Improvements in algal lipid production: a systems biology and gene editing approach

Alkaline Phosphatase PhoD Mutation Induces Fatty Acid and Long-Chain Polyunsaturated Fatty Acid (LC-PUFA)-Bound Phospholipid Production in the Model Diatom Phaeodactylum tricornutum

With rapid growth and high lipid contents, microalgae have become promising environmentally friendly candidates for renewable biodiesel and health supplements in our era of global warming and energy depletion. Various pathways have been explored to enhance algal lipid production, especially gene editing. Previously, we found that the functional loss of PhoD-type alkaline phosphatase (AP), a phosphorus-stress indicator in phytoplankton, could lead to increased lipid contents in the model diatom Phaeodactylum tricornutum, but how the AP mutation may change lipid composition remains unexplored. This study addresses the gap in the research and investigates the effects of PhoD-type AP mutation on the lipid composition and metabolic regulation in P. tricornutum using transcriptomic and lipidomic analyses. We observed significantly modified lipid composition and elevated production of fatty acids, lysophosphatidylcholine, lysophosphatidylethanolamine, ceramide, phosphatidylinositol bisphosphate, and monogalactosylmonoacylglycerol after PhoD_45757 mutation. Meanwhile, genes involved in fatty acid biosynthesis were upregulated in mutant cells. Moreover, the mutant exhibited increased contents of ω-3 long-chain polyunsaturated fatty acid (LC-PUFA)-bound phospholipids, indicating that PhoD_45757 mutation could improve the potential bioavailability of PUFAs. Our findings indicate that AP mutation could influence cellular lipid synthesis and probably redirect carbon toward lipid production and further demonstrate that AP mutation is a promising approach for the development of high-value microalgal strains for biomedical and other applications.

Deciphering the recent trends in pesticide bioremediation using genome editing and multi-omics approaches: a review

Pesticide pollution in recent times has emerged as a grave environmental problem contaminating both aquatic and terrestrial ecosystems owing to their widespread use. Bioremediation using gene editing and system biology could be developed as an eco-friendly and proficient tool to remediate pesticide-contaminated sites due to its advantages and greater public acceptance over the physical and chemical methods. However, it is indispensable to understand the different aspects associated with microbial metabolism and their physiology for efficient pesticide remediation. Therefore, this review paper analyses the different gene editing tools and multi-omics methods in microbes to produce relevant evidence regarding genes, proteins and metabolites associated with pesticide remediation and the approaches to contend against pesticide-induced stress. We systematically discussed and analyzed the recent reports (2015-2022) on multi-omics methods for pesticide degradation to elucidate the mechanisms and the recent advances associated with the behaviour of microbes under diverse environmental conditions. This study envisages that CRISPR-Cas, ZFN and TALEN as gene editing tools utilizing Pseudomonas, Escherichia coli and Achromobacter sp. can be employed for remediation of chlorpyrifos, parathion-methyl, carbaryl, triphenyltin and triazophos by creating gRNA for expressing specific genes for the bioremediation. Similarly, systems biology accompanying multi-omics tactics revealed that microbial strains from Paenibacillus, Pseudomonas putida, Burkholderia cenocepacia, Rhodococcus sp. and Pencillium oxalicum are capable of degrading deltamethrin, p-nitrophenol, chlorimuron-ethyl and nicosulfuron. This review lends notable insights into the research gaps and provides potential solutions for pesticide remediation by using different microbe-assisted technologies. The inferences drawn from the current study will help researchers, ecologists, and decision-makers gain comprehensive knowledge of value and application of systems biology and gene editing in bioremediation assessments.

Multiomics and optobiotechnological approaches for the development of microalgal strain for production of aviation biofuel and biorefinery

Demand and consumption of fossil fuels is increasing daily, and oil reserves are depleting. Technological developments are required towards developing sustainable renewable energy sources and microalgae are emerging as a potential candidate for various application-driven research. Molecular understanding attained through omics and system biology approach empowering researchers to modify various metabolic pathways of microalgal system for efficient extraction of biofuel and important biomolecules. This review furnish insight into different "advanced approaches" like optogenetics, systems biology and multi-omics for enhanced production of FAS (Fatty Acid Synthesis) and lipids in microalgae and their associated challenges. These new approaches would be helpful in the path of developing microalgae inspired technological platforms for optobiorefinery, which could be explored as source material to produce biofuels and other valuable bio-compounds on a large scale.

