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Applied Microbiology and Biotechnology (v.87, #6)

Magnetically recyclable, antimicrobial, and catalytically enhanced polymer-assisted “green” nanosystem-immobilized Aspergillus niger amyloglucosidase by Rocktotpal Konwarh; Dipankar Kalita; Charulata Mahanta; Manabendra Mandal; Niranjan Karak (pp. 1983-1992).

The present work reports the integration of polymer matrix-supported nanomaterial and enzyme biotechnology for development of industrially feasible biocatalysts. Aqueous leaf extract of Mesua ferrea L. was used to prepare silver nanoparticles distributed within a narrow size range (1–12 nm). In situ oxidative technique was used to obtain poly(ethylene glycol)-supported iron oxide nanoparticles (3–5 nm). Sonication-mediated mixing of above nanoparticles generated the immobilization system comprising of polymer-supported silver–iron oxide nanoparticles (20–30 nm). A commercially important enzyme, Aspergillus niger amyloglucosidase was coupled onto the immobilization system through sonication. The immobilization enzyme registered a multi-fold increment in the specific activity (807 U/mg) over the free counterpart (69 U/mg). Considerable initial activity of the immobilized enzyme was retained even after storing the system at room temperature as well as post-repeated magnetic recycling. Evaluation of the commendable starch saccharification rate, washing performance synergy with a panel of commercial detergents, and antibacterial potency strongly forwards the immobilized enzyme as a multi-functional industrially feasible system.

Keywords: Amyloglucosidase immobilization; Polymeric nanocomposite; Antimicrobial potency; Magnetic recyclability; Starch saccharification; Detergent compatibility

l-Ribulose production by an Escherichia coli harboring l-arabinose isomerase from Bacillus licheniformis by Ye-Wang Zhang; Marimuthu Jeya; Jung-Kul Lee (pp. 1993-1999).

Recombinant Escherichia coli harboring the l-arabinose isomerase (BLAI) from Bacillus licheniformis was used as a biocatalyst to produce l-ribulose in the presence of borate. Effects of substrate concentration, the borate to l-arabinose ratio, pH, and temperature on the conversion of l-arabinose to l-ribulose were investigated. l-Ribulose production was efficient when pH was higher than 9 and temperature was higher than 50 °C. Borate addition to the reaction mixture was essential for high conversion of l-arabinose to l-ribulose as it resulted in an equilibrium shift in favor of the product. Under the optimal conditions determined by response surface methodology, the E. coli harboring BLAI produced 375 g l⁻¹ L-ribulose from 500 g l⁻¹ l-arabinose at a reaction time of 60 min, corresponding to a conversion yield of 75% and productivity of 375 g l⁻¹ h⁻¹. When the resting recombinant E. coli cells were recycled, 85% of the yield was obtained even after seven cycles of reuse. The productivity and final concentration of l-ribulose obtained in the present study were the highest yet reported.

Keywords: l-Arabinose; Borate; Isomerization; Response surface methodology; l-Ribulose

Microbial production of meso-2,3-butanediol by metabolically engineered Escherichia coli under low oxygen condition by Zheng-Jun Li; Jia Jian; Xiao-Xing Wei; Xiao-Wen Shen; Guo-Qiang Chen (pp. 2001-2009).

A metabolically engineered Escherichia coli has been constructed for the production of meso-2,3-butanediol (2,3-BD) under low oxygen condition. Genes responsible for 2,3-BD formation from pyruvate were assembled together to generate a high-copy plasmid pEnBD, in which each gene was transcribed with a constitutive promoter. To eliminate by-product formation under low oxygen condition, genes including ldhA, pta, adhE, and poxB which functioned for the mixed acid fermentation pathways were deleted in E. coli JM109. Compared with the wild type, the quadruple gene deletion mutant produced smaller amounts of acetate, succinate, and ethanol from glucose when cultivated in LB medium in shake flasks under low-aeration. When 2,3-BD producing pathway was introduced via pEnBD into the mutant, higher glucose consumption and faster 2,3-BD production rate compared with that of the wild-type control were observed under aerobic condition in shake flasks. In a 6-L fermentor supplied with only 3% dissolved oxygen (DO), the mutant harboring pEnBD converted glucose to 2,3-BD much faster than the control did. When DO supply was further lowered to 1% DO, the recombinant mutant grew much slower but produced 2,3-BD as a major fermentation metabolic product. In addition, the 2,3-BD yield showed an increase from 0.20 g BD/g glucose for the control to 0.43 g BD/g glucose for the mixed acid pathway deleted mutant grown in fermentors under 1% DO. These results reveals the potential of production of enantiomerically pure 2,3-BD isomer by recombinant E. coli under low oxygen condition.

Keywords: meso-2,3-butanediol; Microaerobic; Mixed acid fermentation; Escherichia coli ; Metabolic engineering

Optimized bioprocess for production of fructofuranosidase by recombinant Aspergillus niger by Habib Driouch; Andreas Roth; Petra Dersch; Christoph Wittmann (pp. 2011-2024).

A comprehensive approach of bioprocess design at various levels was used to optimize microbial production of extracellular fructofuranosidase, important as biocatalyst to derive fructooligosaccharides with broad application in food or pharmaceutical industry. For production, the recombinant strain Aspergillus niger SKAn1015 was used, which expresses the fructofuranosidase encoding gene suc1 under control of a strong constitutive promoter. In a first screening towards an optimized medium, glucose, nitrate, Fe²⁺, and Mn²⁺ were identified as beneficial for production. A minimal medium with optimized concentration of these key nutrients, obtained by central composite design experiments and quadratic modelling, provided a threefold increased fructofuranosidase activity in the culture supernatant (400 U/mL) as compared to the originally described medium. Utilizing the optimized medium, the process was then transferred from shake flask into a fed-batch-operated bioreactor. Hereby, the intended addition of talc microparticles allowed engineering the morphology of A. niger into a highly active mycelial form, which strongly boosted production. Fructofuranosidase production was highly specific as confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. The secreted enzyme activity of 2,800 U/mL, corresponding to about 3 g/L of fructofuranosidase, achieved by the microparticle-enhanced fed-batch process, is tenfold higher than that of any other process reported so far, so that the presented bioprocess strategy appears as a milestone towards future industrial fructofuranosidase production.

Keywords: Morphology engineering; Central composite design; Fed-batch; Enzyme; GFP

High-level succinic acid production and yield by lactose-induced expression of phosphoenolpyruvate carboxylase in ptsG mutant Escherichia coli by Dan Wang; Qiang Li; Yu Mao; Jianmin Xing; Zhiguo Su (pp. 2025-2035).

Escherichia coli strains with foreign genes under the isopropyl-β-d-thiogalactopyranoside-inducible promoters such as lac, tac, and trc were engineered and considered as the promising succinic acid-producing bacteria in many reports. The promoters mentioned above could also be induced by lactose, which had not been attempted for succinic acid production before. Here, the efficient utilization of lactose as inducer was demonstrated in cultures of the ptsG, ldhA, and pflB mutant strain DC1515 with ppc overexpression. A fermentative process for succinic acid production at high level by this strain was developed. In flask anaerobic culture, 14.86 g l⁻¹ succinic acid was produced from 15 g l⁻¹ glucose with a yield of 1.51 mol mol⁻¹ glucose. In two-stage culture carried out in a 3-l bioreactor, the overall yield and concentration of succinic acid reached to 1.67 mol mol⁻¹ glucose and 99.7 g l⁻¹, respectively, with a productivity of 1.7 g l⁻¹ h⁻¹ in the anaerobic stage. The efficient utilization of lactose as inducer made recombinant E. coli a more capable strain for succinic acid production at large scale.

