Toward an understanding of lipid and starch accumulation in microalgae: A proteomic study of Neochloris oleoabundans cultivated under N-limited heterotrophic conditions

The dispersant Corexit 9500 and (dispersed) oil are lethal to coral endosymbionts

Endosymbionts (Symbiodiniaceae) play a vital role in the health of corals. Seawater pollution can harm these endosymbionts and dispersants used during oil spill cleanup can be extremely toxic to these organisms. Here, we examined the impact of oil and a specific dispersant, Corexit-9500, on two representative endosymbionts - Symbiodinium and Cladocopium - from the Southwestern endemic coral Mussismilia braziliensis. The survival and photosynthetic potential of the endosymbionts decreased dramatically after exposure to the dispersant and oil by ~25 % after 2 h and ~50 % after 7 days. Low concentrations of dispersant (0.005 ml/l) and dispersed oil (Polycyclic Aromatic Hydrocarbons, 1132 μg/l; Total Petroleum Hydrocarbons, 595 μg/l) proved highly toxic to both Symbiodinium and Cladocopium. These levels triggered a reduction in growth rate, cell size, and cell wall thickness. After a few hours of exposure, cellular organelles were damaged or destroyed. These acute toxic effects underline the fragile nature of coral endosymbionts.

The responding mechanism of indigenous bacteria in municipal wastewater inoculated with different concentrations of exogenous microalgae

Indigenous bacteria popularly exist in real wastewater. Therefore, the potential interaction between bacteria and microalgae is inevitable in microalgae-based wastewater treatment systems. It is likely to affect the performance of systems. Accordingly, the characteristics of indigenous bacteria is worth serious concerning. Here we investigated the response of indigenous bacterial communities to variant inoculum concentrations of Chlorococcum sp. GD in municipal wastewater treatment systems. The removal efficiency of COD, ammonium and total phosphorus were 92.50%-95.55%, 98.00%-98.69%, and 67.80%-84.72%, respectively. The bacterial community responded differently to different microalgal inoculum concentrations, which was mainly affected by microalgal number, ammonium and nitrate. Besides, there were differential co-occurrence patterns and carbon and nitrogen metabolic function of indigenous bacterial communities. All these results indicated that bacterial communities responded significantly to environmental changes caused by the change of microalgal inoculum concentrations. The response of bacterial communities to different microalgal inoculum concentrations was beneficial for forming a stable symbiotic community of both microalgae and bacteria to remove pollutants in wastewater.

Exploiting AGPase genes and encoded proteins to prioritize development of optimum engineered strains in microalgae towards sustainable biofuel production

Although ADP glucose pyrophosphorylase (AGPase), with two large subunits (ls) and two small subunits (ss), is a promising knockout target for increasing the neutral lipid content, the details regarding the sequence-structure features and their distribution within metabolic system in microalgae is rather limited. Against this backdrop, a comprehensive genome-wide comparative analysis on 14 sequenced microalgal genomes was performed. For the first time the heterotetrameric structure of the enzyme and the interaction of the catalytic unit with the substrate was also studied. Novel findings of the present study includes: (i) at the DNA level, the genes controlling the ss are more conserved than those controlling the ls; the variation in both the gene groups is mainly due to exon number, exon length and exon phase distribution; (ii) at protein level, the ss genes are more conserved relative to those for ls; (III) three putative key consensus sequences 'LGGGAGTRLYPLTKNRAKPAV', 'WFQGTADAV' and 'ASMGIYVFRKD' were ubiquitously conserved in all the AGPases; (iv) molecular dynamics investigations revealed that the modeled AGPase heterotetrameric structure, from oleaginous algae Chlamydomonas reinharditii, was completely stable in real time environment; (v) The binding interfaces of catalytic unit, ssAGPase, from C. reinharditii with α-D-glucose 1-phosphate (αGP) was also analyzed. The results of the present study have provided system-based insights into the structure-function of the genes and encoded proteins, which provided clues for exploitation of variability in these genes that, could be further utilized to design site-specific mutagenic experiments for engineering of microalgal strains towards sustainable development of biofuel.

