Paucibacter aquatile sp. nov. isolated from freshwater of the Nakdong River, Republic of Korea.

A Gram-negative, aerobic, motile, and rod-shaped bacterial strain designated CR182T was isolated from freshwater of the Nakdong River, Republic of Korea. Optimal growth conditions for this novel strain were found to be: 25-30 °C, pH 6.5-8.5, and 3% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicates that the strain CR182T belongs to type strains of genus Paucibacter. Strain CR182T showed 98.0% 16S rRNA gene sequence similarity with Paucibacter oligotrophus CHU3T and formed a robust phylogenetic clade with this species. The average nucleotide identity value between strain CR182T and P. oligotrophus CHU3T was 78.4% and the genome-to-genome distance was 22.2% on average. The genomic DNA G+C content calculated from the genome sequence was 66.3 mol%. Predominant cellular fatty acids of strain CR182T were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) (31.2%) and C16:0 (16.0%). Its major respiratory quinine was ubiquinone Q-8. Its polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, and two unidentified phospholipids. Its genomic DNA G+C content was 66.3%. Based on data obtained from this polyphasic taxonomic study, strain CR182T represents a novel species belonging to genus Paucibacter, for which a name of P. aquatile sp. nov. is proposed. The type strain is CR182T (= KCCM 90284T = NBRC 113032T).

Deinococcus koreensis sp. nov., a gamma radiation-resistant bacterium isolated from river water.

A gamma radiation-resistant, Gram-stain-negative, rod-shaped bacterial strain, designated SJW1-2T, was isolated from freshwater samples collected from the Seomjin River, Republic of Korea. The 16S rRNA gene sequence analyses showed that strain SJW1-2T was most closely related to Deinococcus metalli 1PNM-19T (94.3 % sequence similarity) and formed a robust phylogenetic clade with other species of the genus Deinococcus. The optimum growth pH and temperature for the isolate were pH 7.0-7.5 and 25 °C, respectively. Strain SJW1-2T exhibited high resistance to gamma radiation. The predominant respiratory quinone was MK-8. The polar lipid profile consisted of different unidentified glycolipids, two unidentified lipids, two unidentified phospholipids and an unidentified phosphoglycolipid. The major peptidoglycan amino acids were alanine, d-glutamic acid, glycine and l-ornithine. The predominant fatty acids (>10 %) were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (25.2 %) and C16 : 0 (21.2 %), and the DNA G+C content was 69.5 mol%. On the basis of phenotypic, genotypic and phylogenetic analyses, strain SJW1-2T (=KACC 19332T=NBRC 112908T) represents a novel species of the genus Deinococcus, for which the name Deinococcus koreensis sp. nov. is proposed.

Enhanced removal of cesium by potassium-starved microalga, Desmodesmus armatus SCK, under photoheterotrophic condition with magnetic separation.

This study investigated the feasibility of using photoheterotrophic microalga, Desmodesmus armatus SCK, for removal of cesium (Cs+) followed by recovery process using magnetic nanoparticles. The comparison of three microalgae results indicated that D. armatus SCK removed the most Cs+ at both 25 °C and 10 °C. The results also revealed that the use of microalga grown in potassium (K+)-starved condition improves the accumulation of Cs+. Heterotrophic mode with addition of volatile fatty acids (VFAs), especially acetic acids (HAc), also enhanced removal of Cs+ by K+-starved D. armatus SCK; maximum removal efficiency of Cs+ was almost 2-fold higher than that of cells grown without organic carbon source. The Cs+ taken up by this microalga was efficiently harvested using magnetic nanoparticles, polydiallyldimethylammonium (PDDA)-FeO3. Finally, this strain eliminated more than 99% of radioactive 137Cs from solutions of 10, 100, and 1000 Bq mL-1. Therefore, use of K+-starved microalga, D. armatus SCK, with VFAs could be promising means to remove the Cs from the liquid wastes.

Induction of axenic culture of Arthrospira (Spirulina) platensis based on antibiotic sensitivity of contaminating bacteria.

Arthrospira platensis SAG 21.99 and the isolated bacteria (Halomonas spp., Staphylococcus sp., etc.) from the culture of A. platensis SAG 21.99 were treated with five antibiotics to determine the minimal lethal concentrations. The combination of a washing step and a consecutive treatment with antibiotics, imipenem (100 microg ml(-1)), neomycin (100 microg ml(-1)) and cycloheximide (20 microg ml(-1)), treatment step was highly effective in eliminating bacteria. An axenic culture of A. platensis SAG 21.99 could be induced within 3 days using this method. This technique is a simple and rapid method for obtaining axenic cultures of filamentous cyanobacteria.

