Development of PMA-qPCR assay to accurately and reproducible quantify viable bacteria of Paenibacillus polymyxa.

Paenibacillus polymyxa is an important biocontrol bacterium. The combination of propidium monoazide (PMA) and quantitative polymerase chain reactionq (qPCR) has proven effective in quantifying live bacteria from various microorganisms. The objective was to create a PMA-qPCR assay to precisely and consistently measure the number of living bacteria of biocontrol P. polymyxa. The primers were designed for the spo0A gene of P. polymyxa HY96-2. The optimal conditions for treating the target strain with PMA were a PMA concentration of 15 µg/mL, an incubation time of 5 min, and an exposure time of 10 min. The PMA-qPCR method had a limit of quantification (LOQ) of 1.0 × 103 CFU/mL for measuring the amount of viable P. polymyxa bacteria. The PMA-qPCR method is more sensitive than the qPCR method in detecting viable bacteria in the mixtures of viable and dead bacteria. The accuracy and reproducibility of quantifying viable P. polymyxa bacteria using the PMA-qPCR method were higher compared to the plate count method.

Controlling average number of photons received per biomass to promote the growth of Synechocystis sp. PPC 6803.

To investigate the actually received light of cells in the photo bioreactor, a light attenuation model of Synechocystis sp. PCC 6803 was established. The relationship between the average number of photons received per biomass (APRPB) and the growth of cell was analyzed. The results demonstrated, Cornet model was accurately fitted with the light attenuation of Synechocystis sp. PCC 6803 and the cell growth rate was affected by APRPB. When the value of APRPB is 3.2 µmol g-1 s-1, the cell have the maximum light efficiency. A maximum specific growth rate of 0.05 h-1 was achieved with APRPB from 3.2 to 12.8 µmol g-1 s-1. After 156 h cultivation, compared to cells cultured under constant light [light intensity: 100 and 1800 µmol/(m2 s)], the DCW under controlled light intensity (light intensity increasing with the cell density) was higher by 79.1% and 20.0%, respectively. This study indicated that APRPB could be used as a light intensity regulation criterion to improve cell production despite different types of reactor and cell density, which provided a theoretical basis for improving the biomass yield of Synechocystis sp. PCC 6803 or other photosynthetic auto-trophic organism.

Genomic Foundation of Starch-to-Lipid Switch in Oleaginous Chlorella spp.

The ability to rapidly switch the intracellular energy storage form from starch to lipids is an advantageous trait for microalgae feedstock. To probe this mechanism, we sequenced the 56.8-Mbp genome of Chlorella pyrenoidosa FACHB-9, an industrial production strain for protein, starch, and lipids. The genome exhibits positive selection and gene family expansion in lipid and carbohydrate metabolism and genes related to cell cycle and stress response. Moreover, 10 lipid metabolism genes might be originated from bacteria via horizontal gene transfer. Transcriptomic dynamics tracked via messenger RNA sequencing over six time points during metabolic switch from starch-rich heterotrophy to lipid-rich photoautotrophy revealed that under heterotrophy, genes most strongly expressed were from the tricarboxylic acid cycle, respiratory chain, oxidative phosphorylation, gluconeogenesis, glyoxylate cycle, and amino acid metabolisms, whereas those most down-regulated were from fatty acid and oxidative pentose phosphate metabolism. The shift from heterotrophy into photoautotrophy highlights up-regulation of genes from carbon fixation, photosynthesis, fatty acid biosynthesis, the oxidative pentose phosphate pathway, and starch catabolism, which resulted in a marked redirection of metabolism, where the primary carbon source of glycine is no longer supplied to cell building blocks by the tricarboxylic acid cycle and gluconeogenesis, whereas carbon skeletons from photosynthesis and starch degradation may be directly channeled into fatty acid and protein biosynthesis. By establishing the first genetic transformation in industrial oleaginous C. pyrenoidosa, we further showed that overexpression of an NAD(H) kinase from Arabidopsis (Arabidopsis thaliana) increased cellular lipid content by 110.4%, yet without reducing growth rate. These findings provide a foundation for exploiting the metabolic switch in microalgae for improved photosynthetic production of food and fuels.

