Adaptive evolution of microalgae Schizochytrium sp. under high salinity stress to alleviate oxidative damage and improve lipid biosynthesis

Attenuation pathways of erythromycin and biochemical responses related to algal growth and lipid synthesis in a microalga-effluent system

Microalgal cultivation in municipal wastewater treatment plants (WWTPs) can realize the coupling of wastewater treatment and microalgae energy utilization, however, the residual antibiotics in effluents from WWTPs affect the growth of microalgae. In this study, green alga (Scenedesmus obliquus) cells were inoculated into the effluents to ascertain the attenuation pathways of erythromycin (ERY) and the biochemical responses of microalga in a microalga-effluent system. Results showed that hydrolysis, photolysis, and biodegradation (including bioadsorption) cause the attenuation of ERY in a microalga-effluent system, and the biodegradation (including bioadsorption) has the greatest removal rate (reaching a maximum of 57.87%), followed by hydrolysis (reaching a maximum of 34.13%), and photolysis (less than 5%) after five days. The photosynthetic pigment contents in cells of microalga decreased the most (by 35.66% for chlorophyll a), and the production of ROS was stimulated (by 33.75%) after five-day exposure to ERY at an initial concentration of 100 μg/L. Meanwhile, the activity of ribulose-1,5-biphosphate carboxylase (RuBPCase) decreased by 55.65%, and the activity of acetyl-CoA carboxylase (ACCase) increased by 55.65%. The ROS level, photosynthetic pigment content, and RuBPCase activity were extremely significantly correlated with each other (P < 0.01), indicating that exposure to ERY changed those biochemical responses related to the rate of photosynthesis of microalga, inhibiting the growth thereof. On the other hand, exposure to ERY increased lipid production by microalga through the induced ACCase activity.

Synthetic biology-driven microbial production of folates: Advances and perspectives

With the development and application of synthetic biology, significant progress has been made in the production of folate by microbial fermentation using cell factories, especially for using generally regarded as safe (GRAS) microorganism as production host. In this review, the physiological functions and applications of folates were firstly discussed. Second, the current advances of folate-producing GRAS strains development were summarized. Third, the applications of synthetic biology-based metabolic regulatory tools in GRAS strains were introduced, and the progress in the application of these tools for folate production were summarized. Finally, the challenges to folates efficient production and corresponding emerging strategies to overcome them by synthetic biology were discussed, including the construction of biosensors using tetrahydrofolate riboswitches to regulate metabolic pathways, adaptive evolution to overcome the flux limitations of the folate pathway. The combination of new strategies and tools of synthetic biology is expected to further improve the efficiency of microbial folate synthesis.

Toxic mechanism of three azole fungicides and their mixture to green alga Chlorella pyrenoidosa

Currently, few studies have investigated the joint toxicity mechanism of azole fungicides at different exposure times and mixed at the relevant environmental concentrations. In this study, three common azole fungicides, namely, myclobutanil (MYC), propiconazole (PRO), and tebuconazole (TCZ), were used in studying the toxic mechanisms of a single substance and its ternary mixture exposed to ambient concentrations of Chlorella pyrenoidosa. Superoxide dismutase (SOD), catalase (CAT), chlorophyll a (Chla), and total protein (TP), were used as physiological indexes. Results showed that three azole fungicides and ternary mixture presented obvious time-dependent toxicities at high concentrations. MYC induced a hormetic effect on algal growth, whereas PRO and TCZ inhibit algal growth in the entire range of the tested concentrations. The toxicities of the three azole fungicides at 7 days followed the order PRO > TCZ > MYC. Three azole fungicides and their ternary mixture induced different levels of SOD and CAT activities in algae at high concentrations. The ternary mixture showed additive effects after 4 and 7 days exposure, but no effect was observed at actual environmental concentrations. The toxic mechanisms may be related to the continuous accumulation of reactive oxygen species, which not only affected protein structures and compositions but also damaged thylakoid membranes, hindered the synthesis of proteins and chlorophyll a, and eventually inhibited algal growth. These findings increase the understanding of the ecotoxicity of azole fungicides and use of azole fungicides in agricultural production.