Enhanced biomass and gamma-linolenic acid production of mutant strain Arthrospira platensis.

A mutant of Arthrospira platensis PCC 9108, strain M9108, obtained by mutagenesis with UV treatment, was able to mixotrophically grow in an SOT medium containing 40 g of glucose/l. The biomass and specific growth rate of strain M9108 (4.10 g/l and 0.70/d) were 1.9-fold and 1.4-fold higher, respectively, than those of the wild type (2.21 g/l and 0.58/d) under mixotrophic culture condition. In addition, when compared with the wild type, the content of gamma- linolenic acid (GLA) in the mutant was increased when glucose concentration was increased. Compared with the wild type, the GLA content of the mutant was 2-fold higher in autotrophic culture and about 3-fold higher in mixotrophic culture. Thus, the mutant appears to possess more efficient facility to assimilate and metabolize glucose and to produce more GLA than its wild-type strain.

Draft Genome Sequence of Paucibacter aquatile CR182T, a Strain with Antimicrobial Activity Isolated from Freshwater of Nakdong River in South Korea.

This report details a draft genome sequence of Paucibacter aquatile CR182T, isolated from river water, which contains 5,523,543 bp, has a G+C content of 66.3%, and harbors 4,544 protein-coding genes in 4 contigs. These genome data provide insights into the genetic basis of this strain's antibacterial activity and adaptive mechanisms.

Draft Genome Sequence of Deinococcus koreensis SJW1-2T, a Gamma Radiation-Resistant Bacterium Isolated from River Water.

Deinococcus koreensis SJW1-2T was isolated from river water and was observed to be highly resistant to gamma radiation. In this study, we report a draft genome sequence which revealed that SJW1-2T possesses genes involved in nucleotide excision repair. The primary genomic information will aid in elucidating the DNA repair mechanism during ionizing radiation.

Advanced treatment of residual nitrogen from biologically treated coke effluent by a microalga-mediated process using volatile fatty acids (VFAs) under stepwise mixotrophic conditions.

This work describes the development of a microalga-mediated process for simultaneous removal of residual ammonium nitrogen (NH4(+)-N) and production of lipids from biologically treated coke effluent. Four species of green algae were tested using a sequential mixotrophic process. In the first phase-CO2-supplied mixotrophic condition-all microalgae assimilated NH4(+)-N with no evident inhibition. In second phase-volatile fatty acids (VFAs)-supplied mixotrophic condition-removal rates of NH4(+)-N and biomass significantly increased. Among the microalgae used, Arctic Chlorella sp. ArM0029B had the highest rate of NH4(+)-N removal (0.97 mg/L/h) and fatty acid production (24.9 mg/L/d) which were 3.6- and 2.1-fold higher than those observed under the CO2-supplied mixotrophic condition. Redundancy analysis (RDA) indicated that acetate and butyrate were decisive factors for increasing NH4(+)-N removal and fatty acid production. These results demonstrate that microalgae can be used in a sequential process for treatment of residual nitrogen after initial treatment of activated sludge.

Effects of overexpression of a bHLH transcription factor on biomass and lipid production in Nannochloropsis salina.

BACKGROUND: Microalgae are considered promising alternative energy sources because they consume CO2 and accumulate large amounts of lipids that can be used as biofuel. Nannochloropsis is a particularly promising microalga due to its high growth rate and lipid content, and the availability of genomic information. Transcription factors (TFs) are global regulators of biological pathways by up- or down-regulation of related genes. Among these, basic helix-loop-helix (bHLH) TFs regulate growth, development, and stress responses in plants and animals, and have been identified in microalgae. We identified two bHLH TFs in the genome of N. salina CCMP1776, NsbHLH1, and NsbHLH2, and characterized functions of NsbHLH2 that may be involved in growth and nutrient uptake. RESULTS: We obtained NsbHLH2 overexpressing transformants of N. salina CCMP1776 by particle bombardment and confirmed that these were stable transformants. Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting using antibodies against the FLAG tag that was attached at the end of the coding sequence confirmed the expression of the NsbHLH2 protein under various culture conditions. The qRT-PCR results also indicated that the endogenous and transgenic expression of NsbHLH2 was reduced under stressed conditions. Overexpression of NsbHLH2 led to increased growth rate in the early growth period, and concomitantly higher nutrient uptake, than wild type (WT). These enhanced growth and nutrient uptake resulted in increased productivities of biomass and FAME. For example, one of the transformants, NsbHLH2 3-6, showed increased biomass productivity by 36 % under the normal condition, and FAME productivity by 33 % under nitrogen limitation condition. Conclusively, the improved growth in the transformants can be associated with the enhanced nutrient uptake. We are currently assessing their potential for scale-up cultivation with positive outcomes. CONCLUSION: Overexpression of NsbHLH2 led to enhanced growth rate and nutrient uptake during the early growth phase, and increased biomass and FAME productivity, especially in the later period under normal and stressed conditions. Based on these results, we postulate that NsbHLH2 can be employed for the industrial production of biodiesel from N. salina.

