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Applied Microbiology and Biotechnology (v.82, #5)

Bioproducts from Aureobasidium pullulans, a biotechnologically important yeast by Zhenming Chi; Fang Wang; Zhe Chi; Lixi Yue; Guanglei Liu; Tong Zhang (pp. 793-804).

It has been well documented that Aureobasidium pullulans is widely distributed in different environments. Different strains of A. pullulans can produce amylase, proteinase, lipase, cellulase, xylanase, mannanase, transferases, pullulan, siderophore, and single-cell protein, and the genes encoding proteinase, lipase, cellulase, xylanase, and siderophore have been cloned and characterized. Therefore, like Aspergillus spp., it is a biotechnologically important yeast that can be used in different fields. So it is very important to sequence the whole genomic DNA of the yeast cells in order to find new more bioproducts and novel genes from this yeast.

Keywords: A. pullulans ; Pullulan; Extracellular enzymes; Functional genes; Biotechnology

Engineering of bacterial strains and vectors for the production of plasmid DNA by Diana M. Bower; Kristala L. J. Prather (pp. 805-813).

The demand for plasmid DNA (pDNA) is anticipated to increase significantly as DNA vaccines and non-viral gene therapies enter phase 3 clinical trials and are approved for use. This increased demand, along with renewed interest in pDNA as a therapeutic vector, has motivated research targeting the design of high-yield, cost-effective manufacturing processes. An important aspect of this research is engineering bacterial strains and plasmids that are specifically suited to the production of plasmid biopharmaceuticals. This review will survey recent innovations in strain and vector engineering that aim to improve plasmid stability, enhance product safety, increase yield, and facilitate downstream purification. While these innovations all seek to enhance pDNA production, they can vary in complexity from subtle alterations of the host genome or vector backbone to the investigation of non-traditional host strains for higher pDNA yields.

Keywords: Plasmid DNA; Escherichia coli ; DNA vaccines; Gene therapy; Strain engineering

Organosolv pretreatment of lignocellulosic biomass for enzymatic hydrolysis by Xuebing Zhao; Keke Cheng; Dehua Liu (pp. 815-827).

Production of ethanol by bioconversion of lignocellulosic biomass has attracted much interest in recent years. However, the pretreatment process for increasing the enzymatic digestibility of cellulose has become a key step in commercialized production of cellulosic ethanol. During the last decades, many pretreatment processes have been developed for decreasing the biomass recalcitrance, but only a few of them seem to be promising. From the point of view for integrated utilization of lignocellulosic biomass, organosolv pretreatment provides a pathway for biorefining of biomass. This review presents the progress of organosolv pretreatment of lignocellulosic biomass in recent decades, especially on alcohol, organic acid, organic peracid and acetone pretreatments, and corresponding action mechanisms. Evaluation and prospect of organosolv pretreatment were performed. Finally, some recommendations for future investigation of this pretreatment method were given.

Keywords: Lignocellulosic biomass; Organosolv pretreatment; Enzymatic hydrolysis; Biorefining; Delignification

Methanogenesis in membraneless microbial electrolysis cells by Peter Clauwaert; Willy Verstraete (pp. 829-836).

Operation of microbial electrolysis cells (MECs) without an ion exchange membrane could help to lower the construction costs while lowering the ohmic cell resistance and improving MEC conversion rates by minimizing the pH gradient between anode and cathode. In this research, we demonstrate that membraneless MECs with plain graphite can be operated for methane production without pH adjustment and that the ohmic cell resistance could be lowered with approximately 50% by removing the cation exchange membrane. As a result, the current production increased from 66 ± 2 to 156 ± 1 A m⁻³ MEC by removing the membrane with an applied voltage of −0.8 V. Methane was the main energetic product despite continuous operation under carbonate-limited and slightly acidified conditions (pH 6.1–6.2). Our results suggest that continuous production of hydrogen in membraneless MECs will be challenging since methane production might not be avoided easily. The electrical energy invested was not always completely recovered under the form of an energy-rich biogas; however, our results indicate that membraneless MECs might be a viable polishing step for the treatment of the effluent of anaerobic digesters as methane was produced under low organic loading conditions and at room temperature.