High-yield strain of fusidic acid obtained by atmospheric and room temperature plasma mutagenesis and the transcriptional changes involved in improving its production in fungus Fusidium coccineum

AIMS

To obtain the high-yield strain of fusidic acid, which is produced from fungus Fusidium coccineum and is the only fusidane-type antibiotic that has been used clinically, and confirm the changes in the transcription levels involved in increasing its production.

METHODS AND RESULTS

By using the atmospheric and room temperature plasma mutagenesis technology, a high-yield mutant strain of fusidic acid-producing fungus F. coccineum was obtained. Using the genomic analysis of the original strain based on biosynthetic pathways of ergosterol and helvolic acid, we demonstrate that the pathway involved in the biosynthesis of 2,3-oxidosqualene from acetyl coenzyme A was shared by fusidic acid and ergosterol, and fusidic acid was finally synthesized by the catalysis of multiple cytochrome P450s and short-chain dehydrogenase/reductase from 2,3-oxidosqualene. Then, through the transcriptomic analysis of the original and mutagenized strain, it revealed that the proposed pathway from sucrose to fusidic acid was the most significantly up-regulated in the transcription levels of the mutant strain.

CONCLUSIONS

The changes in the transcription levels of fusidic acid during its biosynthesis might result in high-yield of fusidic acid in the mutant strain. This is the first report on the whole biosynthetic pathway of fusidic acid in F. coccineum.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study obtain the genetic basis for the biosynthesis of fusidic acid which could be beneficial for the molecular modifications of F. coccineum to further increase its yield by fermentation in future, and established the foundation to reveal the mechanism of the high-yield of the mutant strain.

Unlocking nature's biosynthetic potential by directed genome evolution

Microorganisms have been increasingly explored as microbial cell factories for production of fuels, chemicals, drugs, and materials. Among the various metabolic engineering strategies, directed genome evolution has emerged as one of the most powerful tools to unlock the full biosynthetic potential of microorganisms. Here we summarize the directed genome evolution strategies that have been developed in recent years, including adaptive laboratory evolution and various targeted genome-scale engineering strategies, and discuss their applications in basic and applied biological research.

Harnessing the Power of Mutagenesis and Adaptive Laboratory Evolution for High Lipid Production by Oleaginous Microalgae and Yeasts

Oleaginous microalgae and yeasts represent promising candidates for large-scale production of lipids, which can be utilized for production of drop-in biofuels, nutraceuticals, pigments, and cosmetics. However, low lipid productivity and costly downstream processing continue to hamper the commercial deployment of oleaginous microorganisms. Strain improvement can play an essential role in the development of such industrial microorganisms by increasing lipid production and hence reducing production costs. The main means of strain improvement are random mutagenesis, adaptive laboratory evolution (ALE), and rational genetic engineering. Among these, random mutagenesis and ALE are straight forward, low-cost, and do not require thorough knowledge of the microorganism’s genetic composition. This paper reviews available mutagenesis and ALE techniques and screening methods to effectively select for oleaginous microalgae and yeasts with enhanced lipid yield and understand the alterations caused to metabolic pathways, which could subsequently serve as the basis for further targeted genetic engineering.

Effect of sequential recycling of spent media wastewater on docosahexaenoic acid production by newly isolated strain Aurantiochytrium sp. ICTFD5

The main aim of this work was the optimization of recycled spent media wastewater (SMW) concentration for high biomass production of Aurantiochytrium sp. ICTFD5. Further, optimization for growth patterns and lipid accumulation capacity with three subsequent recycling runs was also performed. The biomass production after 96 h fermentation for recycling with 50% SMW was; 21.3 ± 1.5, 19.1 ± 1.3, 19 ± 1.2, and 23 ± 1.2 g/L for the first, second, third recycle runs, and control respectively. All the recycle runs were carried out with the same media and cultivation conditions. Subsequent recycling affected lipid accumulation, and it was decreased by ~4 to 9% compared to the control. The compositional shift of fatty acids was observed with sequential recycle runs, changing more towards saturated fatty acids content, suggesting it to be a new potential source for biodiesel feedstock.

