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Applied Microbiology and Biotechnology (v.89, #6)

Fungal arabinan and l-arabinose metabolism by Bernhard Seiboth; Benjamin Metz (pp. 1665-1673).

l-Arabinose is the second most abundant pentose beside d-xylose and is found in the plant polysaccharides, hemicellulose and pectin. The need to find renewable carbon and energy sources has accelerated research to investigate the potential of l-arabinose for the development and production of biofuels and other bioproducts. Fungi produce a number of extracellular arabinanases, including α-l-arabinofuranosidases and endo-arabinanases, to specifically release l-arabinose from the plant polymers. Following uptake of l-arabinose, its intracellular catabolism follows a four-step alternating reduction and oxidation path, which is concluded by a phosphorylation, resulting in d-xylulose 5-phosphate, an intermediate of the pentose phosphate pathway. The genes and encoding enzymes l-arabinose reductase, l-arabinitol dehydrogenase, l-xylulose reductase, xylitol dehydrogenase, and xylulokinase of this pathway were mainly characterized in the two biotechnological important fungi Aspergillus niger and Trichoderma reesei. Analysis of the components of the l-arabinose pathway revealed a number of specific adaptations in the enzymatic and regulatory machinery towards the utilization of l-arabinose. Further genetic and biochemical analysis provided evidence that l-arabinose and the interconnected d-xylose pathway are also involved in the oxidoreductive degradation of the hexose d-galactose.

Keywords: Trichoderma reesei ; Aspergillus niger ; α-l-arabinofuranosidase; d-xylose; d-galactose

Native and artificial forisomes: functions and applications by Gundula A. Noll; Boje Müller; Antonia M. Ernst; Boris Rüping; Richard M. Twyman; Dirk Prüfer (pp. 1675-1682).

Forisomes are remarkable protein bodies found exclusively in the phloem of the Fabaceae. When the phloem is wounded, forisomes are converted from a condensed to a dispersed state in an ATP-independent reaction triggered by Ca²⁺, thereby plugging the sieve tubes and preventing the loss of photoassimilates. Potentially, forisomes are ideal biomaterials for technical devices because the conformational changes can be replicated in vitro and are fully reversible over a large number of cycles. However, the development of technical devices based on forisomes has been hampered by the laborious and time-consuming process of purifying native forisomes from plants. More recently, the problem has been overcome by the production of recombinant artificial forisomes. This is a milestone in the development of forisome-based devices, not only because large quantities of homogeneous forisomes can be produced on demand, but also because their properties can be tailored for particular applications. In this review, we discuss the physical and molecular properties of native and artificial forisomes, focusing on their current applications in technical devices and potential developments in the future.

Keywords: Artificial forisomes; Sieve element occlusion; Phloem; Recombinant production; Smart biomaterial; Mechanoprotein

Bioactive metabolite production and stress-related hormones in Devil’s claw cell suspension cultures grown in bioreactors by Milen Georgiev; Jutta Ludwig-Müller; Jost Weber; Nina Stancheva; Thomas Bley (pp. 1683-1691).

In a previous report, we showed that cell cultures of Harpagophytum procumbens, a South African plant with high medicinal value, accumulate high amounts of anti-inflammatory phenylethanoid glycosides during cultivation in shake-flasks. The aim of the present study was to transfer the phenylethanoid biosynthetic process to a 3-L stirred tank reactor and a 1-L glass-column bioreactor (operated with pulsed aeration). We found that, with stepwise increases in aeration, the stirred tank reactor yielded similar productivities of verbascoside (the major phenylethanoid glycoside in the cells) to those reported for shake-flask cultures (55.68 vs. 54.78 mg verbascoside/L/day, respectively). Transfer in the pulse-aerated column reactor resulted in 165.42 mg verbascoside/L/day, one of the highest yields reported to date. Further, to evaluate the physiological status of the suspended cells in the bioreactors cultures, we examined their hormone levels and compared them to those of cells in shake-flask cultures. While indole-3-acetic acid levels did not differ significantly between the bioreactor and shake-flask cultures, there were considerable differences in their levels of abscisic, jasmonic, and salicylic acids. These results are discussed with respect to relative stress levels in the different cultivation systems.

Keywords: Harpagophytum procumbens ; Indole-3-acetic acid; Pulse-aerated column bioreactor; Phenylethanoid glycosides; Stress-related hormones

Phenolic compounds as enhancers in enzymatic and electrochemical oxidation of veratryl alcohol and lignins by María Díaz-González; Teresa Vidal; Tzanko Tzanov (pp. 1693-1700).

Sixteen phenolic compounds, 14 of which naturally occurring, were compared to the synthetic 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) and violuric acid (VA) in terms of their ability to act as mediators/enhancers in: (1) laccase oxidation of veratryl alcohol as a lignin model compound, and (2) electrochemical oxidation of kraft and flax lignins. HPLC analysis revealed that the syringyl-type phenols methyl syringate and acetosyringone were the most efficient natural enhancers in the laccase oxidation of veratryl alcohol. Both compounds, though far from the performance of ABTS were able to generate veratraldehyde in amount similar to that obtained with VA. By contrast, the best performing phenolic enhancers for the electrochemical oxidation of lignins were sinapinaldehyde, vanillin, acetovanillone, and syringic acid. Catalytic efficiencies close to those achieved with ABTS and VA were calculated for these phenolic compounds.

Keywords: Phenolic compounds; Laccase; Veratryl alcohol; Lignin; Oxidation; Cyclic voltammetry

Influence of growth regulators and elicitors on cell growth and α-tocopherol and pigment productions in cell cultures of Carthamus tinctorius L. by Smita P. Chavan; Vinayak H. Lokhande; Kirti M. Nitnaware; Tukaram D. Nikam (pp. 1701-1707).

The present study examined the effects of plant growth hormones, incubation period, biotic (Trametes versicolor, Mucor sp., Penicillium notatum, Rhizopus stolonifer, and Fusarium oxysporum) and abiotic (NaCl, MgSO₄, FeSO₄, ZnSO₄, and FeCl₃) elicitors on cell growth and α-tocopherol and pigment (red and yellow) productions in Carthamus tinctorius cell cultures. The cell growth and α-tocopherol and pigment contents improved significantly on Murashige and Skoog (MS) liquid medium containing 50.0 μM α-naphthalene acetic acid (NAA) and 2.5 μM 6-Benzyladenine (BA) at 28 days of incubation period. Incorporation of T. versicolor (50 mg l⁻¹) significantly enhanced the production of α-tocopherol (12.7-fold) and red pigment (4.24-fold). Similarly, supplementation of 30 mg l⁻¹ T. versicolor (7.54-fold) and 70 mg l⁻¹ Mucor sp. (7.40-fold) significantly increased the production of yellow pigment. Among abiotic elicitors, NaCl (50–70 mg l⁻¹) and MgSO₄ (10–30 mg l⁻¹) significantly improved production of α-tocopherol (1.24-fold) and red pigment (20-fold), whereas yellow pigment content increased considerably by all the abiotic elicitor treatments. Taken together, the present study reports improved productions of α-tocopherol and the pigment as a stress response of safflower cell cultures exposed to these elicitors.