Development of Microalgae Biodiesel: Current Status and Perspectives

Microalgae are regarded as a promising source of biodiesel. In contrast with conventional crops currently used to produce commercial biodiesel, microalgae can be cultivated on non-arable land, besides having a higher growth rate and productivity. However, microalgal biodiesel is not yet regarded as economically competitive, compared to fossil fuels and crop-based biodiesel; therefore, it is not commercially produced. This review provides an overall perspective on technologies with the potential to increase efficiency and reduce the general costs of biodiesel production from microalgae. Opportunities and challenges for large-scale production are discussed. We present the current scenario of Brazilian research in the field and show a successful case in the research and development of microalgal biodiesel in open ponds by Petrobras. This publicly held Brazilian corporation has been investing in research in this sector for over a decade.

Microbial Remediation: A Promising Tool for Reclamation of Contaminated Sites with Special Emphasis on Heavy Metal and Pesticide Pollution: A Review

Heavy metal and pesticide pollution have become an inevitable part of the modern industrialized environment that find their way into all ecosystems. Because of their persistent nature, recalcitrance, high toxicity and biological enrichment, metal and pesticide pollution has threatened the stability of the environment as well as the health of living beings. Due to the environmental persistence of heavy metals and pesticides, they get accumulated in the environs and consequently lead to food chain contamination. Therefore, remediation of heavy metals and pesticide contaminations needs to be addressed as a high priority. Various physico-chemical approaches have been employed for this purpose, but they have significant drawbacks such as high expenses, high labor, alteration in soil properties, disruption of native soil microflora and generation of toxic by-products. Researchers worldwide are focusing on bioremediation strategies to overcome this multifaceted problem, i.e., the removal, immobilization and detoxification of pesticides and heavy metals, in the most efficient and cost-effective ways. For a period of millions of evolutionary years, microorganisms have become resistant to intoxicants and have developed the capability to remediate heavy metal ions and pesticides, and as a result, they have helped in the restoration of the natural state of degraded environs with long term environmental benefits. Keeping in view the environmental and health concerns imposed by heavy metals and pesticides in our society, we aimed to present a generalized picture of the bioremediation capacity of microorganisms. We explore the use of bacteria, fungi, algae and genetically engineered microbes for the remediation of both metals and pesticides. This review summarizes the major detoxification pathways and bioremediation technologies; in addition to that, a brief account is given of molecular approaches such as systemic biology, gene editing and omics that have enhanced the bioremediation process and widened its microbiological techniques toward the remediation of heavy metals and pesticides.

A conserved MYB transcription factor is involved in regulating lipid metabolic pathways for oil biosynthesis in green algae

Green algae can accumulate high levels of triacylglycerol (TAG), yet knowledge remains fragmented on the regulation of lipid metabolic pathways by transcription factors (TFs). Here, via bioinformatics and in vitro and in vivo analyses, we revealed the roles of a myeloblastosis (MYB) TF in regulating TAG accumulation in green algae. CzMYB1, an R2R3-MYB from Chromochloris zofingiensis, was transcriptionally upregulated upon TAG-inducing conditions and correlated well with many genes involved in the de novo fatty acid synthesis, fatty acid activation and desaturation, membrane lipid turnover, and TAG assembly. Most promoters of these genes were transactivated by CzMYB1 in the yeast one-hybrid assay and contained the binding elements CNGTTA that were recognized by CzMYB1 through the electrophoretic mobility shift assay. CrMYB1, a close homologue of CzMYB1 from Chlamydomonas reinhardtii that recognized similar elements for binding, also transcriptionally correlated with many lipid metabolic genes. Insertional disruption of CrMYB1 severely suppressed the transcriptional expression of CrMYB1, as well as of key lipogenic genes, and impaired TAG level considerably under stress conditions. Our results reveal that this MYB, conserved in green algae, is involved in regulating global lipid metabolic pathways for TAG biosynthesis and accumulation.