Toxic effects of terpinolene on Microcystis aeruginosa: Physiological, metabolism, gene transcription, and growth effects

Bioherbicide terpinolene is widely employed in the agricultural field because of its unique phytotoxic properties. However, little is known about the toxicity of bioherbicide on harmful algal blooms (HABs) and its mechanisms. Therefore, in this study, the inhibiting effect of bioherbicide terpinolene on the growth and physiological change of Microcystis aeruginosa was determined. Results showed that the cell density and photosynthetic activity of microalgae were significantly inhibited by terpinolene. Activities of nitrate reductase (NR) and glutamine synthetase (GS) were decreased separately by 25.38% and 42.75% after 4 d of exposure to 1.47 mM terpinolene, suggesting the inhibiting effect of terpinolene on algal nitrogen metabolism. However, the transcript abundance of genes related to membrane protein cytochrome c oxidase subunit II (COX II) and ATP-binding cassette transporters (ABC transporter) were enhanced separately by 3.15 and 1.69-fold compared with control, suggesting the resistance response of cells to terpinolene stress. Additionally, terpinolene not only increased the content of endogenous phytohormones including indole-3-acetic acid (IAA), zeatin, and brassinolide, but also inhibited the expression of genes related to calcium-binding protein (CaBPs), one kind of calcium (Ca²⁺) sensors, suggesting its regulation on algal signal molecules. These findings helped to understand the ecotoxicity of terpinolene and guide the rational use of bioherbicide in agriculture.

High salinity acclimatization alleviated cadmium toxicity in Dunaliella salina: Transcriptomic and physiological evidence

In the present study, we tested the hypothesis that high salinity acclimatization can mitigate cadmium (Cd) toxicity in the microalga Dunaliella salina. To this end, microalgal cells were subjected to high salinity (60 g/L) for 12 weeks until the growth rate remained stable between generations and were then exposed to 2.5 mg/L of Cd for 4 days. Acute Cd toxicity impaired cell growth by increasing Cd bioaccumulation and lipid peroxidation, which reduced cellular pigment, total protein, and glutathione content. It also significantly weakened photosynthetic efficiency and total antioxidant capacity. However, acclimatization to high salinity alleviated these negative effects under Cd stress. To understand the potential mechanisms behind this phenomenon, 12 cDNA libraries from control, Cd-exposed (Cd), high salinity-acclimated (Salinity), and high salinity-acclimated with Cd exposure (Salinity + Cd) cells were derived using RNA sequencing. A total of 2019, 1799, 2150 and 1256 differentially expressed genes (DEGs) were identified from sample groups Salinity / Control, Cd / Control, Salinity + Cd / Control, and Salinity + Cd / Cd, respectively. Some of these DEGs were significantly enriched in ribosome, photosynthesis, stress defense, and photosynthesis-antenna proteins. Among these genes, 82 ribosomal genes were up-regulated in Salinity / Control (corrected P = 3.8 × 10^-28), while 81 were down-regulated in Cd / Control (corrected P = 1.1 × 10^-24). Moreover, high salinity acclimatization up-regulated 8 photosynthesis genes and 18 stress defense genes compared with the control. Additionally, 3 photosynthesis genes, 11 stress defense genes and 11 genes encoding light harvesting proteins were up-regulated by high salinity acclimatization under Cd exposure. Overall, high salinity acclimatization mitigated Cd toxicity, possibly by up-regulating the transcription of photosynthesis, stress defense, and ribosomal genes. These results provide new insights on cross-tolerance in microalgae.