Keywords: Carthamus tinctorius ; Cell culture; Elicitors; α-Tocopherol; Red and yellow pigment

Titer improvement of iso-migrastatin in selected heterologous Streptomyces hosts and related analysis of mRNA expression by quantitative RT–PCR by Dong Yang; Xiangcheng Zhu; Xueyun Wu; Zhiyang Feng; Lei Huang; Ben Shen; Zhinan Xu (pp. 1709-1719).

iso-Migrastatin (iso-MGS) has been actively pursued recently as an outstanding candidate of antimetastasis agents. Having characterized the iso-MGS biosynthetic gene cluster from its native producer Streptomyces platensis NRRL 18993, we have recently succeeded in producing iso-MGS in five selected heterologous Streptomyces hosts, albeit the low titers failed to meet expectations and cast doubt on the utility of this novel technique for large-scale production. To further explore and capitalize on the production capacity of these hosts, a thorough investigation of these five engineered strains with three fermentation media for iso-MGS production was undertaken. Streptomyces albus J1074 and Streptomyces lividans K4-114 were found to be preferred heterologous hosts, and subsequent analysis of carbon and nitrogen sources revealed that sucrose and yeast extract were ideal for iso-MGS production. After the initial optimization, the titers of iso-MGS in all five hosts were considerably improved by 3–18-fold in the optimized R2YE medium. Furthermore, the iso-MGS titer of S. albus J1074 (pBS11001) was significantly improved to 186.7 mg/L by a hybrid medium strategy. Addition of NaHCO₃ to the latter finally afforded an optimized iso-MGS titer of 213.8 mg/L, about 5-fold higher than the originally reported system. With S. albus J1074 (pBS11001) as a model host, the expression of iso-MGS gene cluster in four different media was systematically studied via the quantitative RT–PCR technology. The resultant comparison revealed the correlation of gene expression and iso-MGS production for the first time; synchronous expression of the whole gene cluster was crucial for optimal iso-MGS production. These results reveal new insights into the iso-MGS biosynthetic machinery in heterologous hosts and provide the primary data to realize large-scale production of iso-MGS for further preclinical studies.

Keywords: iso-Migrastatin; Heterologous Streptomyces hosts; Fermentation optimization; Quantitative RT–PCR

Production of 7,10-dihydroxy-8(E)-octadecenoic acid from olive oil by Pseudomonas aeruginosa PR3 by Min-Jung Suh; Ka-Yeon Baek; Beom-Soo Kim; Ching T. Hou; Hak-Ryul Kim (pp. 1721-1727).

Microbial modification of naturally occurring materials is one of the efficient ways to add new values to them. Hydroxylation of free unsaturated fatty acids by microorganism is a good example of those modifications. Among microbial strains studied for that purpose, a new bacterial isolate Pseudomonas aeruginosa PR3 has been well studied to produce several hydroxy fatty acids from different unsaturated fatty acids. Of those hydroxy fatty acids, 7,10-dihydroxy-8(E)-octadecenoic acid (DOD) was efficiently produced from oleic acid by strain PR3. However, it was highly plausible to use vegetable oil containing oleic acid rather than free oleic acid as a substrate for DOD production by strain PR3. In this study, we firstly tried to use olive oil containing high content of oleic acid as a substrate for DOD production. DOD production from olive oil was confirmed by structural determination with GC, TLC, and GC/MS analysis. DOD production yield from olive oil was 53.5%. Several important environmental factors were also tested. Galactose and glutamine were optimal carbon and nitrogen sources, and magnesium ion was critically required for DOD production from olive oil. Results from this study demonstrated that natural vegetable oils containing oleic acid could be used as efficient substrate for the production of DOD by strain PR3.

Keywords: Hydroxy fatty acid; Olive oil; Bioconversion; Pseudomonas aeruginosa ; DOD

Molasses as fermentation substrate for levan production by Halomonas sp. by Faruk Küçükaşik; Hande Kazak; Dilvin Güney; Ilaria Finore; Annarita Poli; Orhan Yenigün; Barbara Nicolaus; Ebru Toksoy Öner (pp. 1729-1740).

Levan is a homopolymer of fructose with many outstanding properties like high solubility in oil and water, strong adhesiveness, good biocompatibility, and film-forming ability. However, its industrial use has long been hampered by costly production processes which rely on mesophilic bacteria and plants. Recently, Halomonas sp. AAD6 halophilic bacteria were found to be the only extremophilic species producing levan at high titers in semi-chemical medium containing sucrose, and in this study, pretreated sugar beet molasses and starch molasses were both found to be feasible substitutes for sucrose. Five different pretreatment methods and their combinations were applied to both molasses types. Biomass and levan concentrations reached by the Halomonas sp. AAD6 cells cultivated on 30 g/L of pretreated beet molasses were 6.09 g dry cells/L and 12.4 g/L, respectively. When compared with literature, Halomonas sp. was found to stand out with its exceptionally high levan production yields on available fructose. Molecular characterization and monosaccharide composition studies confirmed levan-type fructan structure of the biopolymers. Rheological properties under different conditions pointed to the typical characteristics of low viscosity and pseudoplastic behaviors of the levan polymers. Moreover, levan polymer produced from molasses showed high biocompatibility and affinity with both cancerous and non-cancerous cell lines.

Keywords: Levan; Fructan; Halomonas ; Molasses; Sugar beet; Exopolysaccharide

Continuous d-lactic acid production by a novelthermotolerant Lactobacillus delbrueckii subsp. lactis QU 41 by Yukihiro Tashiro; Wataru Kaneko; Yanqi Sun; Keisuke Shibata; Kentaro Inokuma; Takeshi Zendo; Kenji Sonomoto (pp. 1741-1750).

We isolated and characterized a d-lactic acid-producing lactic acid bacterium (d-LAB), identified as Lactobacillus delbrueckii subsp. lactis QU 41. When compared to Lactobacillus coryniformis subsp. torquens JCM 1166 ^T and L. delbrueckii subsp. lactis JCM 1248 ^T, which are also known as d-LAB, the QU 41 strain exhibited a high thermotolerance and produced d-lactic acid at temperatures of 50 °C and higher. In order to optimize the culture conditions of the QU 41 strain, we examined the effects of pH control, temperature, neutralizing reagent, and initial glucose concentration on d-lactic acid production in batch cultures. It was found that the optimal production of 20.1 g/l d-lactic acid was acquired with high optical purity (>99.9% of d-lactic acid) in a pH 6.0-controlled batch culture, by adding ammonium hydroxide as a neutralizing reagent, at 43 °C in MRS medium containing 20 g/l glucose. As a result of product inhibition and low cell density, continuous cultures were investigated using a microfiltration membrane module to recycle flow-through cells in order to improve d-lactic acid productivity. At a dilution rate of 0.87 h⁻¹, the high cell density continuous culture exhibited the highest d-lactic acid productivity of 18.0 g/l/h with a high yield (ca. 1.0 g/g consumed glucose) and a low residual glucose (<0.1 g/l) in comparison with systems published to date.

Keywords: d-lactic acid fermentation; Lactobacillus delbrueckii subsp. lactis QU 41; Continuous culture; High cell density; Thermotolerant

Fermentation and microencapsulation of the nematophagous fungus Hirsutella rhossiliensis in a novel type of hollow beads by Anant V. Patel; Desiree Jakobs-Schönwandt; Thomas Rose; Klaus-Dieter Vorlop (pp. 1751-1760).

In this work, fermentation and formulation aspects of the nematophagous fungus Hirsutella rhossiliensis BBA were investigated. When incubated in 2% (w/w) glucose and 0.5% (w/w) yeast extract medium in a 1-L Erlenmeyer flask without baffles, heavy pellet formation was observed. Only 40% of the mycelium had a size less than 500 μm. When a flask with three baffles was used, the portion of mycelium <500 μm rose to 95%. In the next step, the influence of aeration rate and stirrer speed on production of finely dispersed mycelium in a stirred tank reactor was investigated. The best fermentation results were obtained at 0.4 vvm and 400 rpm stirrer speed with 90% mycelium <500 μm and 5 g/L biomass. Then, mycelium was microencapsulated in hollow beads based on sulfoethylcellulose (SEC). Experiments on the capsule nutrient reservoir showed that 15% (w/w) corn gluten and 0.5% (w/w) yeast extract could be replaced with 3% (w/w) autoclaved baker's yeast which was never used as capsule additive before. Radial growth of mycelium out of dried hollow beads containing 1% (w/w) biomass and 3% (w/w) baker's yeast was faster than for alginate beads containing equivalent amounts of biomass and yeast indicating a higher bio-control potential.