Keywords: Glucose phosphotransferase (ptsG); Escherichia coli ; Succinic acid; Lactose induction; Phosphoenolpyruvate carboxylase (ppc)

Optimization of growth media components for polyhydroxyalkanoate (PHA) production from organic acids by Ralstonia eutropha by Yung-Hun Yang; Christopher J. Brigham; Charles F. Budde; Paolo Boccazzi; Laura B. Willis; Mohd Ali Hassan; Zainal Abidin Mohd Yusof; ChoKyun Rha; Anthony J. Sinskey (pp. 2037-2045).

We employed systematic mixture analysis to determine optimal levels of acetate, propionate, and butyrate for cell growth and polyhydroxyalkanoate (PHA) production by Ralstonia eutropha H16. Butyrate was the preferred acid for robust cell growth and high PHA production. The 3-hydroxyvalerate content in the resulting PHA depended on the proportion of propionate initially present in the growth medium. The proportion of acetate dramatically affected the final pH of the growth medium. A model was constructed using our data that predicts the effects of these acids, individually and in combination, on cell dry weight (CDW), PHA content (%CDW), PHA production, 3HV in the polymer, and final culture pH. Cell growth and PHA production improved approximately 1.5-fold over initial conditions when the proportion of butyrate was increased. Optimization of the phosphate buffer content in medium containing higher amounts of butyrate improved cell growth and PHA production more than 4-fold. The validated organic acid mixture analysis model can be used to optimize R. eutropha culture conditions, in order to meet targets for PHA production and/or polymer HV content. By modifying the growth medium made from treated industrial waste, such as palm oil mill effluent, more PHA can be produced.

Keywords: Polyhydroxyalkanoate; Ralstonia eutropha ; Organic acid; Mixture model

Selective expression of the soluble product fraction in Escherichia coli cultures employed in recombinant protein production processes by Stefan Gnoth; Rimvydas Simutis; Andreas Lübbert (pp. 2047-2058).

Recombinant proteins produced in Escherichia coli hosts may appear within the cells’ cytoplasm in form of insoluble inclusion bodies (IB’s) and/or as dissolved functional protein molecules. If no efficient refolding procedure is available, one is interested in obtaining as much product as possible in its soluble form. Here, we present a process engineering approach to maximizing the soluble target protein fraction. For that purpose, a dynamic process model was developed. Its essential kinetic component, the specific soluble product formation rate, if represented as a function of the specific growth rate and the culture temperature, depicts a clear maximum. Based on the dynamic model, optimal specific growth rate and temperature profiles for the fed-batch fermentation were determined. In the course of the study reported, the mass of desired soluble protein was increased by about 25%. At the same time, the formation of inclusion bodies was essentially avoided. As the optimal cultivation procedure is rather susceptible to distortions, control measures are necessary to guarantee that the real process can be kept on its desired path. This was possible with robust closed loop control. Experimental process validation revealed that, in this way, high dissolved product fractions could be obtained at an excellent batch-to-batch reproducibility.

Keywords: Specific biomass growth rate; Temperature; Hybrid artificial neural network; Process model; Optimization; Feedback control; PAT

Cellulase production on glucose-based media by the UV-irradiated mutants of Trichoderma reesei by Masakazu Ike; Jeung-yil Park; Mine Tabuse; Ken Tokuyasu (pp. 2059-2066).

From 22,791 mutants of a cellulase hyper-producing strain of Trichoderma reesei (Hypocrea jecorina), ATCC66589, as the parent, we selected two mutants, M2-1 and M3-1, that produce cellulases in media containing both cellulose and glucose. The mutation enabled the mutants to produce cellulases, which were measured as p-nitrophenyl β-d-lactopyranoside-hydrolyzing activities, in media with glucose as a sole carbon source, although M2-1 exhibited different sensitivities to glucose from M3-1. When the mutants were grown for 8 days on a medium with cellulose as a sole carbon source, the filter-paper-degrading activities (FPAs) per gram of cellulose were 257 and 281 U for M2-1 and M3-1, respectively, values that were 1.1–1.2 times higher than that of the parental strain. Cellulase production by M2-1 and M3-1 on a medium with a continuously fed mixture of glucose and cellobiose resulted in 214 and 210 U of FPA/gram carbon sources, respectively, whereas less efficient production (140 U of FPA/gram carbon source) was achieved by the parental strain. The improved cellulase productivity of the mutants allows us to use glucose as a carbon source for efficient on-site production of cellulases with quality/quantity-controlled feeding of soluble carbon sources and inducers.

Keywords: Trichoderma reesei (Hypocrea jecorina); Random mutagenesis; Cellulase production; Glucose-based medium

Characterisation of the flavin-free oxygen-tolerant azoreductase from Xenophilus azovorans KF46F in comparison to flavin-containing azoreductases by Sibylle Bürger; Andreas Stolz (pp. 2067-2076).

The flavin-free azoreductase from Xenophilus azovorans KF46F (AzoB), which has been the very first characterized oxygen-tolerant azoreductase, was analyzed in comparison to various recently described flavin-containing azoreductases from different bacterial sources. Sequence comparisons demonstrated that the azoreductase from X. azovorans KF46F is a member of the NmrA family of proteins and demonstrates 30% sequence identity with a NADPH-dependent quinone oxidoreductase from Escherichia coli (encoded by ytfG). In contrast, it was found that the flavin-containing azoreductases from E. coli OY1-2 (AZR), Bacillus sp. OY1-2 (AZR) and related azoreductases all belong to the FMN_red superfamily of enzymes. The substrate specificity of AzoB was reanalyzed in respect to the recently characterized flavin-containing azoreductases, and it was found that purified AzoB converted in addition to different ortho-hydroxy azo compounds [such as Orange II = 1-(4′-sulfophenylazo)-2-naphthol] also the simple non-hydroxylated non-sulfonated azo dye Methyl Red (4′-dimethylaminoazobenzene-2-carboxylic acid), but no indications for the conversion of quinones were obtained. Significant differences were observed in the substrate specificities between AzoB and the flavin-containing azoreductases. The kinetic analysis of the turn-over of Orange II by AzoB suggested an ordered bireactant reaction mechanism which was different from the ping-pong mechanism suggested for the flavin-containing azoreductases.

Keywords: Biodegradation; Azo dyes; Azoreductase

Characterization of catabolic meta-nitrophenol nitroreductase from Cupriavidus necator JMP134 by Ying Yin; Yi Xiao; Hai-Zhou Liu; Fuhua Hao; Simon Rayner; Huiru Tang; Ning-Yi Zhou (pp. 2077-2085).

Cupriavidus necator JMP134 utilizes meta-nitrophenol (MNP) as a sole source of carbon, nitrogen, and energy. The metabolic reconstruction of MNP degradation performed in silico suggested that the mnp cluster might have played important roles in MNP degradation. In order to experimentally confirm the prediction, we have now characterized mnpA-encoded meta-nitrophenol nitroreductase involved in the initial reaction of MNP degradation. Real-time PCR analysis indicated that mnpA played an essential role in MNP degradation. MnpA was purified to homogeneity as His-tagged proteins and was considered to be a dimer as determined by gel filtration. MnpA was an MNP nitroreductase with a tightly bound flavin mononucleotide (FMN), catalyzing the partial reduction of MNP to meta-hydroxylaminophenol via meta-nitrosophenol in the presence of NADPH and oxygen. The accumulation of meta-nitrosophenol was confirmed with the results of liquid chromatography–diode array detection and time-of-flight mass spectrometry for the first time. The low K _m and high k _cat of MnpA as well as MNP-inducible transcription of mnpA suggested that MNP was the physiological substrate for this nitroreductase. In addition, the phylogenetic analysis revealed that nitroreductases of known physiological function including MnpA constituted a new clade in the nitro-FMN-reductase superfamily.