Impacts of CO2 concentration on growth, lipid accumulation, and carbon-concentrating-mechanism-related gene expression in oleaginous Chlorella.

Biodiesel production by microalgae with photosynthetic CO2 biofixation is thought to be a feasible way in the field of bioenergy and carbon emission reduction. Knowledge of the carbon-concentrating mechanism plays an important role in improving microalgae carbon fixation efficiency. However, little information is available regarding the dramatic changes of cells suffered upon different environmental factors, such as CO2 concentration. The aim of this study was to investigate the growth, lipid accumulation, carbon fixation rate, and carbon metabolism gene expression under different CO2 concentrations in oleaginous Chlorella. It was found that Chlorella pyrenoidosa grew well under CO2 concentrations ranging from 1 to 20 %. The highest biomass and lipid productivity were 4.3 g/L and 107 mg/L/day under 5 % CO2 condition. Switch from high (5 %) to low (0.03 %, air) CO2 concentration showed significant inhibitory effect on growth and CO2 fixation rate. The amount of the saturated fatty acids was increased obviously along with the transition. Low CO2 concentration (0.03 %) was suitable for the accumulation of saturated fatty acids. Reducing the CO2 concentration could significantly decrease the polyunsaturated degree in fatty acids. Moreover, the carbon-concentrating mechanism-related gene expression revealed that most of them, especially CAH2, LCIB, and HLA3, had remarkable change after 1, 4, and 24 h of the transition, which suggests that Chlorella has similar carbon-concentrating mechanism with Chlamydomonas reinhardtii. The findings of the present study revealed that C. pyrenoidosa is an ideal candidate for mitigating CO2 and biodiesel production and is appropriate as a model for mechanism research of carbon sequestration.

The effect of iron on growth, lipid accumulation, and gene expression profile of the freshwater microalga Chlorella sorokiniana.

The effects of iron on the growth, lipid accumulation, and gene expression profiles of the limnetic Chlorella sorokiniana CCTCC M209220 under photoautotrophy were investigated. The addition of iron up to 10(-5) mol l(-l) increased final cell densities by nearly 2-fold at 2.3 × 10(7) cells/ml, growth rate by 2-fold, and the length of the exponential phase by 5 days as compared to unsupplemented controls while 10(-3) mol l(-1) iron was toxic. The lipid content increased from 12 % for unsupplemented cultures to 33 % at 10(-4) mol l(-1) iron while the highest overall lipid yield reached 179 mg l(-1). A genefishing and qPCR comparison between the C. sorokiniana at low and high iron levels indicated increases in the expression of several genes, including carbonic anhydrase involved in microalgal cell growth, as well as acc1 and choline transporter related to lipid synthesis. This study provides insights into changes in gene expression and metabolism that accompany iron supplementation to Chlorella as well as potential metabolic engineering targets for improving growth and lipid synthesis in microalgae.

Artificial neural networks prediction and optimization based on four light regions for light utilization from Synechocystis sp. PCC 6803.

Light is crucial in microalgae growth. However, dividing the microalgae growth region into light and dark regions has limitations. In this study, the light response of Synechocystis sp. PCC 6803 was investigated to define four light regions (FLRs): light compensation region, light limitation region, light saturation region, and photoinhibition region. The proportions of cells' residence time in the FLRs and the number of times cells (NTC) passed through the FLRs in photobioreactors were calculated by using MATLAB. Based on the FLRs and NTC passed through the FLRs, a growth model was established by using artificial neural network (ANN).The ANN model had a validation R2 value of 0.97, which was 76.36% higher than the model based on light-dark regions. The high accuracy of the ANN model was further verified through dynamic adjustment of light intensity experiments.This study confirmed the importance of the FLRs for studying microalgae growth dynamics.

[Advances of studies on culture and product functions of Euglena gracilis].