Keywords: Fermentation; Encapsulation; Formulation; Alginate; Sulfoethylcellulose; Hirsutella rhossiliensis ; Heterodera schachtii ; Biological control

Heterologous expression and characterization of a glucose-stimulated β-glucosidase from the termite Neotermes koshunensis in Aspergillus oryzae by Cristiane Akemi Uchima; Gaku Tokuda; Hirofumi Watanabe; Katsuhiko Kitamoto; Manabu Arioka (pp. 1761-1771).

Neotermes koshunensis is a lower termite that secretes endogenous β-glucosidase in the salivary glands. This β-glucosidase (G1NkBG) was successfully expressed in Aspergillus oryzae. G1NkBG was purified to homogeneity from the culture supernatant through ammonium sulfate precipitation and anion exchange, hydrophobic, and gel filtration chromatographies with a 48-fold increase in purity. The molecular mass of the native enzyme appeared as a single band at 60 kDa after gel filtration analysis, indicating that G1NkBG is a monomeric protein. Maximum activity was observed at 50 °C with an optimum pH at 5.0. G1NkBG retained 80% of its maximum activity at temperatures up to 45 °C and lost its activity at temperatures above 55 °C. The enzyme was stable from pH 5.0 to 9.0. G1NkBG was most active towards laminaribiose and p-nitrophenyl-β-d-fucopyranoside. Cellobiose, as well as cello-oligosaccharides, was also well hydrolyzed. The enzyme activity was slightly stimulated by Mn²⁺ and glycerol. The K _m and V _max values were 0.77 mM and 16 U/mg, respectively, against p-nitrophenyl-β-d-glucopyranoside. An unusual finding was that G1NkBG was stimulated by 1.3-fold when glucose was present in the reaction mixture at a concentration of 200 mM. These characteristics, particularly the stimulation of enzyme activity by glucose, make G1NkBG of great interest for biotechnological applications, especially for bioethanol production.

Keywords: Glucose-stimulated β-glucosidase; Neotermes koshunensis ; Heterologous expression; Aspergillus oryzae

Absolute configuration-dependent epoxide formation from isoflavan-4-ol stereoisomers by biphenyl dioxygenase of Pseudomonas pseudoalcaligenes strain KF707 by Jiyoung Seo; Su-Il Kang; Dongho Won; Mihyang Kim; Ji-Young Ryu; Suk-Woo Kang; Byung-Hun Um; Cheol-Ho Pan; Joong-Hoon Ahn; Youhoon Chong; Robert A. Kanaly; Jaehong Han; Hor-Gil Hur (pp. 1773-1782).

Biphenyl dioxygenase from Pseudomonas pseudoalcaligenes strain KF707 expressed in Escherichia coli was found to exhibit monooxygenase activity toward four stereoisomers of isoflavan-4-ol. LC–MS and LC–NMR analyses of the metabolites revealed that the corresponding epoxides formed between C2′ and C3′ on the B-ring of each isoflavan-4-ol substrate were the sole products. The relative reactivity of the stereoisomers was found to be in the order: (3S,4S)-cis-isoflavan-4-ol > (3R,4S)-trans-isoflavan-4-ol > (3S,4R)-trans-isoflavan-4-ol > (3R,4R)-cis-isoflavan-4-ol and this likely depended upon the absolute configuration of the 4-OH group on the isoflavanols, as explained by an enzyme–substrate docking study. The epoxides produced from isoflavan-4-ols by P. pseudoalcaligenes strain KF707 were further abiotically transformed into pterocarpan, the molecular structure of which is commonly found as part of plant-protective phytoalexins, such as maackiain from Cicer arietinum and medicarpin from Medicago sativa.

Keywords: Biphenyl dioxygenase; Pseudomonas pseudoalcaligene ; Isoflavanol epoxide; Pterocarpan; Medicarpin

Lytic enzyme discovery through multigenomic sequence analysis in Clostridium perfringens by Jonathan E. Schmitz; Maria Cristina Ossiprandi; Kareem R. Rumah; Vincent A. Fischetti (pp. 1783-1795).

With their ability to lyse Gram-positive bacteria, phage lytic enzymes (or lysins) have received a great deal of attention as novel anti-infective agents. The number of known genes encoding these peptidoglycan hydrolases has increased markedly in recent years, due in large part to advances in DNA sequencing technology. As the genomes of more and more bacterial species/strains are sequenced, lysin-encoding open reading frames (ORFs) can be readily identified in lysogenized prophage regions. In the current study, we sought to assess lysin diversity for the medically relevant pathogen Clostridium perfringens. The sequenced genomes of nine C. perfringens strains were computationally mined for prophage lysins and lysin-like ORFs, revealing several dozen proteins of various enzymatic classes. Of these lysins, a muramidase from strain ATCC 13124 (termed PlyCM) was chosen for recombinant analysis based on its dissimilarity to previously characterized C. perfringens lysins. Following expression and purification, various biochemical properties of PlyCM were determined in vitro, including pH/salt-dependence and temperature stability. The enzyme exhibited activity at low μg/ml concentrations, a typical value for phage lysins. It was active against 23 of 24 strains of C. perfringens tested, with virtually no activity against other clostridial or non-clostridial species. Overall, PlyCM shows potential for development as an enzybiotic agent, demonstrating how expanding genomic databases can serve as rich pools for biotechnologically relevant proteins.

Keywords: Lysin; Prophage; Enzybiotic; Muramidase; Clostridium perfringens

Cloning, sequencing, and overexpression in Escherichia coli of the Enterobacter sp. Px6-4 gene for ferulic acid decarboxylase by Wen Gu; Xuemei Li; Jingwen Huang; Yanqing Duan; Zhaohui Meng; Ke-Qin Zhang; Jinkui Yang (pp. 1797-1805).

Ferulic acid decarboxylase (FADase) can catalyze the transformation of ferulic acid into 4-vinyl guaiacol via decarboxylation in microorganisms. In this study, a gene encoding FADase was first isolated from the bacterium Enterobacter sp. Px6-4 using degenerate primers and a genome walking technique. The putative encoding gene (fad) of FADase consists of 507-bp nucleotides, coding a polypeptide of 168 amino acid residues. In addition, a putative gene encoding the transcriptional regulator was identified from the upstream of the fad gene. The deduced peptide sequence of the FADase from Enterobacter sp. Px6-4 showed a 51.2–53.3% sequence identity to decarboxylases from other bacteria. The gene fad was successfully expressed in Escherichia coli BL21, and the recombinant FADase was purified as a protein of ca. 23 kDa with an optimal activity at pH 4.0 and 28 °C. The purified FADase could convert ferulic acid to 4-vinyl guaiacol effectively, and its hydrolytic activity could be inhibited by Cu²⁺ (99%) and Hg²⁺ (99.5%). A phylogenetic analysis of the FADase protein from bacteria revealed several different clades. Our result provided a basis for further studies of the ferulic acid transformation pathway and for enhanced production of vanillin in the future.

Keywords: Enterobacter sp. Px6-4; Ferulic acid decarboxylase; Cloning; Expression; Enzyme analysis

Antitumor therapeutic effects of a genetically engineered Salmonella typhimurium harboring TNF-α in mice by Won Suck Yoon; Yang Seok Chae; Juyeon Hong; Yong Keun Park (pp. 1807-1819).