Keywords: Catabolism; Cupriavidus necator JMP134; meta-Nitrophenol; Nitroreductase

Screening for improved activity of a transglutaminase from Streptomyces mobaraensis created by a novel rational mutagenesis and random mutagenesis by Keiichi Yokoyama; Hiroe Utsumi; Takefumi Nakamura; Daisuke Ogaya; Nobuhisa Shimba; Eiichiro Suzuki; Seiichi Taguchi (pp. 2087-2096).

Microbial transglutaminase (MTG) has been used extensively in academic research and the food industries through its cross-linking or posttranslational modification of proteins. Two enzyme engineering approaches were applied to improve MTG activity. One is a novel method of rational mutagenesis, called water-accessible surface hot-space region-oriented mutagenesis (WASH-ROM). One hundred and fifty-one point mutations were selected at 40 residues, bearing high solvent-accessibility surface area, within a 15 Å space from the active site Cys64. Among them, 32 mutants showed higher specific activity than the wild type. The other is a random mutagenesis of the whole region of the MTG gene, coupled with a new plate assay screening system, using Corynebacterium Expression System CORYNEX®. This in vivo system allowed us to readily distinguish the change in enzymatic activity by monitoring the intensity of enzymatic reaction-derived color zones surrounding recombinant cells. From the library of 24,000 mutants, ten were finally selected as beneficial mutants exhibiting higher specific activity than the wild type. Furthermore, we found that Ser199Ala mutant with additional N-terminal tetrapeptide showed the highest specific activity (1.7 times higher than the wild type). These various beneficial positions leading to increased specific activity of MTG were identified to achieve further enzyme improvements.

Keywords: Transglutaminase; Streptomyces; CORYNEX®; Screening; Solvent-accessibility; Specific activity

Characterization of Xyn10A, a highly active xylanase from the human gut bacterium Bacteroides xylanisolvens XB1A by Caroline Mirande; Pascale Mosoni; Christel Béra-Maillet; Annick Bernalier-Donadille; Evelyne Forano (pp. 2097-2105).

A xylanase gene xyn10A was isolated from the human gut bacterium Bacteroides xylanisolvens XB1A and the gene product was characterized. Xyn10A is a 40-kDa xylanase composed of a glycoside hydrolase family 10 catalytic domain with a signal peptide. A recombinant His-tagged Xyn10A was produced in Escherichia coli and purified. It was active on oat spelt and birchwood xylans and on wheat arabinoxylans. It cleaved xylotetraose, xylopentaose, and xylohexaose but not xylobiose, clearly indicating that Xyn10A is a xylanase. Surprisingly, it showed a low activity against carboxymethylcellulose but no activity at all against aryl-cellobioside and cellooligosaccharides. The enzyme exhibited K _m and V _max of 1.6 mg ml⁻¹ and 118 µmol min⁻¹ mg⁻¹ on oat spelt xylan, and its optimal temperature and pH for activity were 37°C and pH 6.0, respectively. Its catalytic properties (k _cat/K _m = 3,300 ml mg⁻¹ min⁻¹) suggested that Xyn10A is one of the most active GH10 xylanase described to date. Phylogenetic analyses showed that Xyn10A was closely related to other GH10 xylanases from human Bacteroides. The xyn10A gene was expressed in B. xylanisolvens XB1A cultured with glucose, xylose or xylans, and the protein was associated with the cells. Xyn10A is the first family 10 xylanase characterized from B. xylanisolvens XB1A.

Keywords: GH10; Xylanase; Bacteroides xylanisolvens ; Human gut

One-step purification and characterization of a β-1,4-glucosidase from a newly isolated strain of Stereum hirsutum by Ngoc-Phuong-Thao Nguyen; Kyoung-Mi Lee; Kyoung-Min Lee; In-Won Kim; Yeong-Suk Kim; Marimuthu Jeya; Jung-Kul Lee (pp. 2107-2116).

A highly efficient β-1,4-glucosidase (BGL) secreting strain, Stereum hirsutum SKU512, was isolated and identified based on morphological features and sequence analysis of internal transcribed spacer rDNA. A BGL containing a carbohydrate moiety was purified to homogeneity from S. hirsutum culture supernatants using only a single chromatography step on a gel filtration column. The relative molecular weight of S. hirsutum BGL was determined as 98 kDa by sodium dodecyl sulfate polyacrylamide gel electrophoresis or 780 kDa by size exclusion chromatography, indicating that the enzyme is an octamer. S. hirsutum BGL showed the highest activity toward p-nitrophenyl-β-D-glucopyranoside (V _max = 3,028 U mg-protein⁻¹, k _cat = 4,945 s⁻¹) ever reported. The enzyme also showed good stability at an acidic pH ranging from 3.0 to 5.5. The BGL was able to promote transglycosylation with an activity of 42.9 U mg-protein⁻¹ using methanol as an acceptor and glucose as a donor. The internal amino acid sequences of the isolated enzyme showed significant homology with hydrolases from glycoside hydrolase family 1 (GH1), indicating that the S. hirsutum BGL is a member of GH1 family. The characteristics of S. hirsutum BGL could prove to be of interest in several potential applications, especially in enhancing flavor release during the wine fermentation process.

Keywords: β-1; 4-Glucosidase; Glycoside hydrolase family 1; Glucoside; Stereum hirsutum ; Wine fermentation

Cloning, expression, purification, and activity assay of proteins related to D-lactic acid formation in Lactobacillus rhamnosus by Xiuwen Wang; Zhaojuan Zheng; Peipei Dou; Jiayang Qin; Xiaochen Wang; Cuiqing Ma; Hongzhi Tang; Ping Xu (pp. 2117-2123).

Two proteins that might be responsible for D-lactic acid (D-LA) formation were screened from the genome database of Lactobacillus rhamnosus GG. The coding genes of the two proteins in L. rhamnosus CASL, ldhD1 and ldhD2, were cloned and expressed in Escherichia coli Rosetta with an inducible expression vector pETDuet™-1 (Novagen, Darmstadt, Germany), respectively. The two purified proteins, LdhD-1 and LdhD-2, migrated as a single protein band separately, both corresponding to an apparent molecular mass between 35 kDa and 45 kDa on sodium dodecyl sulfate polyacrylamide gel electrophoresis. The specific activities of LdhD-1 and LdhD-2 catalyzing pyruvate to LA were 0.02 U/mg and 0.21 U/mg, respectively. The configuration of LA converted from pyruvate was determined using high-performance liquid chromatography equipped with a chiral column. Only D-LA was detected when LdhD-1 and LdhD-2 were tested. In summary, the two proteins cloned and expressed in this study were most probably responsible for D-LA formation during fermentation of L. rhamnosus CASL.

Keywords: Lactobacillus rhamnosus ; D-Lactic acid; Expression; Purification

Functional analysis of glycoside hydrolase family 8 xylanases shows narrow but distinct substrate specificities and biotechnological potential by Annick Pollet; Jan Schoepe; Emmie Dornez; Sergei V. Strelkov; Jan A. Delcour; Christophe M. Courtin (pp. 2125-2135).

