Can Omics Approaches Improve Microalgal Biofuels under Abiotic Stress?

Key Proteomics Tools for Fundamental and Applied Microalgal Research

Microscopic, photosynthetic prokaryotes and eukaryotes, collectively referred to as microalgae, are widely studied to improve our understanding of key metabolic pathways (e.g., photosynthesis) and for the development of biotechnological applications. Omics technologies, which are now common tools in biological research, have been shown to be critical in microalgal research. In the past decade, significant technological advancements have allowed omics technologies to become more affordable and efficient, with huge datasets being generated. In particular, where studies focused on a single or few proteins decades ago, it is now possible to study the whole proteome of a microalgae. The development of mass spectrometry-based methods has provided this leap forward with the high-throughput identification and quantification of proteins. This review specifically provides an overview of the use of proteomics in fundamental (e.g., photosynthesis) and applied (e.g., lipid production for biofuel) microalgal research, and presents future research directions in this field.

Physiological and transcriptome profiling of Chlorella sorokiniana: A study on azo dye wastewater decolorization

Over decades, synthetic dyes have become increasingly dominated by azo dyes posing a significant environmental risk due to their toxicity. Microalgae-based systems may offer an alternative for treatment of azo dye effluents to conventional physical-chemical methods. Here, microalgae were tested to decolorize industrial azo dye wastewater (ADW). Chlorella sorokiniana showed the highest decolorization efficiency in a preliminary screening test. Subsequently, the optimization of the experimental design resulted in 70% decolorization in a photobioreactor. Tolerance of this strain was evidenced using multiple approaches (growth and chlorophyll content assays, scanning electron microscopy (SEM), and antioxidant level measurements). Raman microspectroscopy was employed for the quantification of ADW-specific compounds accumulated by the microalgal biomass. Finally, RNA-seq revealed the transcriptome profile of C. sorokiniana exposed to ADW for 72 h. Activated DNA repair and primary metabolism provided sufficient energy for microalgal growth to overcome the adverse toxic conditions. Furthermore, several transporter genes, oxidoreductases-, and glycosyltransferases-encoding genes were upregulated to effectively sequestrate and detoxify the ADW. This work demonstrates the potential utilization of C. sorokiniana as a tolerant strain for industrial wastewater treatment, emphasizing the regulation of its molecular mechanisms to cope with unfavorable growth conditions.

The genomes of Vischeria oleaginous microalgae shed light on the molecular basis of hyper-accumulation of lipids

BACKGROUND

With the urgent need to reduce carbon emissions, and the dwindling reserves of easily exploitable fossil fuel, microalgae-based biofuels that can be used for transport systems and CO₂ abatement have attracted great attention worldwide in recent years. One useful characteristic of microalgae is their ability to accumulate high levels of lipid content, in particular under conditions of nitrogen deprivation, with numerous species identified so far. However, a trade-off between levels of lipid accumulation and biomass productivity hinders the commercial applicability of lipids from microalgae. Here, we sequenced the genomes of Vischeria sp. CAUP H4302 and Vischeria stellata SAG 33.83, which can accumulate high content of lipids rich in nutraceutical fatty acids and with excellent biomass yield in nitrogen-limiting culture.

RESULTS

A whole-genome duplication (WGD) event was revealed in V. sp. CAUP H4302, which is a rare event in unicellular microalgae. Comparative genomic analyses showed that a battery of genes encoding pivotal enzymes involved in fatty acids and triacylglycerol biosynthesis, storage polysaccharide hydrolysis, and nitrogen and amino acid-related metabolisms are expanded in the genus Vischeria or only in V. sp. CAUP H4302. The most highlighted is the expansion of cyanate lyase genes in the genus Vischeria, which may enhance their detoxification ability against the toxic cyanate by decomposing cyanate to NH₃ and CO₂, especially under nitrogen-limiting conditions, resulting in better growth performance and sustained accumulation of biomass under the aforementioned stress conditions.

CONCLUSIONS

This study presents a WGD event in microalgae, providing new insights into the genetic and regulatory mechanism underpinning hyper-accumulation of lipids and offering potentially valuable targets for future improvements in oleaginous microalgae by metabolic engineering.

Role of secondary metabolites in distressed microalgae

Proficient photosynthetic microalgae/cyanobacteria produce a remarkable amount of various biomolecules. Secondary metabolites (SM) represent high value products for global biotrend application. Production improvement can be achieved by nutritional, environmental, and physiological stress as a first line tools for their stimulation. In recent decade, an increasing interest in algal stress biology and omics techniques have deepened knowledge in this area. However, deep understanding and connection of specific stress elucidator are missing. Hence, the present review summarizes recent evidence with an emphasis on the carotenoids, phenolic, and less-discussed compounds (glycerol, proline, mycosporins-like amino acids). Even when they are synthesized at very low concentrations, it highlights the need to expand knowledge in this area using genome-editing tools and omics approaches.

