Microalgal multiomics-based approaches in bioremediation of hazardous contaminants.

The enhanced industrial growth and higher living standards owing to the incessant population growth have caused heightened production of various chemicals in different manufacturing sectors globally, resulting in pollution of aquatic systems and soil with hazardous chemical contaminants. The bioremediation of such hazardous pollutants through microalgal processes is a viable and sustainable approach. Accomplishing microalgal-based bioremediation of polluted wastewater requires a comprehensive understanding of microalgal metabolic and physiological dynamics. Microalgae-bacterial consortia have emerged as a sustainable agent for synergistic bioremediation and metabolite production. Effective bioremediation involves proper consortium functioning and dynamics. The present review highlights the mechanistic processes employed through microalgae in reducing contaminants present in wastewater. It discusses the multi-omics approaches and their advantages in understanding the biological processes, monitoring, and dynamics among the partners in consortium through metagenomics. Transcriptomics, proteomics, and metabolomics enable an understanding of microalgal cell response toward the contaminants in the wastewater. Finally, the challenges and future research endeavors are summarised to provide an outlook on microalgae-based bioremediation.

Analysis of endoglucanases production using metatranscriptomics and proteomics approach.

The cellulases are among the most used enzyme in industries for various purposes. They add up to the green economy perspective and cost-effective production of enterprises. Biorefineries, paper industries, and textile industries are foremost in their usage. The production of endoglucanases from microorganisms is a valuable resource and can be exploited with the help of biotechnology. The present review provides some insight into the uses of endoglucanases in different industries and the potent fungal source of these enzymes. The advances in the enzyme technology has helped towards understanding some pathways to increase the production of industrial enzymes from microorganisms. The proteomics analysis and systems biology tools also help to identify these pathways for the enhanced production of such enzymes. This review deciphers the use of proteomics tools to analyze the potent microorganisms and identify suitable culture conditions to increase the output of endoglucanases. The review also includes the role of quantitative proteomics which is a powerful technique to get results faster and more timely. The role of metatranscriptomic approaches are also described which are helpful in the enzyme engineering for their efficient use under industrial conditions. Conclusively, this review helps to understand the challenges faced in the industrial use of endoglucanases and their further improvement.

Engineering regulatory networks of cyanobacteria.

Engineering a cell's regulatory networks to dynamically control gene expression has been considered a new frontier in biological engineering. In cyanobacteria, the lack of well-characterized, modular gene regulatory elements makes regulatory network engineering challenging. Here, we suggest potential tools to modify various gene expression steps in cyanobacterial regulatory networks.

Application of ANN-MOGA for nutrient sequestration for wastewater remediation and production of polyunsaturated fatty acid (PUFA) by Chlorella sorokiniana MSP1.

Chlorella bears excellent potential in removing nutrients from industrial wastewater and lipid production enriched with polyunsaturated fatty acids. However, due to the changing nutrient dynamics of wastewater, growth and metabolic activity of Chlorella are affected. In order to sustain microalgal growth in wastewater with concomitant production of PUFA rich lipids, RSM (Response Surface Methodology) followed by heuristic hybrid computation model ANN-MOGA (Artificial Neural Network- Multi-Objective Genetic Algorithm) were implemented. Preliminary experiments conducted taking one factor at a time and design matrix of RSM with process variables viz. Sodium chloride (1 mM-40 mM), Magnesium sulphate (100 mg-800 mg) and incubation time (4th day to 20th day) were validated by ANN-MOGA. The study reported improved biomass and lipid yield by 54.25% and 12.76%, along with total nitrogen and phosphorus removal by 21.92% and 18.72% respectively using ANN-MOGA. It was evident from FAME results that there was a significantly improved concentration of linoleic acid (19.1%) and γ-linolenic acid (21.1%). Improved PUFA content makes it a potential feedstock with application in cosmeceutical, pharmaceutical and nutraceutical industry. The study further proves that C. sorokiniana MSP1 mediated industrial wastewater treatment with PUFA production is an effective way in providing environmental benefits along with value addition. Moreover, ANN-MOGA is a relevant tool that could control microalgal growth in wastewater.

Protein Engineering in Cyanobacterial Biotechnology: Tools and Recent Updates.