The potential of glycoside hydrolase family (GH) 8 xylanases in biotechnological applications is virtually unexplored. Therefore, the substrate preference and hydrolysis product profiles of two GH8 xylanases were evaluated to investigate their activities and substrate specificities. A GH8 xylanase from an uncultured bacterium (rXyn8) shows endo action but very selectively releases xylotriose from its substrates. It has a higher activity than the Pseudoalteromonas haloplanktis GH8 endo-xylanase (PhXyl) on xylononaose and smaller xylo-oligosaccharides. PhXyl preferably degrades xylan substrates with a high degree of polymerization. It is sterically more hindered by arabinose substituents than rXyn8, producing larger end hydrolysis products. The specificities of rXyn8 and PhXyl differ completely from these of the previously described GH8 xylanases from Bifidobacterium adolescentis (BaRexA) and Bacillus halodurans (BhRex). As reducing-end xylose-releasing exo-oligoxylanases, they selectively release xylose from the reducing end of small xylo-oligosaccharides. The findings of this study show that GH8 xylanases have a narrow substrate specificity, but also one that strongly varies between family members and is distinct from that of GH10 and GH11 xylanases. Structural comparison of rXyn8, PhXyl, BaRexA, and BhRex showed that subtle amino acid changes in the glycon as well as the aglycon subsites probably form the basis of the observed differences between GH8 xylanases. GH8 xylanases, therefore, are an interesting group of enzymes, with potential towards engineering and applications.

Keywords: Xylanase; Glycoside hydrolase family 8; Substrate specificity; Arabinoxylan; Xylo-oligosaccharides

Identification and characterization of a novel xylanase derived from a rice straw degrading enrichment culture by Xin-chun Mo; Chun-lan Chen; Hao Pang; Yi Feng; Jia-xun Feng (pp. 2137-2146).

A metagenomic library containing ca. 3.06 × 10⁸ bp insert DNA was constructed from a rice straw degrading enrichment culture. A xylanase gene, umxyn10A, was cloned by screening the library for xylanase activity. The encoded enzyme Umxyn10A showed 58% identity and 73% similarity with a xylanase from Thermobifida fusca YX. Sequence analyses showed that Umxyn10A contained a glycosyl hydrolase family 10 catalytic domain. The gene was expressed in Escherichia coli, and the recombinant enzyme was purified and characterized biochemically. Recombinant Umxyn10A was highly active toward xylan. However, the purified enzyme could slightly hydrolyze β-1,3/4-glucan and β-1,3/6-glucan. Umxyn10A displayed maximal activity toward oat spelt xylan at a high temperature (75°C) and weak acidity (pH 6.5). The K m and V _max of Umxyn10A toward oat spelt xylan were 3.2 mg ml⁻¹ and 0.22 mmol min⁻¹ mg⁻¹ and were 2.7 mg ml⁻¹ and 1.0 mmol min⁻¹ mg⁻¹ against birchwood xylan, respectively. Metal ions did not appear to be required for the catalytic activity of this enzyme. The enzyme Umxyn10A could efficiently hydrolyze birchwood xylan to release xylobiose as the major product and a negligible amount of xylose. The xylanase identified in this work may have potential application in producing xylobiose from xylan.

Keywords: Rice straw degrading enrichment culture; Metagenomic library; Xylanase; Cloning; Characterization

Efficient soluble protein production on transgenic silkworms expressing cytoplasmic chaperones by Sun Mee Hong; Jun Yamashita; Hitoshi Mitsunobu; Keiro Uchino; Isao Kobayashi; Hideki Sezutsu; Toshiki Tamura; Hideki Nakajima; Yoshitaka Miyagawa; Jae Man Lee; Hiroaki Mon; Yoshihiko Miyata; Yutaka Kawaguchi; Takahiro Kusakabe (pp. 2147-2156).

Baculovirus expression systems (BES) are widely used for recombinant protein production in lepidopteran cells or larvae. However, even in BES, the insolubility of recombinant proteins sometimes makes their expression difficult. In this study, to improve the solubility and yield of foreign proteins, we constructed transgenic silkworms using silkworm heat-shock proteins, Hsp70 and Hsp40, or Hsc70 and Hsp90 co-chaperone Hop. In these transgenic silkworms, the expression levels of the transgenes were under the control of a UAS·hsp mini-promoter driven by a Gal4NFkBp65 activator. When the transgenic silkworm with HSP70 and 40 (TGS-HSP70/40) was infected with BmNPV carrying mC3d and Gal4NFkBp65 under the control of baculovirus polyhedrin or p10 promoters, respectively, the soluble fraction of the His- or His·GST-tagged mC3d increased significantly. Similarly, the transgenic silkworm with HSC70 and HOP (TGS-HOP7) was effective for the expression of a steroid hormone receptor, USP2. In conclusion, the His-tagged baculovirus expression system featuring the chaperone effect TGS-HSP70/40 and TGS-HOP7 silkworms is effective for increasing the yields of soluble and functional foreign gene products.

Keywords: Silkworm; Baculovirus expression system; BmNPV; Heat-shock proteins; Recombinant protein; UAS/GAL4

Analysis of DNA repeats in bacterial plasmids reveals the potential for recurrent instability events by Pedro H. Oliveira; Kristala Jones Prather; Duarte M. F. Prazeres; Gabriel A. Monteiro (pp. 2157-2167).

Structural instability has been frequently observed in natural plasmids and vectors used for protein expression or DNA vaccine development. However, there is a lack of information concerning hotspot mapping, namely, DNA repeats or sequences identical to the host genome. This led us to evaluate the abundance and distribution of direct, inverted, and tandem repeats with high recombination potential in 36 natural plasmids from ten bacterial genera, as well as in several widely used bacterial and mammalian expression vectors. In natural plasmids, we observed an overrepresentation of close direct repeats in comparison to inverted ones and a preferential location of repeats with high recombination potential in intergenic regions, suggesting a highly plastic and dynamic behavior. In plasmid vectors, we found a high density of repeats within eukaryotic promoters and non-coding sequences. As a result of this in silico analysis, we detected a spontaneous recombination between two 21-bp direct repeats present in the human cytomegalovirus early enhancer/promoter (huCMV EEP) of the pCIneo plasmid. This finding is of particular importance, as the huCMV EEP is one of the most frequently used regulatory elements in plasmid vectors. Because pDNA integration into host gDNA can have adverse consequences in terms of plasmid processing and host safety, we also mapped several regions with high probability to mediate integration into the Escherichia coli or human genomes. Like repeated regions, some of these were located in non-coding regions of the plasmids, thus being preferential targets to be removed.

Keywords: Genetic instability; Deletion formation; Genome integration; DNA vaccine

Expression of the antimicrobial peptide cecropin fused with human lysozyme in Escherichia coli by Xue-mei Lu; Xiao-bao Jin; Jia-yong Zhu; Han-fang Mei; Yan Ma; Fu-jiang Chu; Yan Wang; Xiao-bo Li (pp. 2169-2176).

Lysozyme is an abundant, cationic antimicrobial protein that plays an important role in host defense. It targets the β (1–4) glycosidic bond between N-acetylglucosamine and N-acetylmuramic residues that make up peptidoglycan, making lysozyme highly active against Gram-positive bacteria. However, lysozyme alone is inactive against Gram-negative bacteria because it cannot reach the peptidoglycan layer. Cecropins are cationic molecules with a wide range of antimicrobial activities. The main target for these peptides is the cytoplasmic membrane. We resume that cecopin may disrupt the outer membrane, giving the enzyme access to the peptidoglycan in cell wall. So in the present study, novel hybrid protein combining Musca domestica cecropin (Mdc) with human lysozyme (Hly) was designed. The DNA sequence encoding recombination fusion protein Mdc–hly was cloned into the pET-32a vector for protein expression in Escherichia coli strain BL21 (DE3). The protein was expressed as a His-tagged fusion protein, and the Mdc–hly was released from the fusion by enterokinase cleavage and separated from the carrier thioredoxin. Antimicrobial activity assays showed that the recombinant fusion protein Mdc–hly has improved in vitro antimicrobial activity and action spectrum compared to Mdc and hly. Mdc–hly may have important potential application as a future safely administered human drug and food additive.