Enhancement of Sphingolipid Synthesis Improves Osmotic Tolerance of Saccharomyces cerevisiae

To enhance the growth performance of Saccharomyces cerevisiae under osmotic stress, mutant XCG001, which tolerates up to 1.5 M NaCl, was isolated through adaptive laboratory evolution (ALE). Comparisons of the transcriptome data of mutant XCG001 and the wild-type strain identified ELO2 as being associated with osmotic tolerance. In the ELO2 overexpression strain (XCG010), the contents of inositol phosphorylceramide (IPC; t18:0/26:0), mannosylinositol phosphorylceramide [MIPC; t18:0/22:0(2OH)], MIPC (d18:0/22:0), MIPC (d20:0/24:0), mannosyldiinositol phosphorylceramide [M(IP)₂C; d20:0/26:0], M(IP)₂C [t18:0/26:0(2OH)], and M(IP)₂C [d20:0/26:0(2OH)] increased by 88.3 times, 167 times, 63.3 times, 23.9 times, 27.9 times, 114 times, and 208 times at 1.0 M NaCl, respectively, compared with the corresponding values of the control strain XCG002. As a result, the membrane integrity, cell growth, and cell survival rate of strain XCG010 increased by 24.4% ± 1.0%, 21.9% ± 1.5%, and 22.1% ± 1.1% at 1.0 M NaCl, respectively, compared with the corresponding values of the control strain XCG002 (wild-type strain with a control plasmid). These findings provided a novel strategy for engineering complex sphingolipids to enhance osmotic tolerance.IMPORTANCE This study demonstrated a novel strategy for the manipulation of membrane complex sphingolipids to enhance S. cerevisiae tolerance to osmotic stress. Elo2, a sphingolipid acyl chain elongase, was related to osmotic tolerance through transcriptome analysis of the wild-type strain and an osmosis-tolerant strain generated from ALE. Overexpression of ELO2 increased the content of complex sphingolipid with longer acyl chain; thus, membrane integrity and osmotic tolerance improved.

Optimization of algae mixotrophic culture for nutrients recycling and biomass/lipids production in anaerobically digested waste sludge by various organic acids addition

Anaerobically digested waste sludge contains very high concentrations of ammonium and phosphate that are difficult to be purified using traditional processes. Mixotrophic culture of microalgae is a potential way to achieve ammonium and phosphate removal, while harvesting considerable biomass for biodiesel production. In this study, four typical volatile organic acids that could be potentially produced from sludge fermentation were tested for algal mixotrophic culture in anaerobically digested waste sludge. The results showed that the addition of propionate and isovaleric acid had no significant improvement on biomass production, and even inhibited algal growth at low concentration. Fortunately, the addition of acetic and n-butyric acid (initial C/N = 10) increased biomass production by1.9-2.4 times compared to the blank culture. Higher biomass production increased ammonium and orthophosphate removal to 88.3-97.1% and 80.4-93.0%, respectively. Moreover, the optimal addition of volatile organic acids enhanced lipids production by 3.9-6.3 times, while achieving higher saturation degree in biodiesels. The results suggest that adding these optimal volatile organic acids is suitable to enhance nutrients recycling and algal biodiesel production from anaerobically digested waste sludge.

Exergy analysis for docosahexaenoic acid production by fermentation and strain improvement by adaptive laboratory evolution for Schizochytrium sp

Exergy analysis is powerful tool for process optimization and mechanism analysis. In this study, exergy analysis was performed for docosahexaenoic acid (DHA) fermentation process. More than 86% of input exergy was contributed by glucose. The exergy of biomass was about 64.66% of the total output exergy when the phosphate concentration was 4 g L^-1. The exergy efficiencies of DHA (η_DHA) for the starting strains and the evolved strains under high oxygen concentration, low temperature, and two-factor conditions were also investigated. The η_DHA in the collected experimental data was not more than 20.9%. It was proved that there was a positive correlation between η_DHA and the biomass yield. It was indicated that adaptive laboratory evolution (ALE) improved biomass yield which had the most important effect on enhancing η_DHA and DHA yield (or DHA productivity). It is necessary to improve η_DHA through process optimization and ALE in future.