Integrated Omics Approach to Discover Differences in the Metabolism of a New Tibetan Desmodesmus sp. in Two Types of Sewage Treatments

Microalgae are now widely applied in municipal (YH_3) and industrial sewage (YH_4) treatments. Through integrated omics analysis, we studied the similarities and differences at the molecular level between the two different types of sewage treatment processes. The most significantly enriched gene ontology (GO) terms in both types of sewage treatments were the ribosome, photosynthesis, and proteasome pathways. The results show that the pathways of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were enriched for photosynthesis, glyoxylate and dicarboxylate metabolism, and carbon fixation in photosynthetic organisms. Considering YH_3 vs. YH_4, the metabolism of citrate, sedoheptulose-7P, and succinate was significantly upregulated. In addition, the results showed that the pathways of DEGs and DAMs were enriched in terms of amino acid metabolism and carotenoid biosynthesis in YH_4 vs. YH_3. The metabolism of S-Adenosyl-L-homocysteine was significantly downregulated, 2-oxobutanoate was significantly upregulated and downregulated, and the metabolism of abscisic acid glucose ester (ABA-GE) was also significantly upregulated. Overall, the results of this paper will help to improve the basic knowledge of the molecular response of microalgae to sewage treatments, and help design a response strategy based on microalgae for complex, mixed sewage treatments.

How do freshwater microalgae and cyanobacteria respond to antibiotics?

Antibiotic pollution is an emerging environmental challenge. Residual antibiotics from various sources, including municipal and industrial wastewater, sewage discharges, and agricultural runoff, are continuously released into freshwater environments, turning them into reservoirs that contribute to the development and spread of antibiotic resistance. Thus, it is essential to understand the impacts of antibiotic residues on aquatic organisms, especially microalgae and cyanobacteria, due to their crucial roles as primary producers in the ecosystem. This review summarizes the effects of antibiotics on major biological processes in freshwater microalgae and cyanobacteria, including photosynthesis, oxidative stress, and the metabolism of macromolecules. Their adaptive mechanisms to antibiotics exposure, such as biodegradation, bioadsorption, and bioaccumulation, are also discussed. Moreover, this review highlights the important factors affecting the antibiotic removal pathways by these organisms, which will promote the use of microalgae-based technology for the removal of antibiotics. Finally, we offer some perspectives on the opportunities for further studies and applications.

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.

Algae: a frontline photosynthetic organism in the microplastic catastrophe

Recalcitrancy in microplastics (MPs) contributes to white pollution. Bioremediation can remove MPs and facilitate environmental sustainability. Although recent studies have been conducted on the interaction of algae and MPs, the role of algae in MP removal with the simultaneous implementation of 'omics studies has not yet been discussed. Here, we review the adverse effects of MPs on the environment and possible approaches to remove them from the aquatic environment by using algae. We highlight the mechanism of MP biodegradation, the algal species that have been used, and how these are affected by MPs. We propose that algomics, characterization of biodegrading enzymes, and genetic engineering could be effective strategies for optimizing MP degradation.

Integrative chemical and omics analyses reveal copper biosorption and tolerance mechanisms of Bacillus cereus strain T6

A comprehensive understanding of the cellular response of microbes to metal stress is necessary for the rational development of microbe-based biosorbents for metal removal. The present study investigated the copper (Cu) sorption and resistance mechanism of Bacillus cereus strain T6, a newly isolated Cu-resistant bacterium, by integrative analyses of physiochemistry, genomics, transcriptomics, and metabolomics. The growth inhibition assay and biosorption determination showed that this bacterium exhibited high tolerance to Cu, with a minimum inhibitory concentration of 4.0 mM, and accumulated Cu by both extracellular adsorption and intracellular binding. SEM microscopic images and FTIR spectra showed significant cellular surface changes at the high Cu level but not at low, and the involvement of surface functional groups in the biosorption of Cu, respectively. Transcriptomic and untargeted metabolomic analyses detected 362 differentially expressed genes and 60 significantly altered metabolites, respectively. Integrative omics analyses revealed that Cu exposure dramatically induced a broad spectrum of genes involved in Cu transport and iron homeostasis, and suppressed the denitrification pathway, leading to significant accumulation of metabolites for metal transporter synthesis, membrane remolding, and antioxidant activities. The results presented here provide a new perspective on the intricate regulatory network of Cu homeostasis in bacteria.