Keywords: Human lysozyme; Cecropin; Fusion protein; Expression

Expression of 1,3-propanediol oxidoreductase and its isoenzyme in Klebsiella pneumoniae for bioconversion of glycerol into 1,3-propanediol by Bin Zhuge; Cheng Zhang; Huiying Fang; Jian Zhuge; Kugen Permaul (pp. 2177-2184).

In the Klebsiella pneumoniae reduction pathway for 1,3-propanediol (1,3-PD) synthesis, glycerol is first dehydrated to 3-hydroxypropionaldehyde (3-HPA) and then reduced to 1,3-PD with NADH consumption. Rapid conversion of 3-HPA to 1,3-PD is one of the ways to improve the yield of 1,3-PD from glycerol and to avoid 3-HPA accumulation, which depends on enzyme activity of the reaction and the amount of reducing equivalents available from the oxidative pathway of glycerol. In the present study, the yqhD gene, encoding 3-propanediol oxidoreductase isoenzyme from Escherichia coli and the dhaT gene, encoding 3-propanediol oxidoreductase from K. pneumoniae were expressed individually and co-expressed in K. pneumoniae using the double tac promoter expression plasmid pEtac-dhaT-tac-yqhD. The three resultant recombinant strains (K. pneumoniae/pEtac-yqhD, K. pneumoniae/pEtac-dhaT, and K. pneumoniae/pEtac-dhaT-tac-yqhD) were used for fermentation studies. Experimental results showed that the peak values for 3-HPA production in broth of the three recombinant strains were less than 25% of that of the parent strain. Expression of dhaT reduced formation of by-products (ethanol and lactic acid) and increased molar yield of 1,3-PD slightly, while expression of yqhD did not enhance molar yield of 1,3-PD, but increased ethanol concentration in broth as NADPH participation in transforming 3-HPA to 1,3-PD allowed more cellular NADH to be used to produce ethanol. Co-expression of both genes therefore decreased by-products and increased the molar yield of 1,3-PD by 11.8%, by catalyzing 3-HPA conversion to 1,3-propanediol using two cofactors (NADH and NADPH). These results have important implications for further studies involving use of YqhD and DhaT for bioconversion of glycerol into 1,3-PD.

Keywords: 1,3-Propanediol; 1,3-Propanediol oxidoreductase; 1,3-Propanediol oxidoreductase isoenzyme; Coexpression; K. pneumoniae

Improvement of polyunsaturated fatty acids synthesis by the coexpression of CYB5 with desaturase genes in Saccharomyces cerevisiae by Hisashi Yazawa; Hitoshi Iwahashi; Yasushi Kamisaka; Kazuyoshi Kimura; Hiroshi Uemura (pp. 2185-2193).

Since Saccharomyces cerevisiae contains Δ9 fatty acid desaturase (OLE1) as a sole fatty acid desaturase, it produces saturated and monounsaturated fatty acids of 16- and 18-carbon compounds. We showed earlier that Kluyveromyces lactis Δ12 (KlFAD2) and ω3 (KlFAD3) fatty acid desaturase genes enabled S. cerevisiae to make also polyunsaturated fatty acids (PUFAs), linoleic (18:2n-6), and α-linolenic (18:3n-3) acids. Unlike Δ9 fatty acid desaturase Ole1p, the two added fatty acid desaturases (KlFAD2and KlFAD3) do not contain a cytochrome b5 domain, and we now report on effects of the overexpression of K. lactis and S. cerevisiae cytochrome b5 (CYB5) genes as well as temperature effects on PUFA synthesis. Without extra cytochrome b5, while PUFA synthesis is significant at low temperature (20 °C), it was marginal at 30 °C. Overexpression of cytochrome b5 at 20 °C did not affect the fatty acid synthesis so much, but it significantly enhanced the synthesis of PUFA at 30 °C.

Keywords: S. cerevisiae ; Polyunsaturated fatty acids; FAD2 ; FAD3 ; Fatty acid desaturase; Cytochrome b5

Accumulation of gene-targeted Bacillus subtilis mutations that enhance fermentative inosine production by Takayuki Asahara; Yukiko Mori; Natalia P. Zakataeva; Vitaliy A. Livshits; Ken-ichi Yoshida; Kiyoshi Matsuno (pp. 2195-2207).

In order to test a possible approach to enhance fermentative inosine production by Bacillus subtilis, seven gene-targeted mutations were introduced in the laboratory standard strain168 in a stepwise fashion. The mutations were employed in order to prevent inosine 5′-monophosphate (IMP) from being consumed for AMP and GMP synthesis, to minimize inosine degradation, and to expand the intracellular IMP pool. First, the genes for adenylosuccinate synthase (purA) and IMP dehydrogenase (guaB) were inactivated. Second, two genes for purine nucleoside phosphorylase, punA and deoD, were inactivated. Third, to enhance purine nucleotide biosynthesis, the pur operon repressor PurR and the 5′-UTR of the operon, containing the guanine riboswitch, were disrupted. Finally, the -10 sequence of the pur promoter was optimized to elevate its transcription level. The resulting mutant was capable of producing 6 g/L inosine from 30 g/L glucose in culture broth without the detectable by-production of hypoxanthine. This indicates the validity of this approach for the breeding of the next generation of B. subtilis strains for industrial nucleoside production.

Keywords: B. subtilis ; Fermentation; Inosine; Purine nucleoside phosphorylase; Purine operon

A proteomic and transcriptional view of acidogenic and solventogenic steady-state cells of Clostridium acetobutylicum in a chemostat culture by Holger Janssen; Christina Döring; Armin Ehrenreich; Birgit Voigt; Michael Hecker; Hubert Bahl; Ralf-Jörg Fischer (pp. 2209-2226).

The complex changes in the life cycle of Clostridium acetobutylicum, a promising biofuel producer, are not well understood. During exponential growth, sugars are fermented to acetate and butyrate, and in the transition phase, the metabolism switches to the production of the solvents acetone and butanol accompanied by the initiation of endospore formation. Using phosphate-limited chemostat cultures at pH 5.7, C. acetobutylicum was kept at a steady state of acidogenic metabolism, whereas at pH 4.5, the cells showed stable solvent production without sporulation. Novel proteome reference maps of cytosolic proteins from both acidogenesis and solventogenesis with a high degree of reproducibility were generated. Yielding a 21% coverage, 15 protein spots were specifically assigned to the acidogenic phase, and 29 protein spots exhibited a significantly higher abundance in the solventogenic phase. Besides well-known metabolic proteins, unexpected proteins were also identified. Among these, the two proteins CAP0036 and CAP0037 of unknown function were found as major striking indicator proteins in acidogenic cells. Proteome data were confirmed by genome-wide DNA microarray analyses of the identical cultures. Thus, a first systematic study of acidogenic and solventogenic chemostat cultures is presented, and similarities as well as differences to previous studies of batch cultures are discussed.