Developing algae as a sustainable food source

Current agricultural and food production practices are facing extreme stress, posed by climate change and an ever-increasing human population. The pressure to feed nearly 8 billion people while maintaining a minimal impact on the environment has prompted a movement toward new, more sustainable food sources. For thousands of years, both the macro (seaweed and kelp) and micro (unicellular) forms of algae have been cultivated as a food source. Algae have evolved to be highly efficient at resource utilization and have proven to be a viable source of nutritious biomass that could address many of the current food production issues. Particularly for microalgae, studies of their large-scale growth and cultivation come from the biofuel industry; however, this knowledge can be reasonably translated into the production of algae-based food products. The ability of algae to sequester CO₂ lends to its sustainability by helping to reduce the carbon footprint of its production. Additionally, algae can be produced on non-arable land using non-potable water (including brackish or seawater), which allows them to complement rather than compete with traditional agriculture. Algae inherently have the desired qualities of a sustainable food source because they produce highly digestible proteins, lipids, and carbohydrates, and are rich in essential fatty acids, vitamins, and minerals. Although algae have yet to be fully domesticated as food sources, a variety of cultivation and breeding tools exist that can be built upon to allow for the increased productivity and enhanced nutritional and organoleptic qualities that will be required to bring algae to mainstream utilization. Here we will focus on microalgae and cyanobacteria to highlight the current advancements that will expand the variety of algae-based nutritional sources, as well as outline various challenges between current biomass production and large-scale economic algae production for the food market.

Effects of different concentrations of CO2 on Scenedesmus obliquus to overcome sludge extract toxicity and accumulate biomass

Large amounts of toxic excess sludge as well as high concentrations of carbon dioxide can be produced in coal-gasification industry. Microalgae has huge potential in the use of nutrients, the removal of toxic organic matter in excess sludge and CO₂ fixation. At the same time, the cultivation of the microalgae and the accumulation of high-quality biomass are also the key problems of concern. In this study, the growth and biomass synthesis of Scenedesmus obliquus cultured in sludge extract under 0%-15% (v/v) CO₂ were investigated. Results indicated that the highest microalgae biomass yield of 1.609 ± 0.012 g/L can be achieved under 15% CO₂ on the 30th day. The maximal photochemical efficiency of PSⅡ (Fv/Fm) decreased in the first 12 h and then increased with the culture time, and the decline amplitude decreased with the increase of the CO₂ concentration, indicating that CO₂ slowed down the toxic inhibition of sludge extract to Scenedesmus obliquus, which was expressed as the down-regulation of p53 signaling pathway and protein A0A383WFI7. Proteomic analysis showed that under high-concentration CO₂, the protein interaction network with the protein of photosystem II assembly (A0A383VSL5) as the core protein regulated the growth of Scenedesmus obliquus in terms of energy metabolism and material transportation. On the 4th day, Methyltransf_11 domain-containing protein (A0A383VH03) was up-regulated and promoted lipid synthesis, leading to the accumulation of lipids in Scenedesmus obliquus in the early stage and the increase of polysaccharides in the later stage. Collectively, this study revealed the regulation mechanism of CO₂ on toxicity removal and carbon distribution of Scenedesmus obliquus.

Physiological and proteomic responses of Chlamydomonas reinhardtii to arsenate and lead mixtures

Arsenic (As) and lead (Pb) are frequently emitted from various sources into environment, but microbial responses to their combined toxicity have not been systematically investigated. In this study, Chlamydomonas reinhardtii was exposed to two levels of arsenate (As (V), 50, 500 μg/L), Pb (II) (500, 5000 μg/L) and their mixture (50 μg/L As (V) + 500 μg/L Pb (II); 500 μg/L As (V) + 5000 μg/L Pb (II)). The growth of C. reinhardtii was inhibited more remarkably by As (V) than by Pb (II). The As stress was alleviated by Pb in the 50 μg/L As (V) + 500 μg/L Pb (II) treatment, but was enhanced upon the 500 μg/L As (V) + 5000 μg/L Pb (II) exposure, with more pronounced changes in a number of physiological parameters of the algal cells. Proteomic results showed that 71 differently expressed proteins (DEPs) in the treatment of 50 μg/L As (V) + 500 μg/L Pb (II), and 167 DEPs were identified in that of 500 μg/L As (V) + 5000 μg/L Pb (II). These proteins were involved in energy metabolism, photosynthetic carbon fixation, reactive oxygen scavenging and defense, and amino acid synthesis. Taken together, these physiological and proteomic data demonstrated that C. reinhardtii could resist the As (V) and Pb (II) combined treatments through extracellular complexation and intracellular pathways.

Comparative Proteomics Reveals Evidence of Enhanced EPA Trafficking in a Mutant Strain of Nannochloropsis oculata