Keywords: Phosphate buffer; Biocatalyzed electrolysis; Overpotentials; Biocatalysts; Ohmic resistance; Microbial fuel cell

Overexpression of the gene encoding HMG-CoA reductase in Saccharomyces cerevisiae for production of prenyl alcohols by Chikara Ohto; Masayoshi Muramatsu; Shusei Obata; Eiji Sakuradani; Sakayu Shimizu (pp. 837-845).

To develop microbial production method for prenyl alcohols (e.g., (E,E)-farnesol (FOH), (E)-nerolidol (NOH), and (E,E,E)-geranylgeraniol (GGOH)), the genes encoding enzymes in the mevalonate and prenyl diphosphate pathways were overexpressed in Saccharomyces cerevisiae, and the resultant transformants were evaluated as to the production of these alcohols. Overexpression of the gene encoding hydroxymethylglutaryl (HMG)-CoA reductase was most effective among the genes tested. A derivative of S. cerevisiae ATCC 200589, which was selected through screening, was found to be the most suitable host for the production. On cultivation of the resultant transformant, in which the HMG-CoA reductase gene was overexpressed, in a 5-liter bench-scale jar fermenter for 7 d, the production of FOH, NOH, and GGOH reached 145.7, 98.8, and 2.46 mg/l, respectively.

Keywords: Farnesol; Nerolidol; Geranylgeraniol; Prenyl alcohol; Saccharomyces cerevisiae ; Production

Microbial production of 2,3-butanediol from Jerusalem artichoke tubers by Klebsiella pneumoniae by Li-Hui Sun; Xu-Dong Wang; Jian-Ying Dai; Zhi-Long Xiu (pp. 847-852).

2,3-Butanediol is one of the promising bulk chemicals with wide applications. Its fermentative production has attracted great interest due to the high end concentration. However, large-scale production of 2,3-butanediol requires low-cost substrate and efficient fermentation process. In the present study, 2,3-butanediol production by Klebsiella pneumoniae from Jerusalem artichoke tubers was successfully performed, and various technologies, including separate hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF), were investigated. The concentration of target products reached 81.59 and 91.63 g/l, respectively after 40 h in batch and fed-batch SSF processes. Comparing with fed-batch SHF, the fed-batch SSF provided 30.3% higher concentration and 83.2% higher productivity of target products. The results showed that Jerusalem artichoke tuber is a favorable substrate for 2,3-butanediol production, and the application of fed-batch SSF for its conversion can result in a more cost-effective process.

Keywords: 2,3-Butanediol; Jerusalem artichoke; Separate hydrolysis and fermentation; Simultaneous saccharification and fermentation

Metabolism of hydroxylated PCB congeners by cloned laccase isoforms by Satoru Fujihiro; Ryusuke Higuchi; Shin Hisamatsu; Shigenori Sonoki (pp. 853-860).

The white-rot fungus T. versicolor UAMH 8272 produced two groups of laccases, each of which included several isoforms showing different isoelectric points (pI). Group 1 and group 2 laccases, respectively, displayed higher pI 5–6 and lower pI 3–4. Of the four cloned full-length laccase cDNAs, Lac 1 and Lac 4 were expressed in the heterologous protein expression system using Aspergillus oryzae. The measured pI of each Lac 1 and Lac 4 expressed in A. oryzae was lower than that of pI predicted from the amino acid composition. With this regard, isoelectric focusing of Lac 1 showed the presence of multiple protein bands in the 3.0–4.0 pI range, although the predicted pI value of Lac 1 was 4.7. Similarly, Lac 4 exhibited a pI value which was lower than that predicted (3.6 vs. 4.3, respectively). In all tested hydroxyPCBs, higher chlorinated hydroxyPCBs were less susceptible to in vitro degradation by laccase than lower chlorinated hydroxyPCBs. Although Lac 4 showed a generally higher activity than Lac 1, the two laccases were characterized by quite different substrate specificity toward two hydroxy-tetrachlorobiphenyl congeners. Two metabolites were obtained from the metabolism of hydroxy-pentachlorobiphenyl: a ten chlorine-substituted dimer with a C–O bond, and one with a C–C bond.