Cyanobacteria have emerged as a microbial cell factory to produce a variety of bioproducts, including peptides and proteins. Cyanobacteria stand out among other organisms due to their photoautotrophic metabolism and ability to produce a wide range of metabolites. As photoautotrophic hosts can produce industrial compounds and proteins by using minimal resources such as sunlight, atmospheric carbon dioxide, and fewer nutrients, cyanobacteria are cost-effective industrial hosts. Therefore, the use of protein engineering tools for rational protein design, and the desired modification of enzyme activity has become a desirable undertaking in cyanobacterial biology. Protein engineering can improve their biological functions as well as the stability of their intracellular proteins. This review aims to highlight the success of protein engineering in the direction of cyanobacterial biotechnology and outlines the emerging technologies, current challenges, and prospects of protein engineering in cyanobacterial biotechnology.

Molecular insights and omics-based understanding of plant-microbe interactions under drought stress.

The detrimental effects of adverse environmental conditions are always challenging and remain a major concern for plant development and production worldwide. Plants deal with such constraints by physiological, biochemical, and morphological adaptations as well as acquiring mutual support of beneficial microorganisms. As many stress-responsive traits of plants are influenced by microbial activities, plants have developed a sophisticated interaction with microbes to cope with adverse environmental conditions. The production of numerous bioactive metabolites by rhizospheric, endo-, or epiphytic microorganisms can directly or indirectly alter the root system architecture, foliage production, and defense responses. Although plant-microbe interactions have been shown to improve nutrient uptake and stress resilience in plants, the underlying mechanisms are not fully understood. "Multi-omics" application supported by genomics, transcriptomics, and metabolomics has been quite useful to investigate and understand the biochemical, physiological, and molecular aspects of plant-microbe interactions under drought stress conditions. The present review explores various microbe-mediated mechanisms for drought stress resilience in plants. In addition, plant adaptation to drought stress is discussed, and insights into the latest molecular techniques and approaches available to improve drought-stress resilience are provided.

Microalgal-based bioremediation of emerging contaminants: Mechanisms and challenges.

Emerging contaminants (ECs) in different ecosystems have consistently been acknowledged as a global issue due to toxicity, human health implications, and potential role in generating and disseminating antimicrobial resistance. The existing wastewater treatment system is incompetent at eliminating ECs since the effluent water contains significant concentrations of ECs, viz., antibiotics (0.03-13.0 µg L-1), paracetamol (50 µg L-1), and many others in varying concentrations. Microalgae are considered as a prospective and sustainable candidate for mitigating of ECs owing to some peculiar features. In addition, the microalgal-based processes also offer cost and energy-efficient solutions for the bioremediation of ECs than conventional treatment systems. It is pertinent that, microalgal-based processes also provides waste valorization benefits as microalgal biomass obtained after ECs treatment can be potentially applied to generate biofuels. Moreover, microalgae can effectively utilize alternative metabolic (cometabolism) routes for enhanced degradation of ECs. Additionally, the ECs removal via the microalgal biodegradation route is highly promising as it can transform the ECs into less toxic compounds. The present review comprehensively discusses different mechanisms involved in removing ECs and various factors that affect their removal. Also, the technoeconomic feasibility of microalgae than other conventional wastewater treatment methods is summarised. The review also highlighted the different molecular and genetic tools that can augment the activity and robustness of microalgae for better removal of organic contaminants. Finally, we have summarised the challenges and future research required towards microalgal-based bioremediation of emerging contaminants (ECs) as a holistic approach.

Biotechnological potential of microbial bio-surfactants, their significance, and diverse applications.

Globally, there is a huge demand for chemically available surfactants in many industries, irrespective of their detrimental impact on the environment. Naturally occurring green sustainable substances have been proven to be the best alternative for reducing reliance on chemical surfactants and promoting long-lasting sustainable development. The most frequently utilized green active biosurfactants, which are made by bacteria, yeast, and fungi, are discussed in this review. These biosurfactants are commonly originated from contaminated sites, the marine ecosystem, and the natural environment, and it holds great potential for environmental sustainability. In this review, we described the importance of biosurfactants for the environment, including their biodegradability, low toxicity, environmental compatibility, and stability at a wide pH range. In this review, we have also described the various techniques that have been utilized to characterize and screen the generation of microbial biosurfactants. Also, we reviewed the potential of biosurfactants and its emerging applications in the foods, cosmetics, pharmaceuticals, and agricultural industries. In addition, we also discussed the ways to overcome problems with expensive costs such as low-cost substrate media formulation, gravitational techniques, and solvent-free foam fractionation for extraction that could be employed during biosurfactant production on a larger scale.

Metabolic sink engineering in cyanobacteria: Perspectives and applications.