Keywords: Phosphate-limited chemostat; Acidogenesis; Solventogenesis; Proteome reference maps; Transcriptome; CAP0037 and CAP0036

Regulation of acetoin and 2,3-butanediol utilization in Bacillus licheniformis by Trung Nguyen Thanh; Britta Jürgen; Melanie Bauch; Manuel Liebeke; Michael Lalk; Armin Ehrenreich; Stefan Evers; Karl-Heinz Maurer; Haike Antelmann; Florian Ernst; Georg Homuth; Michael Hecker; Thomas Schweder (pp. 2227-2235).

The acoABCL and acuABC operons of Bacillus licheniformis DSM13 are strongly induced at the transcriptional level during glucose starvation conditions. Primer extension analyses of this study indicate that the acoABCL operon is controlled by a sigmaL-dependent promoter and the acuABC operon by a sigmaA-dependent promoter. Transcription at the acoA promoter is repressed by glucose but induced by acetoin as soon as the preferred carbon source glucose is exhausted. The acuA promoter shows a similar induction pattern, but its activity is independent from the presence of acetoin. It is demonstrated that the acoABCL operon is mainly responsible for acetoin and 2,3-butanediol degradation in B. licheniformis.

Keywords: Bacillus licheniformis ; Glucose starvation; Overflow metabolism; Acetoin

Chitosan increases conidiation in fungal pathogens of invertebrates by Javier Palma-Guerrero; Eduardo Larriba; Berenice Güerri-Agulló; Hans-Börje Jansson; Jesus Salinas; Luis Vicente Lopez-Llorca (pp. 2237-2245).

Antifungal activity of chitosan on plant pathogenic fungi has been widely studied, but little is known about the effect of chitosan on fungal biocontrol agents. In this work, we characterize the increase of conidiation induced by chitosan in fungal pathogens of invertebrates (FPI). Chitosan increased conidiation of FPI, including Beauveria bassiana, widely used as mycoinsecticide, and did not affect conidia viability or pathogenicity. Increased conidiation induced by chitosan is shown to be concentration dependent and is not associated to growth inhibition as observed for the mycoparasitic fungus Trichoderma harzianum. Real-time reverse transcription polymerase chain reaction was used to study transcript levels of two genes involved in conidiation in B. bassiana, the regulatory G protein signaling gene Bbrgs1 and the hydrophobin gene hyd1, at different chitosan concentrations. Higher levels of Bbrgs1 and hyd1 transcripts were detected on chitosan-amended media. No correlation with chitosan concentration was observed for expression of Bbrgs1 unlike hyd1. Bbrgs1 deletion mutant ∆Bbrgs1 showed that chitosan-induced conidiation is independent of Bbrgs1, suggesting an alternative mechanism controlling conidiation in B. bassiana. Our data supports that sporulation increases by chitosan, with spores retaining their viability and pathogenicity, which makes chitosan a suitable compound to increase conidia production in fungi with applications in fungal biotechnology.

Keywords: Chitosan; Conidiation; Entomopathogenic fungi; Nematophagous fungi; Beauveria bassiana ; Biological control

Production of polyhydroxyalkanoates by Escherichia coli mutants with defected mixed acid fermentation pathways by Jia Jian; Shao-Qin Zhang; Zhen-Yu Shi; Wei Wang; Guo-Qiang Chen; Qiong Wu (pp. 2247-2256).

A series of Escherichia coli BW25113 mutants with reduced mixed acid fermentation were constructed. Genes ackA-pta, poxB, ldhA, adhE, and pflB encoding acetate kinase, phosphate acetyltransferase, pyruvate oxidase, d-lactate dehydrogenase, acetaldehyde dehydrogenase, and pyruvate formate-lyase, respectively, were deleted successively. When grown under microaerobic condition, the mutants reduced approximately 90% acetate excretion after the deletion of genes ackA-pta and poxB. Production of lactate, ethanol, and formate was also significantly reduced after the deletion of genes ldhA, adhE, and pflB, respectively. The accumulation of biomass and poly(3-hydroxybutyrate) (PHB) were significantly enhanced after deleting the mixed acid fermentation. E. coli mutant BWapld with deletions of ackA-pta, poxB, ldhA, and adhE produced twice the cell dry weight (CDW) and 3.5 times of PHB compared with its wild-type under microaerobic conditions. E. coli mutant BWapl with deletions of ackA-pta, poxB, and ldhA also achieved nearly twice CDW and three times of PHB content in comparison to the wild-type during 48 h static cultivation. Production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] was observed in the mutants under static cultivation. E. coli mutant BWapld could produce approximately 50 wt.% P(3HB-co-3HV) consisting of 5 mol% of 3-hydroxyvalerate (3HV) under aerobic conditions, when the seed culture was inoculated at an appropriate time. When ackA-pta, poxB, ldhA, adhE, and pflB were deleted, E. coli mutant BWapldf accumulated over 70 wt.% P(3HB-co-3HV) consisting of 8 mol% 3HV under aerobic conditions.

Keywords: PHB; P(3HB-co-3HV); Escherichia coli ; Polyhydroxyalkanoates; Mixed acid fermentation; Metabolic engineering

Production of conjugated linoleic acid and conjugated linolenic acid isomers by Bifidobacterium species by Lara Gorissen; Katleen Raes; Stefan Weckx; Dirk Dannenberger; Frédéric Leroy; Luc De Vuyst; Stefaan De Smet (pp. 2257-2266).

Conjugated linoleic acid (CLA) and conjugated linolenic acid (CLNA) isomers have attracted great interest because of their potential health benefits. Formation of CLA and CLNA takes place in the rumen during biohydrogenation. Several studies have indicated that certain types of intestinal bacteria, including bifidobacteria, are able to convert linoleic acid (LA) to CLA. The role of intestinal bacteria in the formation of CLNA isomers is largely unknown. In the present study, a screening of 36 different Bifidobacterium strains for their ability to produce CLA and CLNA from free LA and α-linolenic acid (LNA), respectively, was performed. The strains were grown in MRS broth, to which LA or LNA (0.5 mg ml⁻¹) were added after 7 h of bacterial growth. Cultures were further incubated at 37°C for 72 h. Six strains (four Bifidobacterium breve strains, a Bifidobacterium bifidum strain and a Bifidobacterium pseudolongum strain) were able to produce different CLA and CLNA isomers. Conversion percentages varied from 19.5% to 53.5% for CLA production and from 55.6% to 78.4% for CLNA production among these strains. The CLA isomers produced were further identified with Ag⁺-HPLC. LA was mainly converted to t9t11-CLA and c9t11-CLA. The main CLNA isomers were identified with GC-MS as c9t11c15-CLNA and t9t11c15-CLNA.

Keywords: Bifidobacteria; Conjugated fatty acid; CLA; CLNA; GC-MS; Ag⁺-HPLC

Typical methanogenic inhibitors can considerably alter bacterial populations and affect the interaction between fatty acid degraders and homoacetogens by Kewei Xu; He Liu; Xiufen Li; Jian Chen; Aijie Wang (pp. 2267-2279).

The effects of two typical methanogenic inhibitors [2-bromoethanesulfonate (BES) and chloroform (CHCl₃)] on the bacterial populations were investigated using molecular ecological techniques. Terminal restriction fragment length polymorphism analyses (T-RFLP) in combination with clone library showed that both the toxicants not only inhibited methanogenic activity but also considerably altered the bacterial community structure. Species of low % G + C Gram-positive bacteria (Clostridiales), high % G + C Actinomycetes, and uncultured Chloroflexi showed relatively greater tolerance of CHCl₃, whereas the BES T-RFLP patterns were characterized by prevalence of Geobacter hydrogenophilus and homoacetogenic Moorella sp. In addition, due to indirect thermodynamic inhibition caused by high hydrogen partial pressures, the growth of obligately syntrophic acetogenic Syntrophomonas and Syntrophobacter was also affected by selective inhibition of methanogenesis. Interestingly, by comparing the fermentative intermediates detected in BES- and CHCl₃-treated experiments, it was furthermore found that when methanogenesis is specifically inhibited, the syntrophic interaction between hydrogen-producing fatty acid degraders and hydrogen-utilizating homoacetogens seemed to be strengthened.

