greatly facilitated by the rapid development of high-throughput sequencing and spectroscopic techniques discussed in this review. Despite the availability of high throughput analytical tools, examples of gathering and application of proteomic and metabolomic data for metabolic engineering of microalgae are few and mainly limited to lipid production. The present review highlights the application of contemporary proteomic and metabolomic techniques in eukaryotic microalgae for redesigning pathways for enhanced production of algal metabolites.

Metabolomic Profiling of Drought-Tolerant and Susceptible Peanut (Arachis hypogaea L.) Genotypes in Response to Drought Stress

Peanut is frequently constrained by extreme environmental conditions such as drought. To reveal the involvement of metabolites, TAG 24 (drought-tolerant) and JL 24 (drought-sensitive) peanut genotypes were investigated under control and 20% PEG 6000-mediated water scarcity conditions at the seedling stage. Samples were analyzed by gas chromatography-mass spectrometry (GC-MS) to identify untargeted metabolites and targeted metabolites, i.e., polyamines and polyphenols by high-performance liquid chromatography (HPLC) and ultrahigh-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), respectively. The principal component analysis (PCA), partial least-squares discriminant analysis (PLS-DA), heat map, and cluster analysis were applied to the metabolomics data obtained by the GC-MS technique to determine the important metabolites for drought tolerance. Among 46 resulting metabolites, pentitol, phytol, xylonic acid, d-xylopyranose, stearic acid, and d-ribose were important drought-responsive metabolites. Agmatine and cadaverine were present in TAG 24 leaves and roots, respectively, during water-deficit conditions and believed to be the potential polyamines for drought tolerance. Polyphenols such as syringic acid and vanillic acid were produced more in the leaves of TAG 24, while catechin production was high in JL 24 during stress conditions. Seven metabolic pathways, namely, galactose metabolism, starch and sucrose metabolism, fructose and mannose metabolism, pentose and glucuronate interconversion, propanoate metabolism, amino sugar and nucleotide sugar metabolism, and biosynthesis of unsaturated fatty acids were significantly affected by water-deficit conditions. This study provides valuable information about the metabolic response of peanut to drought stress and metabolites identified, which encourages further study by transcriptome and proteomics to improve drought tolerance in peanut.

Bioengineering of Microalgae: Recent Advances, Perspectives, and Regulatory Challenges for Industrial Application

Microalgae, due to their complex metabolic capacity, are being continuously explored for nutraceuticals, pharmaceuticals, and other industrially important bioactives. However, suboptimal yield and productivity of the bioactive of interest in local and robust wild-type strains are of perennial concerns for their industrial applications. To overcome such limitations, strain improvement through genetic engineering could play a decisive role. Though the advanced tools for genetic engineering have emerged at a greater pace, they still remain underused for microalgae as compared to other microorganisms. Pertaining to this, we reviewed the progress made so far in the development of molecular tools and techniques, and their deployment for microalgae strain improvement through genetic engineering. The recent availability of genome sequences and other omics datasets form diverse microalgae species have remarkable potential to guide strategic momentum in microalgae strain improvement program. This review focuses on the recent and significant improvements in the omics resources, mutant libraries, and high throughput screening methodologies helpful to augment research in the model and non-model microalgae. Authors have also summarized the case studies on genetically engineered microalgae and highlight the opportunities and challenges that are emerging from the current progress in the application of genome-editing to facilitate microalgal strain improvement. Toward the end, the regulatory and biosafety issues in the use of genetically engineered microalgae in commercial applications are described.

Bioremediation of heavy metals using microalgae: Recent advances and mechanisms

Five heavy metals namely, arsenic (As), cadmium (Cd), chromium (Cr), lead (Pb) and mercury (Hg) are carcinogenic and show toxicity even at trace amounts, posing threats to environmental ecology and human health. There is an emerging trend of employing microalgae in phycoremediation of heavy metals, due to several benefits including abundant availability, inexpensive, excellent metal removal efficiency and eco-friendly nature. This review presents the recent advances and mechanisms involved in bioremediation and biosorption of these toxic heavy metals utilizing microalgae. Tolerance and response of different microalgae strains to heavy metals and their bioaccumulation capability with value-added by-products formation as well as utilization of non-living biomass as biosorbents are discussed. Furthermore, challenges and future prospects in bioremediation of heavy metals by microalgae are also explored. This review aims to provide useful insights to help future development of efficient and commercially viable technology for microalgae-based heavy metal bioremediation.

Metabolome response to anthropogenic contamination on microalgae: a review

BACKGROUND

Microalgae play a key role in ecosystems and are widely used in ecological status assessment. Research focusing on such organisms is then well developed and essential. Anyway, approaches for a better comprehension of their metabolome's response towards anthropogenic stressors are only emerging.

AIM OF REVIEW

This review presents the biochemical responses of various microalgae species towards several contaminants including metals and chemicals as pesticides or industrial compounds. We aim to provide a comprehensive and up-to-date overview of analytical approaches deciphering anthropogenic contaminants impact on microalgae metabolome dynamics, in order to bring out relevant biochemical markers that could be used for risk assessment.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Studies to date on ecotoxicological metabolomics on microalgae are highly heterogeneous in both analytical techniques and resulting metabolite identification. There is a real need for studies using complementary approaches to determine biomarkers usable for ecological risk assessment.

Delineating the molecular responses of a halotolerant microalga using integrated omics approach to identify genetic engineering targets for enhanced TAG production

BACKGROUND

Harnessing the halotolerant characteristics of microalgae provides a viable alternative for sustainable biomass and triacylglyceride (TAG) production. Scenedesmus sp. IITRIND2 is a fast growing fresh water microalga that has the capability to thrive in high saline environments. To understand the microalga's adaptability, we studied its physiological and metabolic flexibility by studying differential protein, metabolite and lipid expression profiles using metabolomics, proteomics, real-time polymerase chain reaction, and lipidomics under high salinity conditions.

RESULTS

On exposure to salinity, the microalga rewired its cellular reserves and ultrastructure, restricted the ions channels, and modulated its surface potential along with secretion of extrapolysaccharide to maintain homeostasis and resolve the cellular damage. The algal-omics studies suggested a well-organized salinity-driven metabolic adjustment by the microalga starting from increasing the negatively charged lipids, up regulation of proline and sugars accumulation, followed by direction of carbon and energy flux towards TAG synthesis. Furthermore, the omics studies indicated both de-novo and lipid cycling pathways at work for increasing the overall TAG accumulation inside the microalgal cells.

CONCLUSION

The salt response observed here is unique and is different from the well-known halotolerant microalga; Dunaliella salina, implying diversity in algal response with species. Based on the integrated algal-omics studies, four potential genetic targets belonging to two different metabolic pathways (salt tolerance and lipid production) were identified, which can be further tested in non-halotolerant algal strains.