Euglena gracilis is a unicellular eukaryote between animal and plant cells, which is widely distributed in nature. E. gracilis has both plant and animal characteristics, and can grow photoautotrophically, heterotrophically and mixotrophically. E. gracilis also features on abundant and various cellular composition. Recently, extensive researches on unique cellular components of E. gracilis have revealed its application in the field of medicine, food, and feedstuff, in terms of improving immunity, fighting inflammation, and lowering uric acid levels. The application prospects of paramylon in biomedical area were also discovered. As food ingredients, food additives, feedstuffs and cosmetic ingredients, E. gracilis has been certified domestically and overseas. A series of products have been developed overseas, especially in Japan. However, the research and development of E. gracilis are still in its infancy in China, and there is huge space for development. At present, the research and potential application of cultivation and product functions of E. gracilis have been rarely reviewed. This review systematically examines both the domestic and abroad research of cultivation and production of E. gracilis, as well as the biological activity of E. gracilis powder and paramylon. The existing problems in the application, exploitation, and possible development direction of E. gracilis in the future are prospected. This review might be useful for establishing and optimizing large-scale and efficient heterotrophic technology, as well as developing related products of E. gracilis with specific functions.

The effect of energy substrates on PHB accumulation of Acidiphilium cryptum DX1-1.

The effect of glucose and elemental sulfur on the growth and PHB accumulation of Acidiphilium cryptum DX1-1 was investigated. Meanwhile, the differential expressions of 19 genes related with PHB accumulation, sulfur metabolism and carbon fixed in heterotrophy, phytotrophy and mixotrophy were studied by RT-qPCR. The results showed that strain DX1-1 could accumulate PHB with sulfur as the energy substance and atmospheric CO2 as carbon resource. Glucose could improve the growth of strain DX1-1 cultured in medium with sulfur as the energy substance, and almost all the key enzyme-encoding genes related with PHB, sulfur metabolism and carbon fixed were basically up-regulated. PHB polymerase (Arcy_3030), ribulose-bisphosphate carboxylase (Acry_0825), ribulose-phosphate-epimerase (Acry_0022), and cysteine synthase A (Acry_2560) played important role in PHB accumulation, the modified expression of which could influence the PHB yield. With CO2 as carbon resource, the main initial substance of PHB accumulation for strain DX1-1 was acetyl-CoA, instead of acetate with the glucose as the carbon resource. Because of accumulating PHB by fixed atmospheric CO2 while independent of light, A. cryptum DX1-1 may have specifically potential in production of PHB.

Physiological evaluation of a new Chlorella sorokiniana isolate for its biomass production and lipid accumulation in photoautotrophic and heterotrophic cultures.

A novel green unicellular microalgal isolate from the freshwater of the Inner Mongolia Province of China and named as CCTCC M209220, grows between pH 6 and 11 and temperatures of 20-35°C with optimal conditions at pH 9 and 30°C. Morphological features and the phylogenetic analysis for the 18S rRNA gene reveal that the isolate is a Chlorella sorokiniana strain. A nitrogen source test reveals that this strain can grow well with nitrate and urea, but not ammonium. The strain can grow heterotrophically with glucose as the carbon source and accumulates lipid content as high as 56% (w/w) dry weight after 7 days in high glucose concentrations compared to 19% lipids achieved in 30 days of photoautotrophic culture. The relative neutral lipid content as a fraction of the total lipid is also much higher in heterotrophic culture as compared to photoautotrophic culture.

A new PMA-qPCR method for rapid and accurate detection of viable bacteria and spores of marine-derived Bacillus velezensis B-9987.

Marine-derived Bacillus velezensis B-9987 is an important biocontrol bacterium with a broad-spectrum antibacterial effect. The traditional plate counting method is widely used for quantitative detection of viable bacteria and spores but has some disadvantages such as being laborious and time-consuming (at least 24-48 h). This study aimed to develop a new PMA-qPCR method for rapid and accurate detection of viable bacteria and spores of B-9987. The specific primers were designed for qPCR amplification based on the conserved region of the bmmA gene (encoding a malonyl CoA-ACP transacylase) of B-9987. According to the characteristic that propidium monoazide (PMA) dye can distinguish viable and dead bacteria, the optimal PMA concentration of 10 µg/ml and optimal exposure time of 10 min were achieved under PMA treatment conditions. The B-9987 spores' genomic DNA was successfully extracted after the spore coat was removed and spore germination was induced. The quantification limits of the PMA-qPCR method were determined for viable B-9987 bacteria, spores in pure culture, and spores in marine Bacillus wettable powder (marine Bacillus WP) and were 1.5 × 103 CFU/ml, 6.5 × 102 CFU/ml, and 103 CFU/ml, respectively. Compared with the qPCR method, the PMA-qPCR method could sensitively detect viable bacteria in the viable/dead bacterial mixture. In this study, the developed PMA-qPCR method was found to have excellent sensitivity and specificity in the context of a pure culture of B-9987 strain, which could accurately and rapidly detect viable B-9987 bacteria within 3-4 h and viable B-9987 spores in marine Bacillus WP within 4-6 h.