Recent advances in metabolic engineering have made cyanobacteria emerge as promising and attractive microorganisms for sustainable production, by exploiting their natural capability for producing metabolites. The potential of metabolically engineered cyanobacterium would depend on its source-sink balance in the same way as other phototrophs. In cyanobacteria, the amount of light energy harvested (Source) is incompletely utilized by the cell to fix carbon (sink) resulting in wastage of the absorbed energy causing photoinhibition and cellular damage leading to lowered photosynthetic efficiency. Although regulatory pathways like photo-acclimation and photoprotective processes can be helpful unfortunately they limit the cell's metabolic capacity. This review describes approaches for source-sink balance and engineering heterologous metabolic sinks in cyanobacteria for enhanced photosynthetic efficiency. The advances for engineering additional metabolic pathways in cyanobacteria are also described which will provide a better understanding of the cyanobacterial source-sink balance and approaches for efficient cyanobacterial strains for valuable metabolites.

Computational Approaches for the Structure-Based Identification of Novel Inhibitors Targeting Nucleoid-Associated Proteins in Mycobacterium Tuberculosis.

Implementation of computational tools in the identification of novel drug targets for Tuberculosis (TB) has been a promising area of research. TB has been a chronic infectious disease caused by Mycobacterium tuberculosis (Mtb) localized primarily on the lungs and it has been one of the most successful pathogen in the history of mankind. Extensively arising drug resistivity in TB has made it a global challenge and need for new drugs has become utmost important.The involvement of Nucleoid-Associated Proteins (NAPs) in maintaining the structure of the genomic material and regulating various cellular processes like transcription, DNA replication, repair and recombination makes significant, has opened a new arena to find the drugs targeting Mtb. The current study aims to identify potential inhibitors of NAPs through a computational approach. In the present work we worked on the eight NAPs of Mtb, namely, Lsr2, EspR, HupB, HNS, NapA, mIHF and NapM. The structural modelling and analysis of these NAPs were carried out. Moreover, molecular interaction were checked and binding energy was identified for 2500 FDA-approved drugs that were selected for antagonist analysis to choose novel inhibitors targeting NAPs of Mtb. Drugs including Amikacin, streptomycin, kanamycin, and isoniazid along with eight FDA-approved molecules that were found to be potential novel targets for these mycobacterial NAPs and have an impact on their functions. The potentiality of several anti-tubercular drugs as therapeutic agents identified through computational modelling and simulation unlocks a new gateway for accomplishing the goal to treat TB. Complete framework of the methodology employed in this study to predict inhibitors against mycobacterial NAPs.

Microalgae harvesting techniques: updates and recent technological interventions.

Microalgal biomass has garnered attention as a renewable and sustainable resource for producing biodiesel. The harvesting of microalgal biomass is a significant bottleneck being faced by the industries as it is the crucial cost driver in the downstream processing of biomass. Bioharvesting of microalgal biomass mediated by: microbial, animal, and plant-based polymeric flocculants has gained a higher probability of utility in accumulation due to: its higher dewatering potential, less toxicity, and ecofriendly properties. The present review summarizes the key challenges and the technological advancements associated with various such harvesting techniques. The economic and technical aspects of different microalgal harvesting techniques, particularly the cationic polymeric flocculant-based harvesting of microalgal biomass, are also discussed. Furthermore, interactions of flocculants with microalgal biomass and the effects of these interactions on metabolite and lipid extractions are discussed to offer a promising solution for suitability in selecting the most efficient and economical method of microalgal biomass harvesting for cost-effective biodiesel production.

Microbiome engineering for bioremediation of emerging pollutants.

Axenic microbial applications in the open environment are unrealistic and may not be always practically viable. Therefore, it is important to use mixed microbial cultures and their interactions with the microbiome in the targeted ecosystem to perform robust functions towards their sustainability in harsh environmental conditions. Emerging pollutants like phthalates and hydrocarbons that are toxic to several aquatic and terrestrial life forms in the water bodies and lands are an alarming situation. The present review explores the possibility of devising an inclusive eco-friendly strategy like microbiome engineering which proves to be a unique and crucial technology involving the power of microbial communication through quorum sensing. This review discusses the interspecies and intra-species communications between different microbial groups with their respective environments. Moreover, this review also envisages the efforts for designing the next level of microbiome-host engineering concept (MHEC). The focus of the review also extended toward using omics and metabolic network analysis-based tools for effective microbiome engineering. These approaches might be quite helpful in the future to understand such microbial interactions but it will be challenging to implement in the real environment to get the desired functions. Finally, the review also discusses multiple approaches for the bioremediation of toxic chemicals from the soil environment.

Degradation effectiveness of hexachlorohexane (ϒ-HCH) by bacterial isolate Bacillus cereus SJPS-2, its gene annotation for bioremediation and comparison with Pseudomonas putida KT2440.