Enhanced microalgal growth and lipid accumulation by addition of different nanoparticles under xenon lamp illumination

In this study, the growth and lipid accumulation of Scenedesmus sp. using different nanoparticles and light sources were investigated. Xenon lamp can produce a broad illumination spectrum, and exhibited better performance than light-emitting diode. SiC and g-C₃N₄ nanoparticles improved the biomass and lipid accumulation, whereas TiO₂ and TiC nanoparticles had inhibitory influence on microalgae. Lipid production can be improved by oxidative stress produced by combination of nanoparticles and xenon lamp irradiation. At the optimal SiC nanoparticles concentration of 150 mg L^-1 and photoperiod of 6:18 h, the maximum biomass concentration and total lipid content reached 3.18 g L^-1 and 40.26%, respectively. The addition of SiC nanoparticles could promote the substrate utilization rate and induce stress condition, thereby enhancing the activity of acetyl-CoA carboxylase and lipid biosynthesis. This research shows that SiC nanoparticles addition combined with xenon lamp illumination is a promising strategy to promote microalgal growth and lipid accumulation.

Biological Carbon Recovery from Sugar Refinery Washing Water into Microalgal DHA: Medium Optimization and Stress Induction

Sugar refinery washing water (SRWW) contains abundant levels of carbon sources and lower levels of contaminants than other types of wastewater, which makes it ideal for heterotrophic cultivation of microalgae. Here, carbon sources in SRWW were utilized for conversion into the form of value-added docosahexaenoic acid (DHA) using Aurantiochytrium sp. KRS101. Since SRWW is not a defined medium, serial optimizations were performed to maximize the biomass, lipid, and DHA yields by adjusting the nutrient (carbon, nitrogen, and phosphorus) concentrations as well as the application of salt stress. Optimum growth performance was achieved with 30% dilution of SRWW containing a total organic carbon of 95,488 mg L-1. Increasing the nutrient level in the medium by supplementation of 9 g L-1 KH2PO4 and 20 g L-1 yeast extract further improved the biomass yield by an additional 14%, albeit at the expense of a decrease in the lipid content. Maximum biomass, lipid, and DHA yields (22.9, 6.33, and 2.03 g L-1, respectively) were achieved when 35 g L-1 sea salt was applied on a stationary phase for osmotic stress. These results demonstrate the potential of carbon-rich sugar refinery washing water for DHA production using Aurantiochytrium sp. KRS101 and proper cultivation strategy.

Salinity Stress Responses and Adaptation Mechanisms in Eukaryotic Green Microalgae

High salinity is a challenging environmental stress for organisms to overcome. Unicellular photosynthetic microalgae are especially vulnerable as they have to grapple not only with ionic imbalance and osmotic stress but also with the generated reactive oxygen species (ROS) interfering with photosynthesis. This review attempts to compare and contrast mechanisms that algae, particularly the eukaryotic Chlamydomonas microalgae, exhibit in order to immediately respond to harsh conditions caused by high salinity. The review also collates adaptation mechanisms of freshwater algae strains under persistent high salt conditions. Understanding both short-term and long-term algal responses to high salinity is integral to further fundamental research in algal biology and biotechnology.

Transcriptome Mechanism of Utilizing Corn Steep Liquor as the Sole Nitrogen Resource for Lipid and DHA Biosynthesis in Marine Oleaginous Protist Aurantiochytrium sp