[Effects of directional adaptation on selenium tolerance and accumulation of heterotrophic Chlorella pyrenoidosa].

Selenium (Se) is an essential trace element for organisms. Se deficiency will cause diseases such as Keshan disease and Kashin-Beck in human being, and huge loss to animal husbandry. Currently available Se supplements have such problems as low Se content, poor bioavailability, and poor safety. Chlorella pyrenoidosa can produce bioavailable and safe organic Se under suitable conditions, which is thus a promising Se supplement. Therefore, in this study, we tried to improve the Se tolerance and accumulation of C. pyrenoidosa by directional adaptation. To be specific, we gradually increased the concentration of Na2SeO3 in medium to domesticate C. pyrenoidosa and optimized the adapting time and concentration gradient of Na2SeO3 during the adaptation. The results showed that the adapted C. pyrenoidosa was more tolerant to Se and had stronger Se enrichment ability. In 5 L fermenter, the adapted strains could tolerate 40 mg/L Na2SeO3 and the synthesis rate of organic Se was 175.6% higher. Then, Se addition method in the 5 L fermenter was optimized. The result demonstrated that addition of Na2SeO3 at 40 mg/L during heterotrophic culture achieved the final dry weight of C. pyrenoidosa cells at 106.4 g/L, content of organic Se at 1 227 mg/kg, and synthesis rate of organic Se at 1.36 mg/(L·h). Compared with the reported highest cell density of 75 g/L and the highest organic Se content of 560 mg/kg, the corresponding figures in this study were 41.9% and 119.1% higher, respectively. In conclusion, directional adaptation can remarkably improve the Se tolerance and enrichment of C. pyrenoidosa.

The effect of mixotrophy on microalgal growth, lipid content, and expression levels of three pathway genes in Chlorella sorokiniana.

Nannochloropsis oculata CCMP 525, Dunaliella salina FACHB 435, and Chlorella sorokiniana CCTCC M209220 were compared in mixotrophic and photoautotrophic cultures in terms of growth rate, protein, and lipid content. Growth improved in glucose, and the biomass productivities of N. oculata, D. salina, and C. sorokiniana were found to be 1.4-, 2.2- and 4.2-fold that observed photoautotrophically. However, biomass and lipid production decreased at the highest glucose concentrations. Meanwhile, the content of protein and lipid were significantly augmented for mixotrophic conditions at least for some species. C. sorokiniana was found to be well suited for lipid production based on its high biomass production rate and lipid content reaching 51% during mixotrophy. Expression levels of accD (heteromeric acetyl-CoA carboxylase beta subunit), acc1 (homomeric acetyl-CoA carboxylase), rbcL (ribulose 1, 5-bisphosphate carboxylase/oxygenase large subunit) genes in C. sorokiniana were studied by real-time PCR. Increased expression levels of accD reflect the increased lipid content in stationary phase of mixotrophic growth, but expression of the acc1 gene remains low, suggesting that this gene may not be critical to lipid accumulation. Additionally, reduction of expression of the rbcL gene during mixotrophy indicated that utilization of glucose was found to reduce the role of this gene and photosynthesis.

An improved colony PCR procedure for genetic screening of Chlorella and related microalgae.

A colony PCR technique was applied for both genomic and chloroplast DNA in the green microalgae Chlorella. Of five different lysis buffers, Chelex-100 was superior for DNA extraction, PCR and DNA storage. It also was insensitive to variations in cell density. The conditions established for an improved PCR formulation are applicable for screening of genetically-engineered transformants as well as bioprospecting of natural microalgal isolates. Besides multiple Chlorella species, we also demonstrate the efficacy of Chelex-100 for colony PCR with a number of other microalgal strains, including Chlamydomonas reinhardtii, Dunaliella salina, Nannochloropsis sp., Coccomyxa sp., and Thalassiosira pseudonana.