The marine microalga Nannochloropsis oculata is a bioproducer of eicosapentaenoic acid (EPA), a fatty acid. EPA is incorporated into monogalactosyldiacylglycerol within N. oculata thylakoid membranes, and there is a biotechnological need to remodel EPA synthesis to maximize production and simplify downstream processing. In this study, random mutagenesis and chemical inhibitor-based selection method were devised to increase EPA production and accessibility for improved extraction. Ethyl methanesulfonate was used as the mutagen with selective pressure achieved by using two enzyme inhibitors of lipid metabolism: cerulenin and galvestine-1. Fatty acid methyl ester analysis of a selected fast-growing mutant strain had a higher percentage of EPA (37.5% of total fatty acids) than the wild-type strain (22.2% total fatty acids), with the highest EPA quantity recorded at 68.5 mg/g dry cell weight, while wild-type cells had 48.6 mg/g dry cell weight. Label-free quantitative proteomics for differential protein expression analysis revealed that the wild-type and mutant strains might have alternative channeling pathways for EPA synthesis. The mutant strain showed potentially improved photosynthetic efficiency, thus synthesizing a higher quantity of membrane lipids and EPA. The EPA synthesis pathways could also have deviated in the mutant, where fatty acid desaturase type 2 (13.7-fold upregulated) and lipid droplet surface protein (LDSP) (34.8-fold upregulated) were expressed significantly higher than in the wild-type strain. This study increases the understanding of EPA trafficking in N. oculata, leading to further strategies that can be implemented to enhance EPA synthesis in marine microalgae.

Transcriptomic and fatty acid analyses of Neochloris aquatica grown under different nitrogen concentration

In this study, we characterized the fatty acid production in Neochloris aquatica at transcriptomics and biochemical levels under limiting, normal, and excess nitrate concentrations in different growth phases. At the stationary phase, N. aquatica mainly produced saturated fatty acids such as stearic acid under the limiting nitrate concentration, which is suitable for biodiesel production. However, it produced polyunsaturated fatty acids such as α-linolenic acid under the excess nitrate concentration, which has nutritional values as food supplements. In addition, RNA-seq was employed to identify genes and pathways that were being affected in N. aquatica for three growth phases in the presence of the different nitrate amounts. Genes that are responsible for the production of saturated fatty acids were upregulated in the cells grown under a limiting nitrogen amount while genes that are responsible for the production of polyunsaturated fatty acid were upregulated in the cells grown under excess nitrogen amount. Further analysis showed more genes differentially expressed (DEGs) at the logarithmic phase in all conditions while a relatively steady trend was observed during the transition from the logarithmic phase to the stationary phase under limiting and excess nitrogen. Our results provide a foundation for identifying developmentally important genes and understanding the biological processes in the different growth phases of the N. aquatica in terms of biomass and lipid production.

Comparison of Auxenochlorella protothecoides and Chlorella spp. Chloroplast Genomes: Evidence for Endosymbiosis and Horizontal Virus-like Gene Transfer

Resequencing of the chloroplast genome (cpDNA) of Auxenochlorella protothecoides UTEX 25 was completed (GenBank Accession no. KC631634.1), revealing a genome size of 84,576 base pairs and 30.8% GC content, consistent with features reported for the previously sequenced A. protothecoides 0710, (GenBank Accession no. KC843975). The A. protothecoides UTEX 25 cpDNA encoded 78 predicted open reading frames, 32 tRNAs, and 4 rRNAs, making it smaller and more compact than the cpDNA genome of C. variabilis (124,579 bp) and C. vulgaris (150,613 bp). By comparison, the compact genome size of A. protothecoides was attributable primarily to a lower intergenic sequence content. The cpDNA coding regions of all known Chlorella species were found to be organized in conserved colinear blocks, with some rearrangements. The Auxenochlorella and Chlorella species genome structure and composition were similar, and of particular interest were genes influencing photosynthetic efficiency, i.e., chlorophyll synthesis and photosystem subunit I and II genes, consistent with other biofuel species of interest. Phylogenetic analysis revealed that Prototheca cutis is the closest known A. protothecoides relative, followed by members of the genus Chlorella. The cpDNA of A. protothecoides encodes 37 genes that are highly homologous to representative cyanobacteria species, including rrn16, rrn23, and psbA, corroborating a well-recognized symbiosis. Several putative coding regions were identified that shared high nucleotide sequence identity with virus-like sequences, suggestive of horizontal gene transfer. Despite these predictions, no corresponding transcripts were obtained by RT-PCR amplification, indicating they are unlikely to be expressed in the extant lineage.

A novel two-stage heterotrophic cultivation for starch-to-protein switch to efficiently enhance protein content of Chlorella sp. MBFJNU-17

This work aimed to firstly establish an efficient and novel two-stage cultivation process to produce microalgal biomass rich in protein using a heterotrophic Chlorella sp. MBFJNU-17 strain. In the first-stage cultivation, to reduce the glucose and urea utilization, microalga achieved a high biomass at 40 g/L glucose and 1 g/L urea; meantime, the expression from starch biosynthesis genes of microalga was up-regulated under nitrogen-starvation conditions for starch accumulation (55.01%). In the second-stage cultivation, based on the over-compensation effect, Chlorella cells after the first-stage cultivation were further treated at 5 g/L glucose and 3 g/L urea to up-regulate starch degradation, central carbon metabolism and urea absorption genes expression to drive intracellular starch-to-protein switch for biosynthetic protein (59.75%). Moreover, microalga performed similar characteristics in a 10-L fermenter by the established process. Taken together, Chlorella sp. MBFJNU-17 was the promising candidate to produce high-value biomass enriched in protein by the established two-stage cultivation.