Multi-omics approaches and genetic engineering of metabolism for improved biorefinery and wastewater treatment in microalgae

Microalgae, a group of photosynthetic microorganisms rich in diverse and novel bioactive metabolites, have been explored for the production of biofuels, high value-added compounds as food and feeds, and pharmaceutical chemicals as agents with therapeutic benefits. This article reviews the development of omics resources and genetic engineering techniques including gene transformation methodologies, mutagenesis, and genome-editing tools in microalgae biorefinery and wastewater treatment. The introduction of these enlisted techniques has simplified the understanding of complex metabolic pathways undergoing microalgal cells. The multiomics approach of the integrated omics datasets, big data analysis, and machine learning for the discovery of objective traits and genes responsible for metabolic pathways was reviewed. Recent advances and limitations of multiomics analysis and genetic bioengineering technology to facilitate the improvement of microalgae as the dual role of wastewater treatment and biorefinery feedstock production are discussed. This article is protected by copyright. All rights reserved.

A comprehensive review on oleaginous bacteria: an alternative source for biodiesel production

Due to continuously increasing population, industrialization, and environmental pollution, lead to generating high energy demand which suitable for our environment. Biodiesel is an alternative renewable fuel source. According to the feedstock of production, biodiesel has been categorized into four generations. The main disadvantage of the first and second generation is the raw material processing cost that the challenge for its industrial-level production. Oleaginous bacteria that contain more than 20% lipid of their cellular biomass can be a good alternative and sustainable feedstock. Oleaginous bacteria used as feedstock have numerous advantages, such as their high growth rate, being easy to cultivate, utilizing various substrates for growth, genetic or metabolic modifications possible. In addition, some species of bacteria are capable of carbon dioxide sequestration. Therefore, oleaginous bacteria can be a significant resource for the upcoming generation's biodiesel production. This review discusses the biochemistry of lipid accumulation, screening techniques, and lipid accumulation factors of oleaginous bacteria, in addition to the overall general biodiesel production process. This review also highlights the biotechnological approach for oleaginous bacteria strain improvement that can be future used for biodiesel production and the advantages of using general biodiesel in place of conventional fuel, along with the discussion about global policies and the prospect that promotes biodiesel production from oleaginous bacteria.

Bioprospecting lipid-producing microorganisms: From metagenomic-assisted isolation techniques to industrial application and innovations

Traditionally, lipid-producing microorganisms have been obtained via conventional bioprospecting based on isolation and screening techniques, demanding time and effort. Thus, high-throughput sequencing combined with conventional microbiological approaches has emerged as an advanced and rapid strategy for recovering novel oleaginous microorganisms from target environments. This review highlights recent developments in lipid-producing microorganism bioprospecting, following (i) from traditional cultivation techniques to state-of-the-art metagenomics approaches; (ii) related topics on workflow, next-generation sequencing platforms, and knowledge bioinformatics; and (iii) biotechnological potential of the production of docosahexaenoic acid (DHA) by Aurantiochytrium limacinum, arachidonic acid (ARA) by Mortierella alpina and biodiesel by Rhodosporidium toruloides. These three species have been shown to be highly promising and studied in research articles, patents and commercialized products. Trends, innovations and future perspectives of these microorganisms are also addressed. Thus, these microbial lipids allow the development of food, feed and biofuels as alternative solutions to animal and vegetable oils.

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.

Biofuel production from Macroalgae: present scenario and future scope

The current fossil fuel reserves are not sufficient to meet the increasing demand and very soon will become exhausted. Pollution, global warming, and inflated oil prices have led the quest for renewable energy sources. Macroalgae (green, brown, and red marine seaweed) is gaining popularity as a viable and promising renewable source for biofuels production. Numerous researches have been conducted to access the potential of macroalgae for generating diverse bioproducts such as biofuels. The existence of components such as carbohydrates and lipids, and the lack or deficiency of lignin, create macroalgae an enviable feedstock for biofuels generation. This review briefly covers the potential macroalgal species promoting the production of biofuels and their cultivation methods. It also illustrates the biofuel generation pathway and its efficiency along with the recent techniques to accelerate the product yield. In addition, the current analysis focuses on a cost-effective sustainable generation of biofuel along with commercialization and scaleup.