Pb(II)-phycoremediation mechanism using Scenedesmus obliquus: cells physicochemical properties and metabolomic profiling

This study highlights the mechanisms of Pb(II)-phycoremediation using the Pb(II) tolerant strain of Scenedesmus obliquus. First, monitoring of cell growth kinetics in control and Pb(II)-doped medium revealed significant growth inhibition, while the analyses through flow cytometry and Zetasizer revealed no difference in cell viability and size. Residual weights of control and Pb(II)-loaded cells assessed by thermogravimetric analysis were 31.34% and 57.8%, respectively, indicating the uptake of Pb(II) into S. obliquus cells. Next, the use of chemical extraction to distinguish between the intracellular and extracellular uptake indicated the involvement of both biosorption (85.5%) and bioaccumulation (14.5%) mechanisms. Biosorption interaction of Pb(II) ions and the cell wall was confirmed using SEM-EDX, FTIR, zeta potential, zero-charge pH, and contact angle analyses. Besides, the biochemical characterization of control and Pb(II)-loaded cells revealed that the bioaccumulation of Pb(II) induces significant increases in the carotenoids and lipids content, while it decreases in the chlorophyll, carbohydrates, and proteins content. Finally, the metabolomic analysis indicated an increase in the relative abundance of fatty acid methyl esters, alkanes, aromatic compounds, and sterols. However, the alkenes and monounsaturated fatty acids decreased. Such metabolic adjustment may represent an adaptive strategy that prevents high Pb(II)-bioaccumulation in cellular compartments.

Genetic and non-genetic tailoring of microalgae for the enhanced production of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) - A review

The myriad health benefits associated with eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) laid the path for their application in the functional foods and nutraceutical industries. Fish being primarily exploited for extraction of EPA and DHA are unsustainable sources; thus, oleaginous microalgae turn out to be an alternative sustainable source. This review paper aims to provide the recent developments in the context of enhancing EPA and DHA production by utilising non-genetic tailoring and genetic tailoring methods. We have also summarized the legislation, public perception, and possible risks associated with the usage of genetically modified microalgae focusing on EPA and DHA production.

Insights into the genetic and metabolic engineering approaches to enhance the competence of microalgae as biofuel resource: A review

Conventional fuel resources are overburden with speedy global energy demand which ensued the urgent need of alternate energy resources. Biofuel generation efficiency of microalgae is notable due to their comparatively rapid biomass production rate and high oil content. But, the employment of microalgae as biofuel resource is in infancy due to low productivity and high production cost. The issues can be addressed by employing engineered microalgal strains that would be able to efficiently generate enhanced levels of biomass with augmented lipid and/or carbohydrate content for proficient biofuel production. Genetic alterations and metabolic engineering of microalgal species might be helpful in developing high stress-tolerant strains with improved properties for biofuel generation. Various omics approaches appeared significant to upgrade the microalgal lipid production. Intervention of genetic and metabolic engineering approaches would facilitate the development of microalgae as a competent biofuel resource and inflate the economic commercialization of biofuels.

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.

Engineering microalgae: transition from empirical design to programmable cells

Domesticated microalgae hold great promise for the sustainable provision of various bioresources for human domestic and industrial consumption. Efforts to exploit their potential are far from being fully realized due to limitations in the know-how of microalgal engineering. The associated technologies are not as well developed as those for heterotrophic microbes, cyanobacteria, and plants. However, recent studies on microalgal metabolic engineering, genome editing, and synthetic biology have immensely helped to enhance transformation efficiencies and are bringing new insights into this field. Therefore, this article, summarizes recent developments in microalgal biotechnology and examines the prospects for generating specialty and commodity products through the processes of metabolic engineering and synthetic biology. After a brief examination of empirical engineering methods and vector design, this article focuses on quantitative transformation cassette design, elaborates on target editing methods and emerging digital design of algal cellular metabolism to arrive at high yields of valuable products. These advances have enabled a transition of manners in microalgal engineering from single-gene and enzyme-based metabolic engineering to systems-level precision engineering, from cells created with genetically modified (GM) tags to that without GM tags, and ultimately from proof of concept to tangible industrial applications. Finally, future trends are proposed in microalgal engineering, aiming to establish individualized transformation systems in newly identified species for strain-specific specialty and commodity products, while developing sophisticated universal toolkits in model algal species.