Heterologous overexpression of sfCherry fluorescent protein in Nannochloropsis salina.

Oleaginous microalgae of the Nannochloropsis genus are considered excellent candidates for biofuels and value-added products owing to their high biomass productivity and lipid content. Here, we report the first overexpression and detection of a heterologous sfCherry fluorescent protein in Nannochloropsis salina in order to develop a transformation toolbox for future genetic improvements. Particle bombardment was employed for transformation, and expression of Shble under the control of TUB and UEP promoters, cloned from N. salina, was used to confer resistance to Zeocin antibiotics, resulting in 5.9 and 4.7 transformants per 108 cells, respectively. Stable integration of the markers into the genome was confirmed using a restriction enzyme site-directed amplification (RESDA) PCR. The expression of sfCherry fluorescent protein was confirmed by Western blot analysis and confocal microscopy. These results suggest new possibilities of efficient genetic engineering of Nannochloropsis for the production of biofuels and other biochemicals.

Enzymatic and non-enzymatic degradation of poly (3-hydroxybutyrate-co-3-hydroxyvalerate) copolyesters produced by Alcaligenes sp. MT-16.

Poly(3-hydroxybutyrate-co-3-hydroxyvalerate), poly(3HB-co-3HV), copolyesters with a variety of 3HV contents (ranging from 17 to 60 mol%) were produced by Alcaligenes sp. MT-16 grown on a medium containing glucose and levulinic acid in various ratios, and the effects of hydrophilicity and crystallinity on the degradability of the copolyesters were evaluated. Measurements of thermo-mechanical properties and Fourier-transform infrared spectroscopy in the attenuated total reflectance revealed that the hydrophilicity and crystallinity of poly(3HB-co-3HV) copolyesters decreased as 3HV content in the copolyester increased. When the prepared copolyester film samples were non-enzymatically hydrolysed in 0.01 N NaOH solution, the weights of all samples were found to have undergone no changes over a period of 20 weeks. In contrast, the copolyester film samples were degraded by the action of extracellular polyhydroxybutyrate depolymerase from Emericellopsis minima W2. The overall rate of weight loss was higher in the films containing higher amounts of 3HV, suggesting that the enzymatic degradation of the copolyester is more dependent on the crystallinity of the copolyester than on its hydrophilicity. Our results suggest that the degradability characteristics of poly(3HB-co-3HV) copolyesters, as well as their thermo-mechanical properties, are greatly influenced by the 3HV content in the copolyesters.

Use of orange peel extract for mixotrophic cultivation of Chlorella vulgaris: increased production of biomass and FAMEs.

Mass cultivation of microalgae is necessary to achieve economically feasible production of microalgal biodiesel, but the high cost of nutrients is a major limitation. In this study, orange peel extract (OPE) was used as an inorganic and organic nutrient source for the cultivation of Chlorella vulgaris OW-01. Chemical composition analysis of the OPE indicated that it contains sufficient nutrients for mixotrophic cultivation of C. vulgaris OW-01. Analysis of biomass and FAME production showed that microalgae grown in OPE medium produced 3.4-times more biomass and 4.5-times more fatty acid methyl esters (FAMEs) than cells cultured in glucose-supplemented BG 11 medium (BG-G). These results suggest that growth of microalgae in an OPE-supplemented medium increases lipid production and that OPE has potential for use in the mass cultivation of microalgae.

Ettlia sp. YC001 showing high growth rate and lipid content under high CO2.