Incorporating a molecular antenna in diatom microalgae cells enhances photosynthesis

Diatom microalgae have great industrial potential as next-generation sources of biomaterials and biofuels. Effective scale-up of their production can be pursued by enhancing the efficiency of their photosynthetic process in a way that increases the solar-to-biomass conversion yield. A proof-of-concept demonstration is given of the possibility of enhancing the light absorption of algae and of increasing their efficiency in photosynthesis by in vivo incorporation of an organic dye which acts as an antenna and enhances cells’ growth and biomass production without resorting to genetic modification. A molecular dye (Cy5) is incorporated in Thalassiosira weissflogii diatom cells by simply adding it to the culture medium and thus filling the orange gap that limits their absorption of sunlight. Cy5 enhances diatoms’ photosynthetic oxygen production and cell density by 49% and 40%, respectively. Cy5 incorporation also increases by 12% the algal lipid free fatty acid (FFA) production versus the pristine cell culture, thus representing a suitable way to enhance biofuel generation from algal species. Time-resolved spectroscopy reveals Förster Resonance Energy Transfer (FRET) from Cy5 to algal chlorophyll. The present approach lays the basis for non-genetic tailoring of diatoms’ spectral response to light harvesting, opening up new ways for their industrial valorization.

CRISPR base editing and prime editing: DSB and template-free editing systems for bacteria and plants

CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated) has been extensively exploited as a genetic tool for genome editing. The RNA guided Cas nucleases generate DNA double-strand break (DSB), triggering cellular repair systems mainly Non-homologous end-joining (NHEJ, imprecise repair) or Homology-directed repair (HDR, precise repair). However, DSB typically leads to unexpected DNA changes and lethality in some organisms. The establishment of bacteria and plants into major bio-production platforms require efficient and precise editing tools. Hence, in this review, we focus on the non-DSB and template-free genome editing, i.e., base editing (BE) and prime editing (PE) in bacteria and plants. We first highlight the development of base and prime editors and summarize their studies in bacteria and plants. We then discuss current and future applications of BE/PE in synthetic biology, crop improvement, evolutionary engineering, and metabolic engineering. Lastly, we critically consider the challenges and prospects of BE/PE in PAM specificity, editing efficiency, off-targeting, sequence specification, and editing window.

Effect of Protocatechuic Acid on Euglena gracilis Growth and Accumulation of Metabolites

The development of efficient, environmentally friendly, low-cost approaches used to boost the growth of microalgae is urgently required to meet the increasing demands for food supplements, cosmetics, and biofuels. In this study, the growth promotion effects of protocatechuic acid (PCA) in the freshwater microalga Euglena gracilis were confirmed for the first time. PCA is a simple phenolic compound derived from natural plants and has a range of biological functions. The highest biomass yield, 3.1-fold higher than that of the control, used at 1.3 g·L−1, was obtained at 800 mg·L−1 of PCA. The yields of the metabolites chlorophyll a, carotenoids, and paramylon in the presence of PCA at 800 mg·L−1 were 3.1, 3.3, and 1.7 times higher than those of the control group, respectively. The highest paramylon yield was achieved at a lower dosage of PCA (100 mg·L−1), which is considered to be feasible for economic paramylon production. The growth and biosynthesis of metabolites stimulated by phytochemicals such as PCA could be an efficient and cost-effective strategy to enhance the productivity of microalgae in large-scale cultivations.

Genetic engineering of microalgae for enhanced biorefinery capabilities

Microalgae-based bioproducts are in limelight because of their promising future, novel characteristics, the current situation of population needs, and rising prices of rapidly depleting energy resources. Algae-based products are considered as clean sustainable energy and food resources. At present, they are not commercialized due to their high production cost and low yield. In recent years, novel genome editing tools like RNAi, ZNFs, TALENs, and CRISPR/Cas9 are used to enhance the quality and quantity of the desired products. Genetic and metabolic engineering are frequently applied because of their rapid and precise results than random mutagenesis. Omic approaches help enhance biorefinery capabilities and are now in the developing stage for algae. The future is very bright for transgenic algae with increased biomass yield, carbon dioxide uptake rate, accumulating high-value compounds, reduction in cultivation, and production costs, thus reaching the goal in the global algal market and capital flow. However, microalgae are primary producers and any harmful exposure to the wild strains can affect the entire ecosystem. Therefore, strict regulation and monitoring are required to assess the potential risks before introducing genetically modified microalgae into the natural ecosystem.