Keywords: Methanogenic inhibitor; T-RFLP; Redundancy analysis; Fluorescence in situ hybridization; Syntrophic interaction

Diversity of the total bacterial community associated with Ghanaian and Brazilian cocoa bean fermentation samples as revealed by a 16 S rRNA gene clone library by Tamara Garcia-Armisen; Zoi Papalexandratou; Hugo Hendryckx; Nicholas Camu; Gino Vrancken; Luc De Vuyst; Pierre Cornelis (pp. 2281-2292).

Cocoa bean fermentation is a spontaneous process involving a succession of microbial activities, starting with yeasts, followed by lactic acid bacteria and acetic acid bacteria. So far, all microbiological studies about cocoa bean fermentation were based on culture-dependent (isolation, cultivation, and identification), or, more recently, culture-independent (PCR-DGGE, or polymerase chain reaction denaturing gradient gel electrophoresis) methods. Using a metagenomic approach, total DNA was extracted from heap and box fermentations at different time points and from different locations (Ghana and Brazil, respectively) to generate a 16 S rDNA clone library that was sequenced. The sequencing data revealed a low bacterial diversity in the fermentation samples and were in accordance with the results obtained through culture-dependent and a second, culture-independent analysis (PCR-DGGE), suggesting that almost all bacteria involved in the fermentation process are cultivable. One exception was the identification by 16 S rDNA library sequencing of Gluconacetobacter species of acetic acid bacteria that were not detected by the two other approaches. The presence of Enterobacteriaceae related to Erwinia/Pantoea/Tatumella, as revealed by 16 S rDNA library sequencing, suggests an impact of these bacteria on fermentation.

Keywords: Cocoa fermentation; Lactic acid bacteria; Acetic acid bacteria; Enterobacteria; 16 S rRNA gene clone library sequencing; PCR-DGGE

Extending the alkene substrate range of vinyl chloride utilizing Nocardioides sp. strain JS614 with ethene oxide by Anne E. Taylor; Daniel J. Arp; Peter J. Bottomley; Lewis Semprini (pp. 2293-2302).

Nocardioides sp. strain JS614 grows on the C₂ alkenes ethene (Eth), vinyl chloride, and vinyl fluoride as sole carbon sources. The presence of 400–800 μM ethene oxide (EtO) extended the growth substrate range to propene (C₃) and butene (C₄). Propene-dependent growth of JS614 was CO₂ dependent and was prevented by the carboxylase/reductase inhibitor 2-bromoethanesulfonic acid, sodium salt (BES), while growth on Eth was not CO₂ dependent or BES sensitive. Although unable to promote growth, both propene and propene oxide (PrO)-induced expression of the genes encoding the alpha subunit of alkene monooxygenase (etnC) and epoxyethane CoM transferase (etnE) to similar levels as did Eth and EtO. Propene was transformed by Eth-grown and propene-grown/EtO-induced JS614 to PrO at a rate 4.2 times faster than PrO was consumed. As a result PrO accumulated in growth medium to 900 μM during EtO-induced growth on propene. PrO (50–100 μM) exerted inhibitory effects on growth of JS614 on both acetate and Eth, and on EtO-induced growth on Eth. However, higher EtO concentrations (300–400 μM) overcame the negative effects of PrO on Eth-dependent growth.

Keywords: Propene; Propylene oxide; Ethene oxide; Nocardioides sp. strain JS614

Improving the recovery of qPCR-grade DNA from sludge and sediment by Sébastien Bonot; Sophie Courtois; Jean-Claude Block; Christophe Merlin (pp. 2303-2311).

DNA extraction is often considered as the limiting step of most molecular approaches in ecology and environmental microbiology. Ten existing DNA extraction protocols were compared for recovery of DNA from sludge and a modified version of the protocol described by Porteous et al. (Mol Ecol 6:787–791, 1997) was determined to be the best method for recovery of DNA suitable for PCR. In this respect, it appeared that the commonly used guanidine isothiocyanate could impair the quality of the extracted DNA unless its concentration is lowered. Second, conditioning the samples as liquors as opposed to pellets critically impacts the outcome of the extraction. The suitability of the modified Porteous protocol for quantitative PCR applications is demonstrated in a series of experiments showing the absence of interfering coextracted inhibitors and the linear correspondence between the concentrations of input target DNA and PCR product. Interestingly, it is also shown that the nature of the environmental matrices affects the recovery yield of both circular plasmids and chromosomal DNA, resulting in an apparent fluctuation of the plasmid copy number per cell. This means that quantitative data obtained by PCR remain comparable as long as they apply to an identical target sequence extracted from a similar environment and amplified under the same conditions.

Keywords: DNA extraction; qPCR; Sludge; Sediment; pB10 plasmid

Identifying diazotrophs by incorporation of nitrogen from ¹⁵N₂ into RNA by Sarah L. Addison; Ian R. McDonald; Gareth Lloyd-Jones (pp. 2313-2322).

The diversity and abundance of active diazotrophs was investigated in a New Zealand pulp and paper wastewater by enrichment with ¹⁵N₂. Purified ¹⁵N-RNA was analysed by reverse transcription, molecular cloning and sequence analysis of 16S rRNA to reveal a diverse community of bacteria as indicated by a Shannon Weaver Index value of > 2.8. The major class represented in the enriched culture were the γ-Proteobacteria at 85% with a secondary group of the phylum Firmicutes present at 8.2%, the remaining sequences were affiliated with the α- and β-Proteobacterial classes (1.4% and 4.3%, respectively). Three dominant genera, Aeromonas, Pseudomonas and Bacillus, were identified by comparison with published sequences and phylogenetic analysis. To confirm that representatives of the taxonomic groups identified from the active enriched nitrogen-fixing community were capable of fixing nitrogen Aeromonas and Pseudomonas species were cultivated and shown to possess nifH genes. In wastewater, fluorescence in situ hybridisation probing revealed that the dominant nitrogen-fixing population identified in this study were present in the population, but at lower levels. The population is, therefore, reliant on a small sub-population of diazotrophs to supply the community's nitrogen needs above that already present in the wastewater.

Keywords: Nitrogen fixing; Stable isotope probing (SIP); Wastewater; Pseudomonas ; ¹⁵N₂-labelling

Selection and characterization of DNA aptamers with binding selectivity to Campylobacter jejuni using whole-cell SELEX by Hari P. Dwivedi; R. Derike Smiley; Lee-Ann Jaykus (pp. 2323-2334).

The need for pre-analytical sample processing prior to the application of rapid molecular-based detection of pathogens in food and environmental samples is well established. Although immunocapture has been applied in this regard, alternative ligands such as nucleic acid aptamers have advantages over antibodies such as low cost, ease of production and modification, and comparable stability. To identify DNA aptamers demonstrating binding specificity to Campylobacter jejuni cells, a whole-cell Systemic Evolution of Ligands by EXponential enrichment (SELEX) method was applied to a combinatorial library of FAM-labeled single-stranded DNA molecules. FAM-labeled aptamer sequences with high binding affinity to C. jejuni A9a as determined by flow cytometric analysis were identified. Aptamer ONS-23, which showed particularly high binding affinity in preliminary studies, was chosen for further characterization. This aptamer displayed a dissociation constant (K d value) of 292.8 ± 53.1 nM with 47.27 ± 5.58% cells fluorescent (bound) in a 1.48-μM aptamer solution. Binding assays to assess the specificity of aptamer ONS-23 showed high binding affinity (25–36%) for all other C. jejuni strains screened (inclusivity) and low apparent binding affinity (1–5%) with non-C. jejuni strains (exclusivity). Whole-cell SELEX is a promising technique to design aptamer-based molecular probes for microbial pathogens without tedious isolation and purification of complex markers or targets.