Keywords: Hydroxylated PCBs; Laccase isoforms; cDNA cloning; Trametes versicolor ; Metabolite dimer

Functional analysis of the disulphide loop mutant of staphylococcal enterotoxin C2 by Xiaogang Wang; Mingkai Xu; Yongming Cai; Hongli Yang; Huiwen Zhang; Chenggang Zhang (pp. 861-871).

The superantigen staphylococcal enterotoxin C2 (SEC2) tremendously activate T lymphocytes bearing certain T-cell receptor Vβ domains when binding to MHC II molecules, which launches a powerful response of tumour inhibition in vitro as well as in vivo. However, the toxicity of SEC2 performed in clinic limited its broad application for immunotherapy. The previous studies suggested that the disulphide loop may be important for the toxicity of some SEs, which prompted us to investigate the potential roles of the disulphide loop in biological activity of SEC2. Site-directed mutagenesis was used to disturb the formation of the disulphide bond by substituting Ala or Ser for Cys-93 and Cys-110. The expressed mutants in Escherichia coli were used to determine their superantigen activity and toxicity. Results showed that all of the mutated proteins exhibited reduced abilities to induce T-cell proliferation and cytotoxic effects on tumour cells L929 and Hepa1-6, suggesting that the disulphide loop plays functional role in maintaining the maximal superantigen activity of SEC2. Furthermore, the toxicity assays in vivo showed that all of the mutants induced a reduced emetic and pyrogenic responses compared with native SEC2, which might be important for further construction of lowly toxic superantigen agent.

Keywords: Superantigen; Staphylococcal enterotoxin C2; Immunotherapy; Toxicity; The disulphide loop; Site-directed mutagenesis

Cloning and characterization of an epoxide hydrolase from Novosphingobium aromaticivorans by Jung-Hee Woo; Ji-Hyun Kang; Sung Gyun Kang; Young-Ok Hwang; Sang-Jin Kim (pp. 873-881).

A gene encoding a putative epoxide hydrolase (EHase) was identified by analyzing an open reading frame of the genome sequence of Novosphingobium aromaticivorans, retaining the conserved catalytic residues such as the catalytic triad (Asp177, Glu328, and His355) and the oxyanion hole. The enantioselective EHase gene (neh) was cloned, and the recombinant EHase could be purified to apparent homogeneity by one step of metal affinity chromatography and further characterized. The purified N. aromaticivorans enantioselective epoxide hydrolase (NEH) showed enantioselective hydrolysis toward styrene oxide, glycidyl phenyl ether, epoxybutane, and epichlorohydrin. The optimal EHase activity toward styrene oxide occurred at pH 6.5 and 45°C. The purified NEH could preferentially hydrolyze (R)-styrene oxide with enantiomeric excess of more than 99% and 11.7% yield after 20-min incubation at an optimal condition. The enantioselective hydrolysis of styrene oxide was also confirmed by the analysis of the vicinal diol, 1-phenyl-1,2-ethanediol. The hydrolyzing rates of the purified NEH toward epoxide substrates were not affected by as high as 100 mM racemic styrene oxide.

Keywords: Epoxide hydrolase; Enantioselectivity; Diol configuration; Genome

Double mutation of the PDC1 and ADH1 genes improves lactate production in the yeast Saccharomyces cerevisiae expressing the bovine lactate dehydrogenase gene by Kenro Tokuhiro; Nobuhiro Ishida; Eiji Nagamori; Satoshi Saitoh; Toru Onishi; Akihiko Kondo; Haruo Takahashi (pp. 883-890).