Although the use of TNF-α in the treatment of cancer is restricted due to its non-specific cytotoxicity and narrow range of applications to different cancers in clinical trials, we investigated a safe anti-cancer drug by the use of engineered bacterial capsule harboring TNF-α. The engineered bacterial capsule was designed to target cancer cells, promote a tumor-suppressive environment, and increase the efficacy of existing cancer treatments, including chemotherapy, radiotherapy, and cell therapy. The engineered bacterial capsule was constructed with Salmonella capsulizing TNF-α protein, which was produced and capsulized by Salmonella to reduce side effects of the protein. This bacterial capsule induced a tumor-suppressive environment through the activation of natural killer cells. Engineered bacterial capsule invaded tumor cells, released TNF-α, and induced apoptosis of tumor cells without apparent side effects. In a murine melanoma model, the bacterial capsule of TNF-α significantly inhibited tumor growth by 80–100% and prolonged the survival of the mice. When tested in combination with chemotherapy (cisplatin), antibiotics, and vaccine, recombinant microbial treatment increased the anti-tumor effects of existing therapies. The anti-tumor effects of the bacterial capsule of TNF-α were also observed in cervical cancer, melanoma, breast cancer, colon cancer, and renal carcinoma. These results suggest that the bacterial capsule of TNF-α is a promising strategy for TNF-α treatment.

Keywords: Antitumor effects; Tumor treatments; TNF-α; Salmonella typhimurium

High level expression of a recombinant amylosucrase gene and selected properties of the enzyme by Jens Schneider; Christin Fricke; Heike Overwin; Bernd Hofer (pp. 1821-1829).

Two high-level heterologous expression systems for amylosucrase genes have been constructed. One depends on sigma-70 bacterial RNA polymerase, the other on phage T7 RNA polymerase. Translational fusions were formed between slightly truncated versions of the gene from Neisseria polysaccharea and sequences of expression vectors pQE-81L or pET33b(+), respectively. These constructs were introduced into different Escherichia coli strains. The resulting recombinants yielded up to 170 mg of dissolved enzyme per litre of culture at a moderate cell density of five OD₆₀₀. To our knowledge, this is the highest yield per cell described so far for amylosucrases. The recombinant enzymes could rapidly be purified through the use of histidine tags in the N-terminally attached sequences. These segments did not alter catalytic properties and therefore need not be removed for most applications. Investigations with glucose and malto-oligosaccharides of different lengths identified rate-limiting steps in the elongation (acceptor reaction) and truncation (donor reaction) of these substrates. The elongation of maltotriose and its reversal, the truncation of maltotetraose, were found to be particularly slow reactions. Potential reasons are discussed, based on the crystal structure of the enzyme. It is furthermore shown that amylosucrase is able to synthesise mixed disaccharides. All of the glucose epimers mannose, allose, and galactose served as acceptors, yielding between one and three main products. We also demonstrate that, as an alternative to the use of purified amylosucrase, cells of the constructed recombinant strains can be used to carry out glucosylations of acceptors.

Keywords: Amylosucrase; High level expression; Glucosylation; Acceptor; Rate-limiting step; Whole cells

Purification, characterization, and cloning of a bifunctional molybdoenzyme with hydratase and alcohol dehydrogenase activity by Jianfeng Jin; Adrie J. J. Straathof; Martijn W. H. Pinkse; Ulf Hanefeld (pp. 1831-1840).

A bifunctional hydratase/alcohol dehydrogenase was isolated from the cyclohexanol degrading bacterium Alicycliphilus denitrificans DSMZ 14773. The enzyme catalyzes the addition of water to α,β-unsaturated carbonyl compounds and the subsequent alcohol oxidation. The purified enzyme showed three subunits in SDS gel, and the gene sequence revealed that this enzyme belongs to the molybdopterin binding oxidoreductase family containing molybdopterins, FAD, and iron-sulfur clusters.

Keywords: Michael addition; α,β-Unsaturated carbonyl compounds; Hydratase; Alcohol dehydrogenase; Molybdenum-containing hydroxylase

Oxidation of polycyclic aromatic hydrocarbons by the bacterial laccase CueO from E. coli by Jun Zeng; Xiangui Lin; Jing Zhang; Xuanzhen Li; Ming Hung Wong (pp. 1841-1849).

Laccases produced by white rot fungi are capable of rapidly oxidizing benzo[a]pyrene. We hypothesize that the polycyclic aromatic hydrocarbon (PAH)-degrading bacteria producing laccase can enhance the degree of benzo[a]pyrene mineralization. However, fungal laccases are glycoproteins which cannot be glycosylated in bacteria, and there is no evidence to show that bacterial laccases can oxidize benzo[a]pyrene. In this study, the in vitro oxidation of PAHs by crude preparations of the bacterial laccase, CueO, from Escherichia coli was investigated. The results revealed that the crude CueO catalyzed the oxidation of anthracene and benzo[a]pyrene in the same way as the fungal laccase from Trametes versicolor, but showed specific characteristics such as thermostability and copper dependence. In the presence of 2,2′-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid), high amounts of anthracene and benzo[a]pyrene, 80% and 97%, respectively, were transformed under optimal conditions of 60°C, pH 5, and 5 mmol l⁻¹ CuCl₂ after a 24-h incubation period. Other PAHs including fluorene, acenaphthylene, phenanthrene, and benzo[a]anthracene were also oxidized by the crude CueO. These findings indicated the potential application of prokaryotic laccases in enhancing the mineralization of benzo[a]pyrene by PAH-degrading bacteria.

Keywords: Anthracene; Bacterial laccase; Benzo[a]pyrene; Biotransformation; CueO; Polycyclic aromatic hydrocarbons (PAHs)

An acid and highly thermostable xylanase from Phialophora sp. G5 by Fan Zhang; Pengjun Shi; Yingguo Bai; Huiying Luo; Tiezheng Yuan; Huoqing Huang; Peilong Yang; Lihong Miao; Bin Yao (pp. 1851-1858).

An endo-β-1,4-xylanase gene, designated xyn10G5, was cloned from Phialophora sp. G5 and expressed in Pichia pastoris. The 1,197-bp full-length gene encodes a polypeptide of 399 amino acids consisting of a putative signal peptide at residues 1–20, a family 10 glycoside hydrolase domain, a short Gly/Thr-rich linker and a family 1 carbohydrate-binding module (CBM). The deduced amino acid sequence of XYN10G5 shares the highest identity (53.4%) with a putative xylanase precursor from Aspergillus terreus NIH2624. The purified recombinant XYN10G5 exhibited the optimal activity at pH 4.0 and 70 °C, remained stable at pH 3.0–9.0 (>70% of the maximal activity), and was highly thermostable at 70 °C (retaining ~90% of the initial activity for 1 h). Substrate specificity studies have shown that XYN10G5 had the highest activity on soluble wheat arabinoxylan (350.6 U mg⁻¹), and moderate activity to various heteroxylans, and low activity on different types of cellulosic substrates. Under simulated gastric conditions, XYN10G5 was stable and released more reducing sugars from soluble wheat arabinoxylan; when combined with a glucanase (CelA4), the viscosity of barley–soybean feed was significantly reduced. These favorable enzymatic properties make XYN10G5 a good candidate for application in the animal feed industry.

Keywords: Phialophora sp. G5; Xylanase; Thermostability; Broad substrate specificity

Increased d-allose production by the R132E mutant of ribose-5-phosphate isomerase from Clostridium thermocellum by Soo-Jin Yeom; Eun-Sun Seo; Yeong-Su Kim; Deok-Kun Oh (pp. 1859-1866).