Biotechnological Advances in the Design of Algae-Based Biosensors

In addition to their use in biomass production and bioremediation, algae have been extensively exploited in biosensing applications. Algae-based biosensors have demonstrated potential for sensitive, sustainable, and multiplexed detection of analytes of agroenvironmental and security interest. Their advantages include the availability of different algal bioreceptors including whole cells and their photosynthetic subcomponents, their potential to be integrated into dual transduction miniaturized devices, and the opportunity for continuous environmental monitoring. Despite obstacles including limited stability and selectivity, algae-based biosensing is a realistic prospect that has some recent effective applications. Strategic exploitation of cutting-edge technologies including materials science, nanotechnology, microfluidics, and genome editing will help to achieve the full potential of algae-based sensors.

Improving lipid production by strain development in microalgae: Strategies, challenges and perspectives

Over the past decade, the number of original articles and reviews presenting microalgae as a promising feedstock for biodiesel has increased tremendously. Many improvements of microalgae have been achieved through selection and strain development for industrial applications. However, the large-scale production of lipids for commercialization is not yet realistic because the production is still much more expensive than that of agricultural products. This review summarizes recent research on the induction of lipid biosynthesis in microalgae and the various strategies of genetic and metabolic engineering for enhancing lipid production. Strain engineering targets are proposed based on these strategies. To address current limitations of strain engineering for lipid production, this review provides insights on recent engineering strategies based on molecular tools and methods, and also discusses further perspectives.

Morpho-taxonomic, genetic, and biochemical characterization of freshwater microalgae as potential biodiesel feedstock

In the present study, seven axenic fresh water microchlorophytes were isolated and identified as Tetradesmus dimorphus (NEIST BT-1), Chlorella sorokiniana (NEIST BT-2), Desmodesmus sp. (NEIST BT-10), Selenastrum sp. (NEIST BT-A6), Tetradesmus obliquus (NEIST BT-A1), Tetradesmus sp. (NEIST BT-A10), and Asterarcys sp. (NEIST BT-A15) based on morphological and molecular characterization. Their potential to be used as biodiesel feedstock was evaluated depending on their growth characteristics and lipid profiles. Among the seven isolates, NEIST BT-2 was found to be the most promising candidate owing to its high biomass yield (2.09 ± 0.037 g L^-1) and lipid productivity (107.60 ± 10.175 mg L^-1 day^-1). The gas chromatography analysis confirmed the presence of significant amounts of palmitic acid, linoleic acid, linolenic acid, and oleic acid in the isolate which are some of the major constituents of any biodiesel. The predictive models showed that the biodiesel from this isolate has ideal fuel properties which comply with the ASTM D6751 and EN 14214 specifications. These findings demonstrate that NEIST BT-2 can be used as a prospective candidate for consideration of large-scale biodiesel production.

Gene Editing and Systems Biology Tools for Pesticide Bioremediation: A Review

Bioremediation is the degradation potential of microorganisms to dissimilate the complex chemical compounds from the surrounding environment. The genetics and biochemistry of biodegradation processes in datasets opened the way of systems biology. Systemic biology aid the study of interacting parts involved in the system. The significant keys of system biology are biodegradation network, computational biology, and omics approaches. Biodegradation network consists of all the databases and datasets which aid in assisting the degradation and deterioration potential of microorganisms for bioremediation processes. This review deciphers the bio-degradation network, i.e., the databases and datasets (UM-BBD, PAN, PTID, etc.) aiding in assisting the degradation and deterioration potential of microorganisms for bioremediation processes, computational biology and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation experiments. Besides, the present review also describes the gene editing tools like CRISPR Cas, TALEN, and ZFNs which can possibly make design microbe with functional gene of interest for degradation of particular recalcitrant for improved bioremediation.