Expression of a heterologous l-lactate dehydrogenase (l-ldh) gene enables production of optically pure l-lactate by yeast Saccharomyces cerevisiae. However, the lactate yields with engineered yeasts are lower than those in the case of lactic acid bacteria because there is a strong tendency for ethanol to be competitively produced from pyruvate. To decrease the ethanol production and increase the lactate yield, inactivation of the genes that are involved in ethanol production from pyruvate is necessary. We conducted double disruption of the pyruvate decarboxylase 1 (PDC1) and alcohol dehydrogenase 1 (ADH1) genes in a S. cerevisiae strain by replacing them with the bovine l-ldh gene. The lactate yield was increased in the pdc1/adh1 double mutant compared with that in the single pdc1 mutant. The specific growth rate of the double mutant was decreased on glucose but not affected on ethanol or acetate compared with in the control strain. The aeration rate had a strong influence on the production rate and yield of lactate in this strain. The highest lactate yield of 0.75 g lactate produced per gram of glucose consumed was achieved at a lower aeration rate.

Keywords: Yeast; l-Lactate; ADH1; PDC1; Disruption; l-ldh

The size and ratio of homologous sequence to non-homologous sequence in gene disruption cassette influences the gene targeting efficiency in Beauveria bassiana by Jin-Cheng Ma; Qun Zhou; Yong-Hong Zhou; Xing-Gang Liao; Yong-Jun Zhang; Dan Jin; Yan Pei (pp. 891-898).

Targeted gene replacement via homologous recombination (HR) is a conventional approach for the analysis of gene function. However, this event is rare in Beauveria bassiana, which hampers efficient functional analysis in this widely used entomopathogenic fungus. To improve homologous recombination frequency in B. bassiana, we investigated the effect of the ratio of homologous sequence to non-homologous sequence (HS/NHS) in gene disruption cassette upon the HR frequency by two gene loci BbNtl and BbThi, using the herpes simplex virus thymidine kinase as a negative selectable marker against ectopic transformants. Our data revealed that an increase of the ratio of HS/NHS achieved by either extending homologous sequence or decreasing non-homologous sequence could improve HR frequency in B. bassiana. We determined empirically that (1) at least 700 bp of homology to both sides of a target gene was needed to get a reasonable number of disruptants, e.g., 6.7‰ to 13.3‰ in B. bassiana. (2) When the ratio of HS/NHS was above 0.8, an acceptable HR frequency could be achieved for gene replacement in B. bassiana, while when the ratio was below 0.3, few gene disrupted mutants were obtained.

Keywords: Beauveria bassiana ; Herpes simplex virus thymidine kinase; Homologous recombination frequency; Ratio of homologous sequence to non-homologous sequence

Evaluation and characterization of Trichoderma reesei cellulase and xylanase promoters by Zinnia Rahman; Yosuke Shida; Takanori Furukawa; Yota Suzuki; Hirofumi Okada; Wataru Ogasawara; Yasushi Morikawa (pp. 899-908).

Comprehensive analyses on promoters of four cellulase and one xylanase genes of Trichoderma reesei were performed expressing a single reporter uidA from Escherichia coli to construct highly functional cellulase-overproducing strains. GUS amount expressed under each promoter correlated entirely with each mRNA amount, suggesting that GUS production was controlled at the transcriptional level. The uidA transcript levels were much lower than the native gene mRNAs, but they were produced in proportion to the mRNA of native cellulase and xylanase genes driven by the same promoters except for the cbh2 promoter. Cellulose-degrading activity and protein amount was reduced in cbh1 and cbh2 disruptant mutants compared to the wild-type T. reesei PC-3-7 and other uidA transformants. The cbh1 disruptant strain was observed to produce more CBH II, EG I, EG III, and xylanases than native PC-3-7 and the other uidA transformants with the same amounts of protein in SDS-PAGE gels. This observation was further analyzed by measuring mRNA levels of cellulase and xylanase genes in the disruptants using quantitative real-time PCR. In the Pcbh1-gus, mRNA levels for cbh2 and egl1 genes were higher than those in native T. reesei PC-3-7 and all other disruptant strains. The cbh2 disruptant strain had the highest amount of cbh1 mRNA among the strains tested. Homologous integration of uidA at the egl1, egl3, and xyn3 loci was also found to cause a slight increased level of cbh1 mRNA, whereas mRNA levels for egl1, egl3, and xyn3 in all the disruptants were similar to those of T. reesei PC-3-7.