In the current study, corn steep liquor (CSL) is evaluated as an ideal raw agro-material for efficient lipid and docosahexaenoic acid DHA production by Aurantiochytrium sp. Low CSL level in medium (nitrogen deficiency) stimulated the biosynthesis of lipids and DHA while inhibiting cellular growth. The transcriptomic profiles of the Aurantiochytrium sp. cells are analyzed and compared when cultured under high (H group), normal (N group), and low (L group) levels of CSL in the medium. The discriminated transcriptomic profiles from the three groups indicates that changes in CSL level in medium result in a global change in transcriptome of Aurantiochytrium sp. The overall de novo assembly of cDNA sequence data generated 61,163 unigenes, and 18,129 of them were annotated in at least one database. A total of 5105 differently expressed (DE) genes were found in the N group versus the H group, with 2218 downregulated and 2887 upregulated. A total of 3625 DE genes were found in the N group versus the L group, with 1904 downregulated and 1721 upregulated. The analysis and categorization of the DE genes indicates that the regulation mechanism of CSL involved in the perception and transduction of the limited nitrogen signal, the interactions between the transcription factors (TFs) and multiple downstream genes, and the variations in downstream genes and metabolites, in sequence, are illuminated for the first time in the current study.

Efficient biosynthesis of anticancer polysaccharide by a mutant Chaetomium globosum ALE20 via non-sterilized fermentation

The sterilization process, due to its immense energy consumption, high facilities investment, and loss of raw materials by caramelization, during industrial production has drawn much attention. In this study, a methanol-resistant mutant strain, Chaetomium globosum ALE20, was obtained following 20 cycles of adaptive laboratory evolution process. The titer of anticancer polysaccharide (GCP-M) from C. globosum ALE20 reached 9.2 g/L with glycerol as sole carbon source using non-sterilized and fed-batch fermentation strategy. This titer represents a 200% increase compared with the 3.3 g/L attained with batch fermentation. The GCP-M monosaccharide was comprised of galactose, glucose, mannose and glucuronic acid, in a molar ratio of 3.83:66.37:3.26:1.95, respectively, and its weight-average molecular weight and polydispersity were 3.796 × 10⁴ Da and 1.060, respectively. This work presents an ideal alternative and safer fermentation process without sterilization, and a useful approach for enhancing industrial production.

GREACE-assisted adaptive laboratory evolution in endpoint fermentation broth enhances lysine production by Escherichia coli

BACKGROUND

Late-stage fermentation broth contains high concentrations of target chemicals. Additionally, it contains various cellular metabolites which have leaked from lysed cells, which would exert multifactorial stress to industrial hyperproducers and perturb both cellular metabolism and product formation. Although adaptive laboratory evolution (ALE) has been wildly used to improve stress tolerance of microbial cell factories, single-factor stress condition (i.e. target product or sodium chloride at a high concentration) is currently provided. In order to enhance bacterial stress tolerance to actual industrial production conditions, ALE in late-stage fermentation broth is desired. Genome replication engineering assisted continuous evolution (GREACE) employs mutants of the proofreading element of DNA polymerase complex (DnaQ) to facilitate mutagenesis. Application of GREACE coupled-with selection under stress conditions is expected to accelerate the ALE process.

RESULTS

In this study, GREACE was first modified by expressing a DnaQ mutant KR5-2 using an arabinose inducible promoter on a temperature-sensitive plasmid, which resulted in timed mutagenesis introduction. Using this method, tolerance of a lysine hyperproducer E. coli MU-1 was improved by enriching mutants in a lysine endpoint fermentation broth. Afterwards, the KR5-2 expressing plasmid was cured to stabilize acquired genotypes. By subsequent fermentation evaluation, a mutant RS3 with significantly improved lysine production capacity was selected. The final titer, yield and total amount of lysine produced by RS3 in a 5-L batch fermentation reached 155.0 ± 1.4 g/L, 0.59 ± 0.02 g lysine/g glucose, and 605.6 ± 23.5 g, with improvements of 14.8%, 9.3%, and 16.7%, respectively. Further metabolomics and genomics analyses, coupled with molecular biology studies revealed that mutations SpeB^A302V, AtpB^S165N and SecY^M145V mainly contributed both to improved cell integrity under stress conditions and enhanced metabolic flux into lysine synthesis.

CONCLUSIONS

Our present study indicates that improving a lysine hyperproducer by GREACE-assisted ALE in its stressful living environment is efficient and effective. Accordingly, this is a promising method for improving other valuable chemical hyperproducers.

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.