Enhancing production of microalgal biopigments through metabolic and genetic engineering

The versatile use of biopigments in food, feed, cosmetic, pharmaceutical and analytical industries emphasized to find different and renewable sources of biopigments. Microalgae, including cyanobacteria, are becoming a potential candidate for pigment production as these have fast-growing ability, high pigment content, highly variable and also have "Generally recognized as safe" status. These algal groups are known to produce different metabolites that include hormones, vitamins, biopolythene and biochemicals. We discuss here the potential use of microalgal biopigments in our daily life as well as in food and cosmetic industries. Pigment like carotenoids has many health benefits such as antioxidant, anti-inflammatory properties and also provide photo-protection against UV radiation. This review details the effect of various abiotic and biotic factors such as temperature, light, nutrition on maximizing the pigment content in the microalgal cell. This review also highlights the potential of microalgae, whether in present native or engineered strain including the many metabolic strategies which are used or can be used to produce a higher amount of these valuable biopigments. Additionally, future challenges in the context of pigment production have also been discussed.

Biochemical characteristics and synergistic effect of two novel alginate lyases from Photobacterium sp. FC615

BACKGROUND

Macroalgae and microalgae, as feedstocks for third-generation biofuel, possess competitive strengths in terms of cost, technology and economics. The most important compound in brown macroalgae is alginate, and the synergistic effect of endolytic and exolytic alginate lyases plays a crucial role in the saccharification process of transforming alginate into biofuel. However, there are few studies on the synergistic effect of endolytic and exolytic alginate lyases, especially those from the same bacterial strain.

RESULTS

In this study, the endolytic alginate lyase AlyPB1 and exolytic alginate lyase AlyPB2 were identified from the marine bacterium Photobacterium sp. FC615. These two enzymes showed quite different and novel enzymatic properties whereas behaved a strong synergistic effect on the saccharification of alginate. Compared to that when AlyPB2 was used alone, the conversion rate of alginate polysaccharides to unsaturated monosaccharides when AlyPB1 and AlyPB2 acted on alginate together was dramatically increased approximately sevenfold. Furthermore, we found that AlyPB1 and AlyPB2 acted the synergistic effect basing on the complementarity of their substrate degradation patterns, particularly due to their M-/G-preference and substrate-size dependence. In addition, a novel method for sequencing alginate oligosaccharides was developed for the first time by combining the ¹H NMR spectroscopy and the enzymatic digestion with the exo-lyase AlyPB2, and this method is much simpler than traditional methods based on one- and two-dimensional NMR spectroscopy. Using this strategy, the sequences of the final tetrasaccharide and pentasaccharide product fractions produced by AlyPB1 were easily determined: the tetrasaccharide fractions contained two structures, ΔGMM and ΔMMM, at a molar ratio of 1:3.2, and the pentasaccharide fractions contained four structures, ΔMMMM, ΔMGMM, ΔGMMM, and ΔGGMM, at a molar ratio of ~ 1:1.5:3.5:5.25.

CONCLUSIONS

The identification of these two novel alginate lyases provides not only excellent candidate tool-type enzymes for oligosaccharide preparation but also a good model for studying the synergistic digestion and saccharification of alginate in biofuel production. The novel method for oligosaccharide sequencing described in this study will offer a very useful approach for structural and functional studies on alginate.

High-value bioproducts from microalgae: Strategies and progress

Microalgae have been considered as alternative sustainable resources for high-value bioproducts such as lipids (especially triacylglycerides [TAGs]), polyunsaturated fatty acids (PUFAs), and carotenoids, due to their relatively high photosynthetic efficiency, no arable land requirement, and ease of scale-up. It is of great significance to exploit microalgae for the production of high-value bioproducts. How to improve the content or productivity of specific bioproducts has become one of the most urgent challenges. In this review, we will describe high-value bioproducts from microalgae and their biosynthetic pathways (mainly for lipids, PUFAs, and carotenoids). Recent progress and strategies for the enhanced production of bioproducts from microalgae are also described in detail, and these strategies take advantages of optimized cultivation conditions with abiotic stress, chemical stress (addition of metabolic precursors, phytohormones, chemical inhibitors, and chemicals inducing oxidative stress response), and molecular approaches such as metabolic engineering, transcriptional engineering, and gene disruption strategies (mainly RNAi, antisense RNA, miRNA-based knockdown, and CRISPR/Cas9).