Keywords: Trichoderma reesei; Hypocrea jecorina; Promoter; Cellulase; Xylanase

Impact of overexpressing NADH kinase on glucose and xylose metabolism in recombinant xylose-utilizing Saccharomyces cerevisiae by Jin Hou; Goutham N. Vemuri; Xiaoming Bao; Lisbeth Olsson (pp. 909-919).

During growth of Saccharomyces cerevisiae on glucose, the redox cofactors NADH and NADPH are predominantly involved in catabolism and biosynthesis, respectively. A deviation from the optimal level of these cofactors often results in major changes in the substrate uptake and biomass formation. However, the metabolism of xylose by recombinant S. cerevisiae carrying xylose reductase and xylitol dehydrogenase from the fungal pathway requires both NADH and NADPH and creates cofactor imbalance during growth on xylose. As one possible solution to overcoming this imbalance, the effect of overexpressing the native NADH kinase (encoded by the POS5 gene) in xylose-consuming recombinant S. cerevisiae directed either into the cytosol or to the mitochondria was evaluated. The physiology of the NADH kinase containing strains was also evaluated during growth on glucose. Overexpressing NADH kinase in the cytosol redirected carbon flow from CO₂ to ethanol during aerobic growth on glucose and to ethanol and acetate during anaerobic growth on glucose. However, cytosolic NADH kinase has an opposite effect during anaerobic metabolism of xylose consumption by channeling carbon flow from ethanol to xylitol. In contrast, overexpressing NADH kinase in the mitochondria did not affect the physiology to a large extent. Overall, although NADH kinase did not increase the rate of xylose consumption, we believe that it can provide an important source of NADPH in yeast, which can be useful for metabolic engineering strategies where the redox fluxes are manipulated.

Keywords: NADH kinase; POS5 ; Saccharomyces cerevisiae ; NADPH; Xylose

Optimization of Verticillium lecanii spore production in solid-state fermentation on sugarcane bagasse by Yujie Shi; Xiangqun Xu; Yang Zhu (pp. 921-927).

Verticillium lecanii is an entomopathogen with high potential in biological control of pests. We developed a solid-state fermentation with sugarcane bagasse as carrier absorbing liquid medium to propagate V. lecanii spores. Using statistical experimental design, we optimized the medium composition for spore production. We first used one-factor-at-a-time design to identify corn flour and yeast extract as the best carbon and nitrogen sources for the spore production of V. lecanii. Then, we used two-level fractional factorial design to confirm corn flour, yeast extract, and KH₂PO₄ as important factors significantly affecting V. lecanii spore production. Finally, we optimized these selected variables using a central composite design and response surface method. The optimal medium composition was (grams per liter): corn flour 35.79, yeast 8.69, KH₂PO₄ 1.63, K₂HPO₄ 0.325, and MgSO₄ 0.325. Under optimal conditions, spore production reached 1.1 × 10¹⁰ spores/g dried carrier, much higher than that on wheat bran (1.7 × 10⁹ spores/g initial dry matter).

Keywords: Verticillium lecanii ; Spore production; Central composite design; Solid-state fermentation; Biological control; Response surface methodology

Analysis of composition and structure of Clostridium thermocellum membranes from wild-type and ethanol-adapted strains by Michael D. Timmons; Barbara L. Knutson; Sue E. Nokes; Herbert J. Strobel; Bert C. Lynn (pp. 929-939).