Ribose-5-phosphate isomerase from Clostridium thermocellum converted d-psicose to d-allose, which may be useful as a pharmaceutical compound, with no by-product. The 12 active-site residues, which were obtained by molecular modeling on the basis of the solved three-dimensional structure of the enzyme, were substituted individually with Ala. Among the 12 Ala-substituted mutants, only the R132A mutant exhibited an increase in d-psicose isomerization activity. The R132E mutant showed the highest activity when the residue at position 132 was substituted with Ala, Gln, Ile, Lys, Glu, or Asp. The maximal activity of the wild-type and R132E mutant enzymes for d-psicose was observed at pH 7.5 and 80°C. The half-lives of the wild-type enzyme at 60°C, 65°C, 70°C, 75°C, and 80°C were 11, 7.0, 4.2, 1.5, and 0.6 h, respectively, whereas those of the R132E mutant enzymes were 13, 8.2, 5.1, 3.1, and 0.9 h, respectively. The specific activity and catalytic efficiency (k _cat/K _m) of the R132E mutant for d-psicose were 1.4- and 1.5-fold higher than those of the wild-type enzyme, respectively. When the same amount of enzyme was used, the conversion yield of d-psicose to d-allose was 32% for the R132E mutant enzyme and 25% for the wild-type enzyme after 80 min.

Keywords: Ribose-5-phosphate isomerase; Clostridium thermocellum ; Site-directed mutagenesis; d-Allose; d-Psicose

Biotransformation of 4-halophenols to 4-halocatechols using Escherichia coli expressing 4-hydroxyphenylacetate 3-hydroxylase by Lydie Coulombel; Louise C. Nolan; Jasmina Nikodinovic; Evelyn M. Doyle; Kevin E. O’Connor (pp. 1867-1875).

Escherichia coli cells, expressing 4-hydroxyphenylacetate 3-hydroxylase, fully transformed 4-halogenated phenols to their equivalent catechols as single products in shaken flasks. 4-Fluorophenol was transformed at a rate 1.6, 1.8, and 3.4-fold higher than the biotransformation of 4-chloro-, 4-bromo-, and 4-iodo-phenol, respectively. A scale-up from shaken flask to a 5 L stirred tank bioreactor was undertaken to develop a bioprocess for the production of 4-substituted halocatechols at higher concentrations and scale. In a stirred tank reactor, the optimized conditions for induction of 4-HPA hydroxylase expression were at 37 °C for 3 h. The rate of biotransformation of 4-fluorophenol to 4-fluorocatechol by stirred tank bioreactor grown cells was the same at 1 and 4.8 mM (5.13 μmol/min/g CDW) once the ratio of biocatalyst (E. coli CDW) to substrate concentration (mM) was maintained at 2:1. At 10.8 mM 4-fluorophenol, the rate of 4-fluorocatechol formation decreased by 4.7-fold. However, the complete transformation of 1.3 g of 4-fluorophenol (10.8 mM) to 4-fluorocatechol was achieved within 7 h in a 1 L reaction volume. Similar to 4-fluorophenol, other 4-substituted halophenols were completely transformed to 4-halocatechols at 2 mM within a 1–2 h period. An increase in 4-halophenol concentration to 4.8 mM resulted in a 2.5–20-fold decrease in biotransformation efficiency depending on the substrate tested. Organic solvent extraction of the 4-halocatechol products followed by column chromatography resulted in the production of purified products with a final yield of between 33% and 38%.

Keywords: Biotransformation; 4-Halogenated catechols; 4-Hydroxyphenylacetate 3-hydroxylase; Scale-up process

Site-specific recombination system based on actinophage TG1 integrase for gene integration into bacterial genomes by Nobutaka Hirano; Tetsurou Muroi; Yoshihiko Kihara; Ryuichi Kobayashi; Hideo Takahashi; Mitsuru Haruki (pp. 1877-1884).

Phage integrases are enzymes that catalyze unidirectional site-specific recombination between the attachment sites of phage and host bacteria, attP and attB, respectively. We recently developed an in vivo intra-molecular site-specific recombination system based on actinophage TG1 serine-type integrase that efficiently acts between attP and attB on a single plasmid DNA in heterologous Escherichia coli cells. Here, we developed an in vivo inter-molecular site-specific recombination system that efficiently acted between the att site on exogenous non-replicative plasmid DNA and the corresponding att site on endogenous plasmid or genomic DNA in E. coli cells, and the recombination efficiencies increased by a factor of ~10^1–3 in cells expressing TG1 integrase over those without. Moreover, integration of attB-containing incoming plasmid DNA into attP-inserted E. coli genome was more efficient than that of the reverse substrate configuration. Together with our previous result that purified TG1 integrase functions efficiently without auxiliary host factors in vitro, these in vivo results indicate that TG1 integrase may be able to introduce attB-containing circular DNAs efficiently into attP-inserted genomes of many bacterial species in a site-specific and unidirectional manner. This system thus may be beneficial to genome engineering for a wide variety of bacterial species.

Keywords: Bacteriophage; Serine-type phage integrase; Site-specific recombination; Microbial genome engineering

Protection of mice against enterotoxigenic E. coli by immunization with a polyvalent enterotoxin comprising a combination of LTB, STa, and STb by Jiansong You; Yongping Xu; Maolong He; Tim A. McAllister; Philip A. Thacker; Xiaoyu Li; Tingting Wang; Liji Jin (pp. 1885-1893).

Currently available enterotoxigenic Escherichia coli (ETEC) vaccines are based on colonization factors and/or the heat-labile enterotoxin B subunit (LTB). However, the induction of antitoxic responses against heat-stable enterotoxin a (STa) and b (STb) has merit as these two poorly immunogenic toxins are frequently associated with ETEC strains. In this study, we genetically constructed a trivalent enterotoxin fusion protein (STa–LTB–STb, abbreviated to SLS) in an effort to develop a single toxoid containing these three enterotoxins for vaccination against ETEC. Mutagenesis at one disulfide-bridge-forming cysteine in STa led to a dramatic reduction in the STa toxicity of SLS; however, the fusion peptide retained the STb-associated toxicity. Immunization of mice with SLS protein elicited significant antibody responses to LTB, STa, and STb. Significantly, the mice antisera were able to neutralize the biological activity of both STa and STb. In the experiment to assess the protective effect of SLS immunization, the mortality of mice receiving SLS was significantly lower than their control cohorts (P < 0.01) after intraperitoneal challenge with ETEC. These results show that the trivalent fusion enterotoxin SLS has the potential to serve as a useful toxin-based vaccine against ETEC-induced diarrheal disease via a single immunogen.

Keywords: Enterotoxigenic Escherichia coli ; Diarrhea; Fusion enterotoxin; Linker; Immunization; Toxoid

Overexpression of a cuticle-degrading protease Ver112 increases the nematicidal activity of Paecilomyces lilacinus by Jinkui Yang; Xuna Zhao; Lianming Liang; Zhenyuan Xia; Liping Lei; Xuemei Niu; Chenggang Zou; Ke-Qin Zhang (pp. 1895-1903).

Due to their ability to degrade the proteins in nematode cuticle, serine proteases play an important role in the pathogenicity of nematophagous fungi against nematodes. The serine protease Ver112 was identified from the nematophagous fungus Lecanicillium psalliotae capable of degrading the nematode cuticle and killing nematodes effectively. In this study, the gene ver112 was introduced into the commercial biocontrol fungal agent Paecilomyces lilacinus by the restriction enzyme-mediated integration transformation. Compared to the wild strain, the transformant P. lilacinus 112 showed significantly greater protease activity, with nematicidal activities increased by 79% and 96% to Panagrellus redivivus and Caenorhabditis elegans at the second day, respectively. The crude protein extract isolated from the culture filtrate of P. lilacinus 112 also showed 20–25% higher nematicidal activity than that of the wild-type strain. Reverse transcription PCR results showed that the expression of gene ver112 in P. lilacinus 112 was correlated to protease activity of the culture filtrate. Our results demonstrated the first successful transfer of a virulence gene from one nematophagous fungus to another nematophagous fungus, and improved the pathogenicity of the recipient fungus against pest nematodes.