The optimization of centrifugal pump driving horizontal tubular photobioreactor for enhancing astaxanthin production using heterotrophic Haematococcus pluvialis.

Haematococcus pluvialis is the prime source of natural astaxanthin for commercial exploitation. The large-scale cultivation of H. pluvialis is one of the key technologies for the development of natural astaxanthin industry. So far, horizontal tubular photobioreactor (HTPBR) circulated by a centrifugal pump has been the main PBR for the large-scale cultivation of H. pluvialis. Shear stress is a negative factor in microalgal cultivation at different scales, particularly for large-scale cultivation. To reduce the adverse impact of shear stress, the tolerance of H. pluvialis to the shear stress during the induction stage was first investigated in this study. H. pluvialis aplanospore was not sensitive to stresses between 19.18 and 27.32 Pa, but was resulted in about 30% cell death under shear stress between 27.32 and 63.84 Pa. Accordingly, two centrifugal pumps with different impellers was selected in 400 L HTPBRs to study the outdoor photoinduction for astaxanthin accumulation. The highest astaxanthin productivity and astaxanthin concentration were obtained in HTPBRs using a centrifugal pump equipped with three unshrouded backward-bladed impellers. The HTPBR was then successfully scaled up to 800 L with a similar performance, showing good scalability.

A novel paradigm for the high-efficient production of phycocyanin from Galdieria sulphuraria.

A novel cultivation strategy called "Sequential Heterotrophy-Dilution-Photoinduction" was successfully applied in the cultivation of Galdieria sulphuraria for efficient production of phycocyanin (PC). Algae cells were firstly cultivated heterotrophically to achieve high cell density. The maximal dry cell weight of 17.8gL(-1) and maximal biomass productivity of 103.1mgL(-1)h(-1) were obtained. Then, a dilution step was applied to obtain a suitable cell concentration and finally these cells were transferred to high light condition for phycocyanin accumulation. During the photoinduction step, cells could accumulate phycocyanin up to 13.88% of dry cell weight in a cultivation period of 8days. By this technology, total PC productivity far surpassed those reported in all literatures of Galdieria sulphuraria, and was 147-fold and 12-fold of those in photoautotrophic and heterotrophic technologies, respectively. Therefore, this strategy provides a promising approach for high-efficient phycocyanin production from Galdieria sulphuraria to meet its mass cultivation and commercialization application.

Sequential Heterotrophy-Dilution-Photoinduction Cultivation of Haematococcus pluvialis for efficient production of astaxanthin.

A novel cultivation strategy called "Sequential Heterotrophy-Dilution-Photoinduction" was successfully applied in the cultivation of Haematococcus pluvialis to produce astaxanthin effectively. Cells were first cultivated heterotrophically to achieve a high cell density, then were diluted to a suitable concentration and switched to a favorable environment for cells acclimation. Finally, the culture was transferred to high light environment for astaxanthin accumulation. By this strategy, the dry cell weight of 26 g/L and biomass productivity of 64.1mg/L/h were obtained in heterotrophy stage which surpassed ever before reported in literatures. Meanwhile, the cells could accumulate considerable astaxanthin up to 4.6% of dry cell weight after 10 days of photoinduction. Furthermore, the application prospects of the strategy were confirmed further by outdoor experiments. Therefore, this novel strategy provided a promising approach for high-efficient production of natural astaxanthin from H. pluvialis to meet the huge demand of this high value product.

Improving performance of flat-plate photobioreactors by installation of novel internal mixers optimized with computational fluid dynamics.

A novel mixer was developed to improve the performance of flat-plate photobioreactors (PBRs). The effects of mixer were theoretically evaluated using computational fluid dynamics (CFD) according to radial velocity of fluid and light/dark cycles within reactors. The structure parameters, including the riser width, top clearance, clearance between the baffles and walls, and number of the chambers were further optimized. The microalgae culture test aiming at validating the simulated results was conducted indoor. The results showed the maximum biomass concentrations in the optimized and archetype reactors were 32.8% (0.89 g L(-1)) and 19.4% (0.80 g L(-1)) higher than that in the control reactor (0.67 g L(-1)). Therefore, the novel mixer can significantly increase the fluid velocity along the light attenuation and light/dark cycles, thus further increased the maximum biomass concentration. The PBRs with novel mixers are greatly applicable for high-efficiency cultivation of microalgae.