Clostridium thermocellum is a candidate organism for consolidated bioprocessing of lignocellulosic biomass into ethanol. However, commercial use is limited due to growth inhibition at modest ethanol concentrations. Recently, an ethanol-adapted strain of C. thermocellum was produced. Since ethanol adaptation in microorganisms has been linked to modification of membrane lipids, we tested the hypothesis that ethanol adaptation in C. thermocellum involves lipid modification by comparing the fatty acid composition and membrane anisotropy of wild-type and ethanol-adapted strains. Derivatization to fatty acid methyl esters provided quantitative lipid analysis. Compared to wild-type, the ethanol-adapted strain had a larger percentage of fatty acids with chain lengths >16:0 and showed a significant increase in the percentage of 16:0 plasmalogens. Structural identification of fatty acids was confirmed through mass spectral fragmentation patterns of picolinyl esters. Ethanol adaptation did not involve modification at sites of methyl branching or the unsaturation index. Comparison of steady-state fluorescence anisotropy experiments, in the absence and presence of ethanol, provided evidence for the effects of ethanol on membrane fluidity. In the presence of ethanol, both strains displayed increased fluidity by approximately 12%. These data support the model that ethanol adaptation was the result of fatty acid changes that increased membrane rigidity that counter-acted the fluidizing effect of ethanol.

Keywords: Clostridium thermocellum ; Biofuels; Ethanol; Anisotropy; Fatty acid methyl esters (FAMEs); Picolinyl esters; Consolidated bioprocessing

Sustainable and practical degradation of intact chicken feathers by cultivating a newly isolated thermophilic Meiothermus ruber H328 by Tatsunobu Matsui; Yukie Yamada; Hideki Mitsuya; Yasushi Shigeri; Yasukazu Yoshida; Yoshiro Saito; Hiroshi Matsui; Kunihiko Watanabe (pp. 941-950).

The sustainable and practical degradation of intact chicken feathers by a newly isolated thermophilic bacterium Meiothermus ruber H328 was presented with extensive data. Aerobic cultivation with moderately thermophilic strain H328 at 55°C for 6 days led to the apparently complete decay of the truly intact feathers and provided 1.89 mmol free amino acids and 7.32 mmol acid-hydrolyzed amino acids from 50 ml of culture containing 3% (w/v) intact chicken feathers. The amino acid components in the soluble fraction of the culture conspicuously agreed with those calculated from the intact feathers. This demonstrated that more than 55% of total keratin proteins were solubilized from the intact chicken feathers into the culture in the forms of free amino acid and/or soluble oligopeptide, and most of them are directly derived from the intact feathers by proteolytic digestion. Feather degradation by strain H328 surpasses that by any other microorganisms with regard to degradation efficiency, absence of requirement for pretreatment of the feathers, and product fidelity in the amino acid component. Furthermore, the culture containing the degradative products from the intact feathers was subjected to matrix-assisted laser desorption ionization mass spectrometry-time-of-flight analysis, and it was revealed that the molecular masses of the solubilized products, oligopeptides, were less than 1,000. This result allows us to investigate the bioactivities of oligopeptides derived from the degradation of chicken feathers by cultivation with strain H328 as well as the production of amino acids for feedstuffs.

Keywords: Thermophile; Protease; Keratin; Hard-to-degrade

Peptide diversity in strains of the cyanobacterium Microcystis aeruginosa isolated from Portuguese water supplies by Joana Martins; Martin L. Saker; Cristiana Moreira; Martin Welker; Jutta Fastner; Vitor M. Vasconcelos (pp. 951-961).

Strains of the cyanobacterium Microcystis aeruginosa were isolated into pure culture from a variety of lakes, rivers, and reservoirs in Portugal. Samples were tested with matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry (MALDI-TOF MS) to investigate the presence of various peptide groups including aeruginosins, microginins, anabaenopeptins, cyanopeptilins, microcystins, and microviridins and other peptide-like compounds. Binary data, based on the presence and absence of different peptide groups, were analyzed by phylogenetic inference. DNA was also extracted from the samples and tested using a range of primers. Those strains that gave positive results for a Microcystis-specific primer pair were further analyzed for the presence of genes linked to the biosynthesis of microginin and microcystin. The results showed that a wide range of microcystin forms were produced by the strains among which MC-LR, -FR, -RR, -WR, and -YR were the most common. The peptide profiles obtained from the MALDI analysis were assessed using cluster analysis which resulted in the formation of distinct groups or chemotypes.

Keywords: Microcystis ; Peptides

Simultaneous biodegradation of pyridine and quinoline by two mixed bacterial strains by Yaohui Bai; Qinghua Sun; Cui Zhao; Donghui Wen; Xiaoyan Tang (pp. 963-973).