Keywords: Nematophagous fungi; Serine protease; Paecilomyces lilacinus ; Nematicidal activity; REMI transformation

Identification of mannose uptake and catabolism genes in Corynebacterium glutamicum and genetic engineering for simultaneous utilization of mannose and glucose by Miho Sasaki; Haruhiko Teramoto; Masayuki Inui; Hideaki Yukawa (pp. 1905-1916).

Here, focus is on Corynebacterium glutamicum mannose metabolic genes with the aim to improve this industrially important microorganism’s ability to ferment mannose present in mixed sugar substrates. cgR_0857 encodes C. glutamicum’s protein with 36% amino acid sequence identity to mannose 6-phosphate isomerase encoded by manA of Escherichia coli. Its deletion mutant did not grow on mannose and exhibited noticeably reduced growth on glucose as sole carbon sources. In effect, C. glutamicum manA is not only essential for growth on mannose but also important in glucose metabolism. A double deletion mutant of genes encoding glucose and fructose permeases (ptsG and ptsF, respectively) of the phosphoenolpyruvate-dependent phosphotransferase system (PTS) was not able to grow on mannose unlike the respective single deletion mutants with mannose utilization ability. A mutant deficient in ptsH, a general PTS gene, did not utilize mannose. These indicate that the glucose-PTS and fructose-PTS are responsible for mannose uptake in C. glutamicum. When cultured with a glucose and mannose mixture, mannose utilization of manA-overexpressing strain CRM1 was significantly higher than that of its wild-type counterpart, but with a strong preference for glucose. ptsF-overexpressing strain CRM2 co-utilized mannose and glucose, but at a total sugar consumption rate much lower than that of the wild-type strain and CRM1. Strain CRM3 overexpressing both manA and ptsF efficiently co-utilized mannose and glucose. Under oxygen-deprived conditions, high volumetric productivity of organic acids concomitant with the simultaneous consumption of the mixed sugars was achieved by the densely packed growth-arrested CRM3 cells.

Keywords: Corynebacterium glutamicum ; Mannose; ptsF ; manA ; Simultaneous utilization

Proteomic understanding of intracellular responses of recombinant Chinese hamster ovary cells cultivated in serum-free medium supplemented with hydrolysates by Jee Yon Kim; Yeon-Gu Kim; Young Kue Han; Hyun Soo Choi; Young Hwan Kim; Gyun Min Lee (pp. 1917-1928).

In order to understand the intracellular responses in recombinant CHO (rCHO) cells producing antibody in serum-free medium (SFM) supplemented with optimized hydrolysates mixtures, yielding the highest specific growth rate (μ, SFM#S1) or the highest specific antibody productivity (q _Ab, SFM#S2), differentially expressed proteins in rCHO cells are measured by two-dimensional gel electrophoresis combined with nano-LC-ESI-Q-TOF tandem MS. The comparative proteomic analysis with basal SFM without hydrolysates revealed that the addition of hydrolysate mixtures significantly altered the profiles of CHO proteome. In SFM#S1, the expression of metabolism-related proteins, cytoskeleton-associated proteins, and proliferation-related proteins was up-regulated. On the other hand, the expression of anti-proliferative proteins and pro-apoptotic protein was down-regulated. In SFM#S2, the expression of various chaperone proteins and proliferation-linked proteins was altered. 2D-Western blot analysis of differentially expressed proteins confirmed the proteomic results. Taken together, identification of differentially expressed proteins in CHO cells by a proteomic approach can provide insights into understanding the effect of hydrolysates on intracellular events and clues to find candidate genes for cell engineering to maximize the protein production in rCHO cells.

Keywords: CHO cells; Proteomics; Hydrolysates; Cell growth; Productivity

A novel l-isoleucine metabolism in Bacillus thuringiensis generating (2S,3R,4S)-4-hydroxyisoleucine, a potential insulinotropic and anti-obesity amino acid by Jun Ogawa; Tomohiro Kodera; Sergey V. Smirnov; Makoto Hibi; Natalia N. Samsonova; Ryoukichi Koyama; Hiroyuki Yamanaka; Junichi Mano; Takashi Kawashima; Kenzo Yokozeki; Sakayu Shimizu (pp. 1929-1938).

4-Hydroxyisoleucine (HIL) found in fenugreek seeds has insulinotropic and anti-obesity effects and is expected to be a novel orally active drug for insulin-independent diabetes. Here, we show that the newly isolated strain Bacillus thuringiensis 2e2 and the closely related strain B. thuringiensis ATCC 35646 operate a novel metabolic pathway for l-isoleucine (l-Ile) via HIL and 2-amino-3-methyl-4-ketopentanoic acid (AMKP). The HIL synthesis was catalyzed stereoselectively by an α-ketoglutaric acid-dependent dioxygenase and to be useful for efficient production of a naturally occurring HIL isomer, (2S,3R,4S)-HIL. The (2S,3R,4S)-HIL was oxidized to (2S,3R)-AMKP by a NAD⁺-dependent dehydrogenase. The metabolic pathway functions as an effective bypass pathway that compensates for the incomplete tricarboxylic acid (TCA) cycle in Bacillus species and also explains how AMKP, a vitamin B₁₂ antimetabolite with antibiotic activity, is synthesized. These novel findings pave a new way for the commercial production of HIL and also for AMKP.

Keywords: l-Isoleucine dioxygenase; 4-Hydroxyisoleucine; NAD⁺-dependent dehydrogenase; 2-Amino-3-methyl-4-ketopentanoic acid; Bacillus thuringiensis ; TCA cycle

Comparison of endoglucanase-1 (EG1) induction in the edible straw mushroom Volvariella volvacea by lactose and/or cellobiose with or without added sorbose by Liang Zhang; Yun Pei; Zengtao Xing; Shaojun Ding; John A. Buswell (pp. 1939-1946).

We have compared the induction of an endoglucanase (EG1) by α-lactose and/or cellobiose, with or without added l-sorbose, in submerged cultures of Volvariella volvacea, to better understand the mechanism whereby cellulase formation is triggered by these soluble disaccharides. EG1 levels induced by α-lactose and cellobiose were 28.6% and 6.7%, respectively of the highest levels recorded with crystalline cellulose. Sorbose did not induce EG1 and strongly repressed enzyme levels when added to α-lactose but not cellobiose-containing cultures. EG1 levels in cultures containing all three saccharides were similar to those recorded with sorbose and cellobiose although enzyme induction was delayed by 12 h. When V. volvacea was pre-grown for 24 h in medium containing sorbose as the sole carbon source, followed by addition of α-lactose or cellobiose or a mixture of the two, EG1 levels recorded in the α-lactose-supplemented cultures were again markedly lower compared with cultures containing only α-lactose. Maximal enzyme levels in cultures with added cellobiose or cellobiose and α-lactose were not affected although appearance of EG1 in culture supernatants was again delayed by 12 h. Semi-quantitative RT-PCR revealed that higher, more prolonged, levels of eg1 transcription occurred in V. volvacea cultures induced with α-lactose compared with cellobiose- or α-lactose + cellobiose-induced cultures. However, eg1 transcription levels in cultures induced with cellobiose or with cellobiose + lactose, and the corresponding cultures with added sorbose, were not markedly different.