Lipid accumulation and biosynthesis genes response of the oleaginous Chlorella pyrenoidosa under three nutrition stressors.

BACKGROUND: Microalgae can accumulate considerable amounts of lipids under different nutrient-deficient conditions, making them as one of the most promising sustainable sources for biofuel production. These inducible processes provide a powerful experimental basis for fully understanding the mechanisms of physiological acclimation, lipid hyperaccumulation and gene expression in algae. In this study, three nutrient-deficiency strategies, viz nitrogen-, phosphorus- and iron-deficiency were applied to trigger the lipid hyperaccumulation in an oleaginous Chlorella pyrenoidosa. Regular patterns of growth characteristics, lipid accumulation, physiological parameters, as well as the expression patterns of lipid biosynthesis-related genes were fully analyzed and compared. RESULTS: Our results showed that all the nutrient stress conditions could enhance the lipid content considerably compared with the control. The total lipid and neutral lipid contents exhibit the most marked increment under nitrogen deficiency, achieving 50.32% and 34.29% of dry cell weight at the end of cultivation, respectively. Both photosynthesis indicators and reactive oxygen species parameters reveal that physiological stress turned up when exposed to nutrient depletions. Time-course transcript patterns of lipid biosynthesis-related genes showed that diverse expression dynamics probably contributes to the different lipidic phenotypes under stress conditions. By analyzing the correlation between lipid content and gene expression level, we pinpoint several genes viz. rbsL, me g6562, accA, accD, dgat g2354, dgat g3280 and dgat g7063, which encode corresponding enzymes or subunits of malic enzyme, ACCase and diacylglycerol acyltransferase in the de novo TAG biosynthesis pathway, are highly related to lipid accumulation and might be exploited as target genes for genetic modification. CONCLUSION: This study provided us not only a comprehensive picture of adaptive mechanisms from physiological perspective, but also a number of targeted genes that can be used for a systematic metabolic engineering. Besides, our results also represented the feasibility of lipid production through trophic transition cultivation modes, throwing light on a two-stage microalgal lipid production strategy with which heterotrophy stage provides sufficient robust seed and nitrogen-starvation photoautotrophy stage enhances the overall lipid productivity.

The effect of temperature on cell growth and astaxanthin accumulation of Haematococcus pluvialis during a light-dark cyclic cultivation.

Haematococcus pluvialis is the best source of natural astaxanthin known as "the king of antioxidants". The mass outdoor culture is the most workable strategy for astaxanthin production, but the effects of daytime and night temperatures on the biomass concentration and astaxanthin content of H. pluvialis have received little attention. This study indicated that, raising the daytime or night temperature could stimulate night accumulation of astaxanthin until temperature up to 28°C; the night biomass loss increased firstly and then decreased along with the daytime temperature reducing; decreasing the night temperature can lessen night biomass loss; the daytime temperature of 28°C and the night temperature below 28°C were optimal for achieving high biomass and astaxanthin content. Subsequently, the outdoor culture strategy has been improved and can increase the net biomass and astaxanthin productivities by 5 and 2.9-fold as compared to the former strategy.

The effect of nutrition pattern alteration on Chlorella pyrenoidosa growth, lipid biosynthesis-related gene transcription.

Heterotrophy to photoautotrophy transition leads to the accumulation of lipids in Chlorella, which has potential to produce both healthy food and biofuels. Therefore, it is of key interest to study the metabolism shift and gene expression changes that influenced by the transition. Both total and neutral lipids contents were increased rapidly within 48 h after the switch to light environment, from 24.5% and 18.0% to 35.3% and 27.4%, respectively, along with the sharp decline of starch from 42.3% to 10.4% during 24h photoinduction phase. By analyzing the correlation between lipid content and gene expression, results revealed several genes viz. me g3137, me g6562, pepc g6833, dgat g3280 and dgat g7566, which encode corresponding enzymes in the de novo lipid biosynthesis pathway, are highly related to lipid accumulation and might be exploited as target genes for genetic modification. These results represented the feasibility of lipid production through trophic converting cultivation.