Experiments were conducted to provide data on the effectiveness of bioaugmentation in the removal of pyridine and quinoline from different wastewaters. A pyridine-degrading bacterial strain (Paracoccus sp. BW001) and a quinoline-degrading strain (Pseudomonas sp. BW003) were isolated from the activated sludge of a coking wastewater treatment plant. In this study, a consortium of these two bacterial strains was used as inoculum to simultaneously degrade pyridine and quinoline in three types of wastewaters: sterile synthetic, domestic, and industrial. In addition, variation of the bacterial community structures during degradation was monitored by denaturing gradient gel electrophoresis and amplicon length heterogeneity polymerase chain reaction techniques. The results of our experiments indicate that pyridine and quinoline can be removed efficiently using this inoculum but that the degradation process results in the production of ammonium as a by-product. Also, in the two actual wastewaters investigated, we observed that several autochthonous strains of bacteria in both the domestic and industrial wastewater were tolerant of pyridine and quinoline and grew rapidly.

Keywords: Pyridine; Quinoline; Biodegradation; Mixed bacteria; Bacterial community

Analysis of rhamnolipid biosurfactants by methylene blue complexation by Neissa M. Pinzon; Lu-Kwang Ju (pp. 975-981).

Rhamnolipids, produced by Pseudomonas aeruginosa, represent an important group of biosurfactants having various industrial, environmental, and medical applications. Current methods for rhamnolipid quantification involve the use of strong hazardous acids/chemicals, indirect measurement of the concentration of sugar moiety, or require the availability of expensive equipment (HPLC-MS). A safer, easier method that measures the whole rhamnolipid molecules would significantly enhance strain selection, metabolic engineering, and process development for economical rhamnolipid production. A semi-quantitative method was reported earlier to differentiate between the rhamnolipid-producing and non-producing strains using agar plates containing methylene blue and cetyl trimethylammonium bromide (CTAB). In this study, a rapid and simple method for rhamnolipid analysis was developed by systematically investigating the complexation of rhamnolipids and methylene blue, with and without the presence of CTAB. The method relies on measuring the absorbance (at 638 nm) of the rhamnolipid−methylene blue complex that partitions into the chloroform phase. With P. aeruginosa fermentation samples, the applicability of this method was verified by comparison of the analysis results with those obtained from the commonly used anthrone reaction technique.

Keywords: Biosurfactant; Pseudomonas aeruginosa ; Rhamnolipid; Methylene blue; Analysis

Different influences of DNA purity indices and quantity on PCR-based DGGE and functional gene microarray in soil microbial community study by Jing Ning; Jost Liebich; Matthias Kästner; Jizhong Zhou; Andreas Schäffer; Peter Burauel (pp. 983-993).

Based on the comparative study of the DNA extracts from two soil samples obtained by three commercial DNA extraction kits, we evaluated the influence of the DNA quantity and purity indices (the absorbance ratios A260/280 and A260/230, as well as the absorbance value A320 indicating the amount of humic substances) on polymerase chain reaction (PCR)-based denaturing gradient gel electrophoresis (DGGE) and a functional gene microarray used in the study of microbial communities. Numbers and intensities of the DGGE bands are more affected by the A260/280 and A320 values than by the ratio A260/230 and conditionally affected by the DNA yield. Moreover, we demonstrated that the DGGE band pattern was also affected by the preferential extraction due to chemical agents applied in the extraction. Unlike DGGE, microarray is more affected by the A260/230 and A320 values. Until now, the successful PCR performance is the mostly used criterion for soil DNA purity. However, since PCR was more influenced by the A260/280 ratio than by A260/230, it is not accurate enough any more for microbial community assessed by non-PCR-based methods such as microarray. This study provides some useful hints on how to choose effective DNA extraction method for the subsequent assessment of microbial community.

Keywords: DNA purity indices; DNA yield; DGGE; Functional gene microarray; Microbial community analyses

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Applied Microbiology and Biotechnology (v.82, #5)