Keywords: Endoglucanase 1 (EG1); Volvariella volvacea ; Induction; Lactose; Cellobiose; Sorbose

Quantitative study of lipase secretion, extracellular lipolysis, and lipid storage in the yeast Yarrowia lipolytica grown in the presence of olive oil: analogies with lipolysis in humans by Amal Najjar; Sylvie Robert; Clémence Guérin; Michèle Violet-Asther; Frédéric Carrière (pp. 1947-1962).

Lipase secretion, extracellular lipolysis, and fatty acid uptake were quantified in the yeast Yarrowia lipolytica grown in the presence of olive oil and/or glucose. Specific lipase assays, Western blot analysis, and ELISA indicated that most of the lipase activity measured in Y. lipolytica cultures resulted from the YLLIP2 lipase. Lipase production was triggered by olive oil and, during the first hours of culture, most of the lipase activity and YLLIP2 immunodetection remained associated with the yeast cells. YLLIP2 was then released in the culture medium before it was totally degraded by proteases. Olive oil triglycerides were largely degraded when the lipase was still attached to the cell wall. The fate of lipolysis products in the culture medium and inside the yeast cell, as well as lipid storage, was investigated simultaneously by quantitative TLC–FID and GC analysis. The intracellular levels of free fatty acids (FFA) and triglycerides increased transiently and were dependent on the carbon sources. A maximum fat storage of 37.8% w/w of yeast dry mass was observed with olive oil alone. A transient accumulation of saturated FFA was observed whereas intracellular triglycerides became enriched in unsaturated fatty acids. So far, yeasts have been mainly used for studying the intracellular synthesis, storage, and mobilization of neutral lipids. The present study shows that yeasts are also interesting models for studying extracellular lipolysis and fat uptake by the cell. The quantitative data obtained here allow for the first time to establish interesting analogies with gastrointestinal and vascular lipolysis in humans.

Keywords: Carbon source; Fatty acid; Lipid metabolism; Lipolysis; LIP2 lipase; Microbial growth; Triglyceride; Yeast

Metallic copper corrosion rates, moisture content, and growth medium influence survival of copper ion-resistant bacteria by Jutta Elguindi; Stuart Moffitt; Henrik Hasman; Cassandra Andrade; Srini Raghavan; Christopher Rensing (pp. 1963-1970).

The rapid killing of various bacteria in contact with metallic copper is thought to be influenced by the influx of copper ions into the cells, but the exact mechanism is not fully understood. This study showed that the kinetics of contact killing of copper surfaces depended greatly on the amount of moisture present, copper content of alloys, type of medium used, and type of bacteria. We examined antibiotic- and copper ion-resistant strains of Escherichia coli and Enterococcus faecium isolated from pig farms following the use of copper sulfate as feed supplement. The results showed rapid killing of both copper ion-resistant E. coli and E. faecium strains when samples in rich medium were spread in a thin, moist layer on copper alloys with 85% or greater copper content. E. coli strains were rapidly killed under dry conditions, while E. faecium strains were less affected. Electroplated copper surface corrosion rates were determined from electrochemical polarization tests using the Stern–Geary method and revealed decreased corrosion rates with benzotriazole and thermal oxide coating. Copper ion-resistant E. coli and E. faecium cells suspended in 0.8% NaCl showed prolonged survival rates on electroplated copper surfaces with benzotriazole coating and thermal oxide coating compared to surfaces without anti-corrosion treatment. Control of surface corrosion affected the level of copper ion influx into bacterial cells, which contributed directly to bacterial killing.

Keywords: Copper ion-resistant bacteria; Metallic copper surface corrosion; Corrosion inhibitors; Survival assay

Modification of yeast characteristics by soy peptides: cultivation with soy peptides represses the formation of lipid bodies by Kayo Ikeda; Sayuri Kitagawa; Takakiyo Tada; Haruyuki Iefuji; Yoshiharu Inoue; Shingo Izawa (pp. 1971-1977).

We have previously reported that the cultivation of yeast cells with soy peptides can improve the tolerance of yeast to freeze–thaw stress (Izawa et al. Appl Microbiol Biotechnol 75:533–538, 2007), indicating that soy peptides can modify the characteristics of yeast cells. To gain a greater understanding of the potencies of soy peptides, we further investigated the effects of cultivation with soy peptides on yeast physiology and found that soy peptides repress the formation of lipid bodies (also called lipid droplets or lipid particles), in which neutral lipids are accumulated. Compared with casein peptone, bacto peptone, yeast nitrogen base, and free amino acid mixtures having the same amino acid composition as soy peptides, cultivation with soy peptides caused decreased levels of mRNAs of neutral lipid synthesis-related genes, such as DGA1, and repressed the formation of lipid bodies and accumulation of triacylglycerol. These results indicate that soy peptides affect the lipid metabolism in yeast cells, and also demonstrate a potentiality of edible natural ingredients as modifiers of the characteristics of food microorganisms.

Keywords: Lipid bodies; Soy peptide; Food microorganisms; Triacylglycerol; Saccharomyces cerevisiae

Development of a single base extension-tag microarray for the detection of pathogenic Vibrio species in seafood by Wanyi Chen; Shuijing Yu; Chunxiu Zhang; Jilun Zhang; Chunlei Shi; Yu Hu; Biao Suo; Huan Cao; Xianming Shi (pp. 1979-1990).

In this study, a single base extension-tag array on glass slides (SBE-TAGS) microarray was established to detect the seven leading seafood-borne pathogens, including Vibrio parahaemolyticus, Vibrio cholerae, Vibrio vulnificus, Vibrio mimicus, Vibrio alginolyticus, Vibrio anguillarum, and Vibrio harveyi. Three multiplex PCR assays were developed to specifically target the following species with individual gene markers, which are aadS, tdh, and trh for V. parahaemolyticus; col, toxR, and vvh for V. alginolyticus, V. mimicus, and V. vulnificus; and empA, vhh1, and tcpA for V. anguillarum, V. harveyi, and V. cholerae, respectively. The purified PCR products were used as template DNA for single base extension-tag reactions, labeled with Cy3 fluorescent dye and hybridized to DNA microarrays. The detection specificity of this microarray method was 100%, with the sensitivity for pure genomic DNA at 200 fg to 2 pg per reaction. Application of the DNA microarray methodology to 55 naturally contaminated seafood samples (shrimp, fish, and oysters) revealed the presence of V. parahaemolyticus at 50.9% and V. alginolyticus at 32.7%. This corresponds with traditional assays (microbiological and biochemical tests) except one sample which was identified as negative in V. parahaemolyticus by the microarray assay but as positive by the conventional method. Therefore, a combination of multiplex PCR with DNA microarray hybridization based on SBE-TAGS ensures rapid and accurate detection of pathogenic Vibrio species in seafood, thereby providing safer seafood products for consumers at a low financial burden to the aquaculture industry.

Keywords: Vibrio species; Single base extension-tag on glass slides (SBE-TAGS); Microarray; Multiplex PCR

Bacterial community structure in experimental methanogenic bioreactors and search for pathogenic clostridia as community members by Anja B. Dohrmann; Susann Baumert; Lars Klingebiel; Peter Weiland; Christoph C. Tebbe (pp. 1991-2004).