Targeted Metabolomic and Biochemical Changes During Nitrogen Stress Mediated Lipid Accumulation in Scenedesmus quadricauda CASA CC202

Scenedesmus quadricauda CASA CC202, a potent freshwater microalga is being used as a biofuel feedstock, which accumulates 2.27 fold lipid during nitrogen stress induction. Upon nitrogen starvation, S. quadricauda undergoes biochemical and metabolic changes that perturb the cell to cope up the stress condition. The nitrogen stress-induced biochemical changes in mitochondrion exhibits due to the oxidative stress-induced Reactive Oxygen species (ROS) generation at high membrane potential (Δψ_m). The predominant ROS generated during nitrogen starvation was H₂O₂, OH^–, O₂⋅⁻ and to suppress them, scavenging enzymes such as peroxidase and catalase increased to about 23.16 and 0.79 U/ml as compared to control (20.2, 0.19 U/ml). The targeted metabolic analysis showed, stress-related non-proteinogenic amino acids and energy equivalents elevated during the initial hours of nitrogen starvation. The nitrogen stress-triggered biochemical and metabolic changes along with other cellular events eventually lead to lipid accumulation in S. quadricauda.

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.

Real-Time Volatilomics: A Novel Approach for Analyzing Biological Samples

The use of the 'omics techniques in environmental research has become common-place. The most widely implemented of these include metabolomics, proteomics, genomics, and transcriptomics. In recent years, a similar approach has also been taken with the analysis of volatiles from biological samples, giving rise to the so-called 'volatilomics' in plant analysis. Developments in direct infusion mass spectrometry (DI-MS) techniques have made it possible to monitor the changes in the composition of volatile flux from parts of plants, single specimens, and entire ecosystems in real-time. The application of these techniques enables a unique insight into the dynamic metabolic processes that occur in plants. Here, we provide an overview of the use of DI-MS in real-time volatilomics research involving plants.

Highest accumulated microalgal lipids (polar and non-polar) for biodiesel production with advanced wastewater treatment: Role of lipidomics

Microalgal lipids consist of non-polar and polar lipids. Triacyleglyceride (TAG), a non-polar lipid, is convertible to biodiesel, whereas glycolipids and phospholipids are polar and not convertible to biodiesel owing to their high degree of unsaturation (polyunsaturated fatty acids), which makes the production process insufficient and expensive. In this review, microalgal species that contain the highest lipid content (≥40%) in the literature till 2019 are highlighted. The differentiation between non-polar and polar lipids and the limitations in the conversion of polar lipids to biodiesel are reported. The basic and advanced factors contributing to the accumulation of lipids convertible to biodiesel is discussed. Microalgal species including Scenedesmus obliquus, Ourococcus multisporus, Chlamydomonas pitschmannii, Micractinium reisseri, and Botryococcus braunii with high lipid content are potential candidates for biomass/biodiesel production and nutrient removal from wastewater. Application of lipidomics and transcriptomics to manipulate the lipid associated gene acetyl-CoA synthetase in microalgae improves the accumulative lipid content.

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.

Omics approaches for microalgal applications: Prospects and challenges

In recent impetus of phycological research, microalgae have emerged as a potential candidate for various arena of application-driven research. Omics-based tactics are used for disentangling the regulation and network integration for biosynthesis/degradation of metabolic precursors, intermediates, end products, and identifying the networks that regulate the metabolic flux. Multi-omics coupled with data analytics have facilitated understanding of biological processes and allow ample access to diverse metabolic pathways utilized for genetic manipulations making microalgal factories more efficient. The present review discusses state-of-art "Algomics" and the prospect of microalgae and their role in symbiotic association by using omics approaches including genomics, transcriptomics, proteomics and metabolomics. Microalgal based uni- and multi-omics approaches are critically analyzed in wastewater treatment, metal toxicity and remediation, biofuel production, and therapeutics to provide an imminent outlook for an array of environmentally sustainable and economically viable microalgal applications.

De novo whole genome sequencing data of two mangrove-isolated microalgae from Terengganu coastal waters

Interest in harvesting potential benefits from microalgae renders it necessary to have the many ecological niches of a single species to be investigated. This dataset comprises de novo whole genome assembly of two mangrove-isolated microalgae (from division Chlorophyta); Chlorella vulgaris UMT-M1 and Messastrum gracile SE-MC4 from Universiti Malaysia Terengganu, Malaysia. Library runs were carried out with 2 × 150 base paired-ends reads, whereas sequencing was conducted using Illumina Novaseq 2500 platform. Sequencing yielded raw reads amounting to ∼11 Gb in total bases for both species and was further assembled de novo. Genome assembly resulted in a 50.15 Mbp and 60.83 Mbp genome size for UMT-M1 and SE-MC4, respectively. All filtered and assembled genomic data sequences have been submitted to National Centre for Biotechnology Information (NCBI) and can be located at DDBJ/ENA/GenBank under the accession of VJNP00000000 (UMT-M1) and VIYE00000000 (SE-MC4).