Over 100 green-colored colonies were isolated from environmental samples when cultivating on a BG11 agar medium, and 4 strains showing different morphologies were selected based on light microscopic observation. Among these strains, the microalgal species with the highest growth rate under 10% CO(2) was identified as Ettlia sp. YC001 using an 18S rDNA-based phylogenetic analysis and morphological comparison. The highest cell density of 3.10 g/L (based on dry cell weight) and biomass productivity of 0.19 g/L/d were obtained under 5% CO(2) after 16 days. The lipid content and productivity were also up to 42% of the dry cell weight and 80.0mg/L/d, respectively. The color of the Ettlia sp. YC001 culture changed from green to red after a month due to the accumulation of certain carotenoids. Therefore, it would seem that Ettlia sp. YC001 is appropriate for mitigating CO(2) due to its high biomass productivity, and a suitable candidate for producing biodiesel and high-value products.

Novel approach for the development of axenic microalgal cultures from environmental samples.

We demonstrated a comprehensive approach for development of axenic cultures of microalgae from environmental samples. A combination of ultrasonication, fluorescence-activated cell sorting (FACS), and micropicking was used to isolate axenic cultures of Chlorella vulgaris Beyerinck (Beijerinck) and Chlorella sorokiniana Shihira & R.W. Krauss from swine wastewater, and Scenedesmus sp. YC001 from an open pond. Ultrasonication dispersed microorganisms attached to microalgae and reduced the bacterial population by 70%, and when followed by cell sorting yielded 99.5% pure microalgal strains. The strains were rendered axenic by the novel method of micropicking and were tested for purity in both solid and liquid media under different trophic states. Denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene confirmed the absence of unculturable bacteria, whereas fluorescence microscopy and scanning electron microscopy (SEM) further confirmed the axenicity. This is the most comprehensive approach developed to date for obtaining axenic microalgal strains without the use of antibiotics and repetitive subculturing.

Dynamics of microcystin production and quantification of potentially toxigenic Microcystis sp. using real-time PCR.

Cyanobacterial blooms in eutrophied water body are generally composed of various genotypes with or without microcystin-producing genes (mcy gene cluster). Thus there is a need for quantification of potent toxin producing strains. The present study aimed at identifying microcystin variants and its producer strains in Durgakund pond, Varanasi, India, based on quantification of cpcBA-IGS and mcyA (condensation domain) genes using real-time PCR and LC-MS. Increase in microcystin concentrations was correlated with increase in mcyA copy number and the level of pigments (chlorophyll a, phycocyanin and carotenoids). Also, selected environmental factors (water temperature, light irradiance, rainfall, pH, N and P) and the concentration of microcystin variants (MC-LR, -RR and -YR) were also assessed in samples during May 2010 to April 2011 to establish the possible correlation among these parameters. Nutrients favored cyanobacterial bloom but it could not be correlated with the levels of microcystin variants and seemed to be geographically specific. Microcystis sp. dominant in the pond comprised potentially toxigenic cells. The ratio of potentially toxigenic Microcystis sp. to that of total Microcystis sp. ranged from 0% to 14%. Such studies paved the way to identify and quantify the most potent microcystin producer in the tropical aquatic body.

Effective screening of Scenedesmus sp. from environmental microalgae communities using optimal sonication conditions predicted by statistical parameters of fluorescence-activated cell sorting.

The effects of the sonication parameters, including the power and time, were investigated for the effective isolation of Scenedesmus sp. from environmental microalgae communities when using fluorescence-activated cell sorting (FACS). The selectivity, defined as the percentage of Scenedesmus sp. successfully isolated and grown in microplates, appeared as peaks in contour plots spanned by the sonication power and time. For fast screening of the optimal sonication conditions, correlations between the selectivity and the statistical parameters from the FACS analysis were investigated. A graphical comparison analysis of the contour plots showed a pattern similarity of over 82% between the coefficients of variation for the side scatter (SSC-CV) and the selectivity. This predictability of the optimal sonication conditions enabled a Scenedesmus sp. selectivity of ca. 2 times using only one-third of the sonication condition sets arbitrarily chosen around the peaks of the SSC-CV, thereby saving resources and time for subsequent processes.

Recent trends in development of biosensors for detection of microcystin.