The contamination of Hexachlorohexane (Lindane) in soil and water has toxic effects due to its persistent nature. In our study, an indigenous HCH (gamma isomer) degrading bacterium viz Bacillus cereus SJPS-2 was isolated from Yamuna river water using enrichment culture method. The growth curve indicated that Bacillus cereus SJPS-2 was able to degrade ϒ-HCH effectively with 80.98% degradation. Further, process was improved by using immobilization using alginate beads which showed enhanced degradation (89.34%). Interestingly, in presence of fructose, the ϒ-HCH degradation was up to 79.24% with exponential growth curve whereas the degradation was only 5.61% in presence of glucose revealing diauxic growth curve. Furthermore, The FTIR results confirmed the potential lindane degradation capability of Bacillus cereus SJPS-2 and the bonds were recorded at wavelengths viz. 2900-2500 cm-1, 3300-2800 cm-1 and 785-540 cm-1. Similarity, the GC studies also reconfirmed the degradation potential with retention time (RT) of ethyl acetate and lindane was 2.12 and 11.0 respectively. Further, we studied the metabolic pathway involved for lindane utilization in Bacillus cereus using KEGG-KASS and functional gene annotation through Rapid Annotation using Subsystems Technology (RAST) resulted in the annotation of the lin genes (lin A, lin B, lin C, lin X, lin D, lin E) and respective encoding enzymes. The comparative ϒ-HCH degradation potential of B. cereus and P. putida KT2440 was also evaluated. The island viewer showed the different colors on circular genome indicate the coordinates of genomic islands resulted with some common genomic islands (GEIs) between both bacteria indicating the possibility of horizontal gene transfer at contaminated site or natural environment. These genomic islands (GEIs) contribute in the rearrangement genetic material or to evolve bacteria in stress conditions, as a result the metabolic pathways evolve by formation of catabolic genes. This study establishes the potential of Bacillus cereus SJPS-2 for effectual ϒ-HCH degradation.

Multi-efficient endoglucanase from Aspergillus niger MPS25 and its potential applications in saccharification of wheat straw and waste paper deinking.

The deinking in the paper industry is in great demand, and microbial enzymes are key players. In the present study, the endoglucanase production from newly isolated fungi Aspergillus niger MPS25 is reported. The optimization of endoglucanase production was carried out using one factor at a time approach resulting in endoglucanase activity (2.37 IU/ml) at 45 °C and pH 8 in submerged fermentation (SmF), which shows optimum enzyme activity at 60 °C. Interestingly, the metal ions viz. Co2+ stimulated the endoglucanase activity, whereas Mn2+ reduced the enzyme activity, which shows that this enzyme can be used for effluent treatment released through deinking. The enzymatic hydrolysis of wheat straw produced 26.96 ± 0.108 mg/g of reducing sugars, indicating its potential in saccharification and the biofuel industry. Furthermore, the validation of the deinking efficiency of this enzyme resulted in improved deinking of mixed office waste and old newspapers by 31.5% and 20.4%, respectively. The strength properties, viz. burst factor and tear index, breaking length, and tensile index of the handmade paper sheets, were also improved which were analyzed by the scanning electron micrographs. The FTIR and XRD analysis of pulp provided insights into the changes in functional groups and cellulose crystallinity, respectively. These results indicate that multi-efficient endoglucanase from Aspergillus niger MPS25 is suitable for enzyme-based eco-friendly deinking for waste paper recycling and lignocellulosic biomass saccharification.

Optimization of endoglucanase-lipase-amylase enzyme consortium from Thermomyces lanuginosus VAPS25 using Multi-Objective genetic algorithm and their bio-deinking applications.

In this study, the enzyme consortium of endoglucanase, lipase, and amylase was obtained and optimized using artificial intelligence-based tools. After optimization using a multi-objective genetic algorithm and artificial neural network, the enzyme activity was 8.8 IU/g, 153.68 U/g, and 19.2 IU/g for endoglucanase, lipase, and amylase, respectively, using Thermomyces lanuginosus VAPS25. The highest enzyme activity was obtained at parameters 77.69% moisture content, 52.7 °C temperature, 98 h, and 3.1 eucalyptus leaves: wheat bran ratio. The endoglucanase-lipase-amylase (END-LIP-AMY) enzyme consortium showed reliable characteristics in terms of catalytic activity at 50-80 °C and pH 6.0-9.0. The increase in deinking efficiency of 27.8% and 11.1% were obtained compared to control for mixed office waste and old newspaper, respectively, using the enzyme consortium. The surface chemical composition and fiber morphology of deinked pulp was investigated using Attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) and Scanning electron microscopy (SEM).