Keywords: Food-borne pathogen; Molecular-based assay; Rapid microbial method; Aptamers

Discovery of commonly existing anode biofilm microbes in two different wastewater treatment MFCs using FLX Titanium pyrosequencing by Tae Kwon Lee; Tuan Van Doan; Kyuseon Yoo; Soojung Choi; Changwon Kim; Joonhong Park (pp. 2335-2343).

In microbial fuel cells (MFC), wastewater is used as a fuel while organic and nutrient pollution in the wastewater are being treated. In the present study, commonly existing microbial populations in MFC anode biofilms were identified using high throughput FLX Titanium pyrosequencing to provide much more extensive information of anode microbial communities than previously possible. Using 454 FLX Titanium pyrosequencing, 31,901 sequence reads with an average length of 430 bp were obtained from 16S rRNA gene amplicons from different MFC anodes with different substrate exposure and respiration conditions, and microbial community structure and population identification were then analyzed using high-throughput bioinformatics methods. Although community profiles from the four samples were significantly different, hierarchical clustering analysis revealed several bacterial populations that commonly exist in the anode biofilm samples. These bacteria were phylogenetically distributed in Firmicutes and the alpha-, beta-, gamma-, and delta-subclasses of Proteobacteria. In addition, most of these populations were found to be novel anode bacteria and exhibited oligotrophic or substrate-concentration-insensitive growth. These findings suggest that commonly existing anode bacteria may play a key role in the stable operations of MFCs, combined with wastewater treatment plants, under fluctuating substrate and respiration conditions.

Keywords: Microbial Fuel Cell (MFC); Microbial community; Pyrosequencing; Anode biofilm; Renewable energy; Wastewater

Yeasts isolated from olive mill wastewaters from southern Italy: technological characterization and potential use for phenol removal by Milena Sinigaglia; Nilde Di Benedetto; Antonio Bevilacqua; Maria Rosaria Corbo; Angela Capece; Patrizia Romano (pp. 2345-2354).

Olive mill wastewater (OMW) samples from two traditional varieties (Peranzana and Ogliarola Garganica) of Apulian region (southern Italy) and produced through continuous and traditional methods were microbiologically and chemically examined; thus, 104 yeasts were isolated and selected for further analyses. The strains were identified as Candida boidinii, Pichia holstii, Pichia membranifaciens, and Saccharomyces cerevisiae and analyzed to assess their suitability to metabolize phenols. Based on phenol metabolism, 27 strains were selected and inoculated into OMW aliquots to determine their ability to reduce phenols in vivo; then, five strains (identified with the codes 682—C. boidinii and 625, 642, 647, and 941—P. holstii) were used as a cocktail in wastewaters for a final validation step. In this last experiment, the effects of the temperature (10–30°C) and (NH₄)₂SO₄ (0.0–6.0 g l⁻¹) were studied through a central composite design approach, and the results highlighted that the cocktail was able to reduce phenols by 40% at 10°C with 6.0 g l⁻¹ of (NH₄)₂SO₄ added.

Keywords: Olive mill wastewater; Yeasts; Bioremediation; Phenols; Microbial cocktail

Copper enhances the activity and salt resistance of mixed methane-oxidizing communities by David van der Ha; Sven Hoefman; Pascal Boeckx; Willy Verstraete; Nico Boon (pp. 2355-2363).

Effluents of anaerobic digesters are an underestimated source of greenhouse gases, as they are often saturated with methane. A post-treatment with methane-oxidizing bacterial consortia could mitigate diffuse emissions at such sites. Semi-continuously fed stirred reactors were used as model systems to characterize the influence of the key parameters on the activity of these mixed methanotrophic communities. The addition of 140 mg L⁻¹ NH ₄ ⁺ –N had no significant influence on the activity nor did a temperature increase from 28°C to 35°C. On the other hand, addition of 0.64 mg L⁻¹ of copper(II) increased the methane removal rate by a factor of 1.5 to 1.7 since the activity of particulate methane monooxygenase was enhanced. The influence of different concentrations of NaCl was also tested, as effluents of anaerobic digesters often contain salt levels up to 10 g NaCl L⁻¹. At a concentration of 11 g NaCl L⁻¹, almost no methane-oxidizing activity was observed in the reactors without copper addition. Yet, reactors with copper addition exhibited a sustained activity in the presence of NaCl. A colorimetric test based on naphthalene oxidation showed that soluble methane monooxygenase was inhibited by copper, suggesting that the particulate methane monooxygenase was the active enzyme and thus more salt resistant. The results obtained demonstrate that the treatment of methane-saturated effluents, even those with increased ammonium (up to 140 mg L⁻¹ NH ₄ ⁺ –N) and salt levels, can be mitigated by implementation of methane-oxidizing microbial consortia.

Keywords: Greenhouse gas; Biofilter; Osmotic pressure; Salt stress

Electricity generation from mixed volatile fatty acids using microbial fuel cells by Shao-Xiang Teng; Zhong-Hua Tong; Wen-Wei Li; Shu-Guang Wang; Guo-Ping Sheng; Xian-Yang Shi; Xian-Wei Liu; Han-Qing Yu (pp. 2365-2372).

Fermentative hydrogen production, as a process for clean energy recovery from organic wastewater, is limited by its low hydrogen yield due to incomplete conversion of substrates, with most of the fermentation products being volatile fatty acids (VFAs). Thus, further recovery of the energy from VFAs is expected. In this work, microbial fuel cell (MFC) was applied to recover energy in the form of electricity from mixed VFAs of acetate, propionate, and butyrate. Response surface methodology was adopted to investigate the relative contribution and possible interactions of the three components of VFAs. A stable electricity generation was demonstrated in MFCs after the enrichment of electrochemically active bacteria. Analysis showed that power density was more sensitive to the composition of mixed VFAs than coulombic efficiency. The electricity generation could mainly be attributed to the portion of acetate and propionate. However, the two components showed an antagonistic effect when propionate exceeded 19%, causing a decrease in coulombic efficiency. Butyrate was found to exert a negative impact on both power density and coulombic efficiency. Denaturing gradient gel electrophoresis profiles revealed the enrichment of electrochemically active bacteria from the inoculum sludge. Proteobacteria (Beta-, Delta-) and Bacteroidetes were predominant in all VFA-fed MFCs. Shifts in bacterial community structures were observed when different compositions of VFA mixtures were used as the electron donor. The overall electron recovery efficiency may be increased from 15.7% to 27.4% if fermentative hydrogen production and MFC processes are integrated.

Keywords: Anaerobic fermentation; Microbial fuel cell (MFC); Response surface methodology (RSM); Volatile fatty acids (VFAs)

Erratum to: Analysis of DNA repeats in bacterial plasmids reveals the potential for recurrent instability events by Pedro H. Oliveira; Kristala Jones Prather; Duarte M. F. Prazeres; Gabriel A. Monteiro (pp. 2373-2373).

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Applied Microbiology and Biotechnology (v.87, #6)

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Applied Microbiology and Biotechnology (v.87, #6)