Microalgae for the production of lipid and carotenoids: a review with focus on stress regulation and adaptation

Microalgae have drawn great attention as promising sustainable source of lipids and carotenoids. Their lipid and carotenoids accumulation machinery can be trigged by the stress conditions such as nutrient limitation or exposure to the damaging physical factors. However, stressful conditions often adversely affect microalgal growth and cause oxidative damage to the cells, which can eventually reduce the yield of the desired products. To overcome these limitations, two-stage cultivation strategies and supplementation of growth-promoting agents have traditionally been utilized, but developing new highly adapted strains is theoretically the simplest strategy. In addition to genetic engineering, adaptive laboratory evolution (ALE) is frequently used to develop beneficial phenotypes in industrial microorganisms during long-term selection under specific stress conditions. In recent years, many studies have gradually introduced ALE as a powerful tool to improve the biological properties of microalgae, especially for improving the production of lipid and carotenoids. In this review, strategies for the manipulation of stress in microalgal lipids and carotenoids production are summarized and discussed. Furthermore, this review summarizes the overall state of ALE technology, including available selection pressures, methods, and their applications in microalgae for the improved production of lipids and carotenoids.

Advances in metabolic modeling of oleaginous microalgae

Production of biofuels and bioenergy precursors by phototrophic microorganisms, such as microalgae and cyanobacteria, is a promising alternative to conventional fuels obtained from non-renewable resources. Several species of microalgae have been investigated as potential candidates for the production of biofuels, for the most part due to their exceptional metabolic capability to accumulate large quantities of lipids. Constraint-based modeling, a systems biology approach that accurately predicts the metabolic phenotype of phototrophs, has been deployed to identify suitable culture conditions as well as to explore genetic enhancement strategies for bioproduction. Core metabolic models were employed to gain insight into the central carbon metabolism in photosynthetic microorganisms. More recently, comprehensive genome-scale models, including organelle-specific information at high resolution, have been developed to gain new insight into the metabolism of phototrophic cell factories. Here, we review the current state of the art of constraint-based modeling and computational method development and discuss how advanced models led to increased prediction accuracy and thus improved lipid production in microalgae.

Recent developments in synthetic biology and metabolic engineering in microalgae towards biofuel production

In the wake of the uprising global energy crisis, microalgae have emerged as an alternate feedstock for biofuel production. In addition, microalgae bear immense potential as bio-cell factories in terms of producing key chemicals, recombinant proteins, enzymes, lipid, hydrogen and alcohol. Abstraction of such high-value products (algal biorefinery approach) facilitates to make microalgae-based renewable energy an economically viable option. Synthetic biology is an emerging field that harmoniously blends science and engineering to help design and construct novel biological systems, with an aim to achieve rationally formulated objectives. However, resources and tools used for such nuclear manipulation, construction of synthetic gene network and genome-scale reconstruction of microalgae are limited. Herein, we present recent developments in the upcoming field of microalgae employed as a model system for synthetic biology applications and highlight the importance of genome-scale reconstruction models and kinetic models, to maximize the metabolic output by understanding the intricacies of algal growth. This review also examines the role played by microalgae as biorefineries, microalgal culture conditions and various operating parameters that need to be optimized to yield biofuel that can be economically competitive with fossil fuels.

Foodomics for human health: current status and perspectives

INTRODUCTION

In the post-genomic era, the opportunity to combine and integrate cutting-edge analytical platforms and data processing systems allowed the birth of foodomics, 'a discipline that studies the Food and Nutrition domains through the application of advanced omics technologies to improve consumer's well-being, health, and confidence'. Since then, this discipline has rapidly evolved and researchers are now facing the daunting tasks to meet consumers' needs in terms of food traceability, sustainability, quality, safety and integrity. Most importantly, today it is imperative to provide solid evidence of the mechanisms through which food can promote human health and well-being. Areas covered: In this review, the complex relationships connecting food, nutrition and human health will be discussed, with emphasis on the relapses for the development of functional foods and nutraceuticals, personalized nutrition approaches, and the study of the interplay among gut microbiota, diet and health/diseases. Expert commentary: Evidence has been provided supporting the role of various omic platforms in studying the health-promoting effects of food and customized dietary interventions. However, although associated to major analytical challenges, only the proper integration of multi-omics studies and the implementation of bioinformatics tools and databases will help translate findings from clinical practice into effective personalized treatment strategies.