Role of regulatory pathways and multi-omics approaches for carbon capture and mitigation in cyanobacteria.

Cyanobacteria are known for their metabolic potential and carbon capture and sequestration capabilities. These cyanobacteria are not only an effective source for carbon minimization and resource mobilization into value-added products for biotechnological gains. The present review focuses on the detailed description of carbon capture mechanisms exerted by the various cyanobacterial strains, the role of important regulatory pathways, and their subsequent genes responsible for such mechanisms. Moreover, this review will also describe effectual mechanisms of central carbon metabolism like isoprene synthesis, ethylene production, MEP pathway, and the role of Glyoxylate shunt in the carbon sequestration mechanisms. This review also describes some interesting facets of using carbon assimilation mechanisms for valuable bio-products. The role of regulatory pathways and multi-omics approaches in cyanobacteria will not only be crucial towards improving carbon utilization but also will give new insights into utilizing cyanobacterial bioresource for carbon neutrality.

Cyanobacterial myxoxanthophylls: biotechnological interventions and biological implications.

Cyanobacteria safeguard their photosynthetic machinery from oxidative damage caused by adverse environmental factors such as high-intensity light. Together with many photoprotective compounds, they contain myxoxanthophylls, a rare group of glycosidic carotenoids containing a high number of conjugated double bonds. These carotenoids have been shown to: have strong photoprotective effects, contribute to the integrity of the thylakoid membrane, and upregulate in cyanobacteria under a variety of stress conditions. However, their metabolic potential has not been fully utilized in the stress biology of cyanobacteria and the pharmaceutical industry due to a lack of mechanistic understanding and their insufficient biosynthesis. This review summarizes current knowledge on: biological function, genetic regulation, biotechnological production, and pharmaceutical potential of myxoxanthophyll, with a focus on strain engineering and parameter optimization strategies for increasing their cellular content. The summarized knowledge can be utilized in cyanobacterial metabolic engineering to improve the stress tolerance of useful strains and enhance the commercial-scale synthesis of myxoxanthophyll for pharmaceutical uses.

Correction to: A Comparative Analysis for the Production of Xylooligosaccharides via Enzymatic Hydrolysis from Sugarcane Bagasse and Coconut Coir.

[This corrects the article DOI: 10.1007/s12088-022-01010-3.].

Microbiome systems biology advancements for natural well-being.

Throughout the years all data from epidemiological, physiological and omics have suggested that the microbial communities play a considerable role in modulating human health. The population of microorganisms residing in the human intestine collectively known as microbiota presents a genetic repertoire that is higher in magnitude than the human genome. They play an essential role in host immunity and neuronal signaling. Rapid enhancement of sequence based screening and development of humanized gnotobiotic model has sparked a great deal of interest among scientists to probe the dynamic interactions of the commensal bacteria. This review focuses on systemic analysis of the gut microbiome to decipher the complexity of the host-microbe intercommunication and gives a special emphasis on the evolution of targeted precision medicine through microbiome engineering. In addition, we have also provided a comprehensive description of how interconnection between metabolism and biochemical reactions in a specific organism can be obtained from a metabolic network or a flux balance analysis and combining multiple datasets helps in the identification of a particular metabolite. The review highlights how genetic modification of the critical components and programming the resident microflora can be employed for targeted precision medicine. Inspite of the ongoing debate on the utility of gut microbiome we have explored on the probable new therapeutic avenues like FMT (Fecal microbiota transplant) can be utilized. This review also recapitulates integrating human-relevant 3D cellular models coupled with computational models and the metadata obtained from interventional and epidemiological studies may decipher the complex interactome of diet-microbiota-disease pathophysiology. In addition, it will also open new avenues for the development of therapeutics derived from microbiome or implementation of personalized nutrition. In addition, the identification of biomarkers can also help towards the development of new diagnostic tools and eventually will lead to strategic management of the disease. Inspite of the ongoing debate on the utility of the gut microbiome we have explored how probable new therapeutic avenues like FMT (Fecal microbiota transplant) can be utilized. This review also summarises integrating human-relevant 3D cellular models coupled with computational models and the metadata obtained from interventional and epidemiological studies may decipher the complex interactome of diet- microbiota-disease pathophysiology. In addition, it will also open new avenues for the development of therapeutics derived from the microbiome or implementation of personalized nutrition. In addition, the identification of biomarkers can also help towards the development of new diagnostic tools and eventually will lead to strategic management of disease.