Molecular characterization of water extractable Euglena gracilis cellular material composition using asymmetrical flow field-flow fractionation and high-resolution mass spectrometry

Asymmetrical flow field-flow fractionation (AF4) and high-resolution Orbitrap mass spectrometry (HRMS) were used to separate and characterize cellular fractions of the dark- and light-grown Euglena gracilis cellular material. Biological replicates analyzed by HRMS shared 21-73% of commonly detected m/z values. Greater variability in shared features was found in light-grown cellular fractions (p < 0.05), likely due to small variations in growth stage. Significant differences in molecular composition were observed between AF4 cellular fractions, with dark cell fractions showing a propensity towards carbohydrate-like and tannin-like compounds, and higher double-bond equivalent (DBE) and modified aromatic index (AI_mod) were associated with light-grown cell fractions. Fractionation and high-resolution mass spectrometry aided characterization demonstrated the power of the AF4 to selectively cater to certain compounds/cellular entities with distinct compositional classes and double-bond equivalents and aromaticity index characteristics. Graphical abstract.

Storage of starch and lipids in microalgae: Biosynthesis and manipulation by nutrients

Microalgae accumulate starch and lipid as storage metabolites under nutrient depletion, which can be used as sustainable feedstock for biorefinery. Omics analysis coupled with enzymatic and genetic verifications uncovered a partial picture of pathways and important enzymes or regulators related to starch and lipid biosynthesis as well as the carbon partitioning between them under nutrient depletion conditions. Depletion of macronutrients (N, P, and S) resulted in considerable enhancement of starch and/or lipid content in microalgae, but the accompanying declined photosynthesis hampered the achievements of high concentrations. This review summarized the current knowledge on the pathways and the committed steps as well as their carbon allocation involved in starch and lipid biosynthesis, and focused on the manipulation of different nutrients and the alleviation of oxidative stress for enhanced storage metabolites production. The biological and engineering approaches to cope with the conflict between biomass production and storage metabolites accumulation are proposed.

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

BACKGROUND

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

RESULTS

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

CONCLUSION

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

Leveraging algal omics to reveal potential targets for augmenting TAG accumulation

Ongoing global efforts to commercialize microalgal biofuels have expedited the use of multi-omics techniques to gain insights into lipid biosynthetic pathways. Functional genomics analyses have recently been employed to complement existing sequence-level omics studies, shedding light on the dynamics of lipid synthesis and its interplay with other cellular metabolic pathways, thus revealing possible targets for metabolic engineering. Here, we review the current status of algal omics studies to reveal potential targets to augment TAG accumulation in various microalgae. This review specifically aims to examine and catalog systems level data related to stress-induced TAG accumulation in oleaginous microalgae and inform future metabolic engineering strategies to develop strains with enhanced bioproductivity, which could pave a path for sustainable green energy.

Neochloris oleoabundans is worth its salt: Transcriptomic analysis under salt and nitrogen stress

Neochloris oleoabundans is an oleaginous microalgal species that can be cultivated in fresh water as well as salt water. Using salt water gives the opportunity to reduce production costs and the fresh water footprint for large scale cultivation. Production of triacylglycerols (TAG) usually includes a biomass growth phase in nitrogen-replete conditions followed by a TAG accumulation phase under nitrogen-deplete conditions. This is the first report that provides insight in the saline resistance mechanism of a fresh water oleaginous microalgae. To better understand the osmoregulatory mechanism of N. oleoabundans during growth and TAG accumulating conditions, the transcriptome was sequenced under four different conditions: fresh water nitrogen-replete and -deplete conditions, and salt water (525 mM dissolved salts, 448mM extra NaCl) nitrogen-replete and -deplete conditions. In this study, several pathways are identified to be responsible for salt water adaptation of N. oleoabundans under both nitrogen-replete and -deplete conditions. Proline and the ascorbate-glutathione cycle seem to be of importance for successful osmoregulation in N. oleoabundans. Genes involved in Proline biosynthesis were found to be upregulated in salt water. This was supported by Nuclear magnetic resonance (NMR) spectroscopy, which indicated an increase in proline content in the salt water nitrogen-replete condition. Additionally, the lipid accumulation pathway was studied to gain insight in the gene regulation in the first 24 hours after nitrogen was depleted. Oil accumulation is increased under nitrogen-deplete conditions in a comparable way in both fresh and salt water. The mechanism behind the biosynthesis of compatible osmolytes can be used to improve N. oleoabundans and other industrially relevant microalgal strains to create a more robust and sustainable production platform for microalgae derived products in the future.