Increased cyanobacterial blooms, a source of cyanotoxins are linked with climate change and eutrophication in aquatic bodies, a major concern worldwide. Microcystins are potently hepatotoxic, nephrotoxic as well as carcinogenic. Thus microcystins are threat to tourism, agriculture and animal's health. However, there is a still lacuna in the knowledge of regulation of microcystins production. Presence of toxic and non-toxic cyanobacterial strains together and occurrence of various microcystin variants in aquatic bodies compounded the problem. Although several analytical techniques for microcystin detection such as bioassay, ELISA, HPLC and LC-MS etc. have been already prevalent, the development of biosensors offered rapid and accurate detection, high reproducibility and portability. Sequencing of Microcystis spp., opened the new vistas towards the development of biosensor at molecular and genetic level. This review incorporates the current trends in the development of biosensors for microcystin detection in the light of state-of-the-art techniques.

Simple, rapid and cost-effective method for high quality nucleic acids extraction from different strains of Botryococcus braunii.

This study deals with an effective nucleic acids extraction method from various strains of Botryococcus braunii which possesses an extensive extracellular matrix. A method combining freeze/thaw and bead-beating with heterogeneous diameter of silica/zirconia beads was optimized to isolate DNA and RNA from microalgae, especially from B. braunii. Eukaryotic Microalgal Nucleic Acids Extraction (EMNE) method developed in this study showed at least 300 times higher DNA yield in all strains of B. braunii with high integrity and 50 times reduced working volume compared to commercially available DNA extraction kits. High quality RNA was also extracted using this method and more than two times the yield compared to existing methods. Real-time experiments confirmed the quality and quantity of the input DNA and RNA extracted using EMNE method. The method was also applied to other eukaryotic microalgae, such as diatoms, Chlamydomonas sp., Chlorella sp., and Scenedesmus sp. resulting in higher efficiencies. Cost-effectiveness analysis of DNA extraction by various methods revealed that EMNE method was superior to commercial kits and other reported methods by >15%. This method would immensely contribute to area of microalgal genomics.

Determination of cyanobacterial diversity during algal blooms in Daechung Reservoir, Korea, on the basis of cpcBA intergenic spacer region analysis.

The detection and prevention of cyanobacterial blooms are important issues in water quality management. As such, the diversity and community dynamics of cyanobacteria during cyanobacterial bloom in the Daechung Reservoir, Korea, were studied by analyzing the intergenic spacer (IGS) region between phycocyanin subunit genes cpcB and cpcA (cpcBA IGS). To amplify the cpcBA IGS from environmental samples, new PCR primers that could cover a wider range of cyanobacteria than previously known primers were designed. In the samples taken around the bloom peak (2 September 2003), seven groups of cpcBA IGS sequences were detected, and none of the amplified cpcBA IGSs was closely related to the cpcBA IGS from chloroplasts. Apart from the Microcystis-, Aphanizomenon (Anabaena)-, Pseudanabaena-, and Planktothrix (Oscillatoria)-like groups, the three other groups of cpcBA IGS sequences were only distantly related to previously reported sequences (<85% similarity to their closest relatives). The most prominent changes during the bloom were the gradual decrease and eventual disappearance of the Aphanizomenon (Anabaena)-like group before the bloom peak and the gradual increase and sudden disappearance of Planktothrix (Oscillatoria)-like groups right after the bloom peak. The community succession profile obtained based on the cpcBA IGS analysis was also supported by a PCR-denaturing gradient gel electrophoresis analysis of the 16S rRNA genes.

Production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) with high molar fractions of 3-hydroxyvalerate by a threonine-overproducing mutant of Alcaligenes sp. SH-69.

A threonine overproducing mutant of Alcaligenes sp. SH-69 was isolated and its ability to produce poly(3-hydroxybutyrate-co-3-hydroxyvalerate), poly(3HB-co-3HV), was investigated. The 3HV fraction in poly(3HB-co-3HV) produced from glucose as the sole carbon source exceeded 22 mol%, which is approximately six times higher than that achieved by the wild type under the same culture conditions. Furthermore, the addition of a relatively low concentration (10 mM) of propionic acid, valeric acid or levulinic acid to the glucose medium greatly increased the molar fraction of 3HV in the copolyester, to 38-77 mol%. The results suggest that metabolic engineering of the biosynthetic pathways supplying polyhydroxyalkanoate monomers, such as the threonine biosynthetic pathway, can lead to new poly(3HB-co-3HV)-producing strains.