Microbial conversion of organic waste or harvested plant material into biogas has become an attractive technology for energy production. Biogas is produced in reactors under anaerobic conditions by a consortium of microorganisms which commonly include bacteria of the genus Clostridium. Since the genus Clostridium also harbors some highly pathogenic members in its phylogenetic cluster I, there has been some concern that an unintended growth of such pathogens might occur during the fermentation process. Therefore this study aimed to follow how process parameters affect the diversity of Bacteria in general, and the diversity of Clostridium cluster I members in particular. The development of both communities was followed in model biogas reactors from start-up during stable methanogenic conditions. The biogas reactors were run with either cattle or pig manures as substrates, and both were operated at mesophilic and thermophilic conditions. The structural diversity was analyzed independent of cultivation using a PCR-based detection of 16S rRNA genes and genetic profiling by single-strand conformation polymorphism (SSCP). Genetic profiles indicated that both bacterial and clostridial communities evolved in parallel, and the community structures were highly influenced by both substrate and temperature. Sequence analysis of 16S rRNA genes recovered from prominent bands from SSCP profiles representing Clostridia detected no pathogenic species. Thus, this study gave no indication that pathogenic clostridia would be enriched as dominant community members in biogas reactors fed with manure.

Keywords: Biogas production; Bioreactors; Manure; 16S rRNA genes; Single-strand conformation polymorphism (SSCP); Bacterial community; Clostridia

The effect of co-substrate activation on indigenous and bioaugmented PCB dechlorinating bacterial communities in sediment microcosms by Joong-Wook Park; Valdis Krumins; Birthe V. Kjellerup; Donna E. Fennell; Lisa A. Rodenburg; Kevin R. Sowers; Lee J. Kerkhof; Max M. Häggblom (pp. 2005-2017).

Microbial reductive dechlorination by members of the phylum Chloroflexi, including the genus Dehalococcoides, may play an important role in natural detoxification of highly chlorinated environmental pollutants, such as polychlorinated biphenyls (PCBs). Previously, we showed the increase of an indigenous bacterial population belonging to the Pinellas subgroup of Dehalococcoides spp. in Anacostia River sediment (Washington DC, USA) microcosms treated with halogenated co-substrates (“haloprimers”), tetrachlorobenzene (TeCB), or pentachloronitrobenzene (PCNB). The PCNB-amended microcosms exhibited enhanced dechlorination of weathered PCBs, while TeCB-amended microcosms did not. We therefore developed and used different phylogenetic approaches to discriminate the effect of the two different haloprimers. We also developed complementary approaches to monitor the effects of haloprimer treatments on 12 putative reductive dehalogenase (rdh) genes common to Dehalococcoides ethenogenes strain 195 and Dehalococcoides sp. strain CBDB1. Our results indicate that 16S rRNA gene-based phylogenetic analyses have a limit in their ability to distinguish the effects of two haloprimer treatments and that two of rdh genes were present in high abundance when microcosms were amended with PCNB, but not TeCB. rdh gene-based phylogenetic analysis supports that these two rdh genes originated from the Pinellas subgroup of Dehalococcoides spp., which corresponds to the 16S rRNA gene-based phylogenetic analysis.

Keywords: PCB; Dehalogenation; Dechlorination; Dehalococcoides ; rdh genes; Sediments

Electrokinetic remediation and microbial community shift of β-cyclodextrin-dissolved petroleum hydrocarbon-contaminated soil by Chunli Wan; Maoan Du; Duu-Jong Lee; Xue Yang; Wencheng Ma; Lina Zheng (pp. 2019-2025).

Electrokinetic (EK) migration of β-cyclodextrin (β-CD), which is inclusive of total petroleum hydrocarbon (TPH), is an economically beneficial and environmentally friendly remediation process for oil-contaminated soils. Remediation studies of oil-contaminated soils generally prepared samples using particular TPHs. This study investigates the removal of TPHs from, and electromigration of microbial cells in field samples via EK remediation. Both TPH content and soil respiration declined after the EK remediation process. The strains in the original soil sample included Bacillus sp., Sporosarcina sp., Beta proteobacterium, Streptomyces sp., Pontibacter sp., Azorhizobium sp., Taxeobacter sp., and Williamsia sp. Electromigration of microbial cells reduced the biodiversity of the microbial community in soil following EK remediation. At 200 V m⁻¹ for 10 days, 36% TPH was removed, with a small population of microbial cells flushed out, demonstrating that EK remediation is effective for the present oil-contaminated soils collected in field.

Keywords: Petroleum hydrocarbons; β-cyclodextrin; Electrokinetic remediation; Denaturing gradient gel electrophoresis (DGGE); Bacterial community

Molecular- and cultivation-based analyses of microbial communities in oil field water and in microcosms amended with nitrate to control H₂S production by Raji Kumaraswamy; Sara Ebert; Murray R. Gray; Phillip M. Fedorak; Julia M. Foght (pp. 2027-2038).

Nitrate injection into oil fields is an alternative to biocide addition for controlling sulfide production (‘souring’) caused by sulfate-reducing bacteria (SRB). This study examined the suitability of several cultivation-dependent and cultivation-independent methods to assess potential microbial activities (sulfidogenesis and nitrate reduction) and the impact of nitrate amendment on oil field microbiota. Microcosms containing produced waters from two Western Canadian oil fields exhibited sulfidogenesis that was inhibited by nitrate amendment. Most probable number (MPN) and fluorescent in situ hybridization (FISH) analyses of uncultivated produced waters showed low cell numbers (≤10³ MPN/ml) dominated by SRB (>95% relative abundance). MPN analysis also detected nitrate-reducing sulfide-oxidizing bacteria (NRSOB) and heterotrophic nitrate-reducing bacteria (HNRB) at numbers too low to be detected by FISH or denaturing gradient gel electrophoresis (DGGE). In microcosms containing produced water fortified with sulfate, near-stoichiometric concentrations of sulfide were produced. FISH analyses of the microcosms after 55 days of incubation revealed that Gammaproteobacteria increased from undetectable levels to 5–20% abundance, resulting in a decreased proportion of Deltaproteobacteria (50–60% abundance). DGGE analysis confirmed the presence of Delta- and Gammaproteobacteria and also detected Bacteroidetes. When sulfate-fortified produced waters were amended with nitrate, sulfidogenesis was inhibited and Deltaproteobacteria decreased to levels undetectable by FISH, with a concomitant increase in Gammaproteobacteria from below detection to 50–60% abundance. DGGE analysis of these microcosms yielded sequences of Gamma- and Epsilonproteobacteria related to presumptive HNRB and NRSOB (Halomonas, Marinobacterium, Marinobacter, Pseudomonas and Arcobacter), thus supporting chemical data indicating that nitrate-reducing bacteria out-compete SRB when nitrate is added.

Keywords: Anaerobic microbes; Nitrate reduction; Sulfidogenesis; Reservoir souring; MPN; DGGE

Bacteria and archaea involved in anaerobic digestion of distillers grains with solubles by Ayrat M. Ziganshin; Thomas Schmidt; Frank Scholwin; Olga N. Il’inskaya; Hauke Harms; Sabine Kleinsteuber (pp. 2039-2052).

Cereal distillers grains, a by-product from bioethanol industry, proved to be a suitable feedstock for biogas production in laboratory scale anaerobic digesters. Five continuously stirred tank reactors were run under constant conditions and monitored for biogas production and composition along with other process parameters. Iron additives for sulfide precipitation significantly improved the process stability and efficiency, whereas aerobic pretreatment of the grains had no effect. The microbial communities in the reactors were investigated for their phylogenetic composition by terminal restriction fragment length polymorphism analysis and sequencing of 16S rRNA genes. The bacterial subcommunities were highly diverse, and their composition did not show any correlation with reactor performance. The dominant phylotypes were affiliated to the Bacteroidetes. The archaeal subcommunities were less diverse and correlated with the reactor performance. The well-performing reactors operated at lower organic loading rates and amended with iron chloride were dominated by aceticlastic methanogens of the genus Methanosaeta. The well-performing reactor operated at a high organic loading rate and supplemented with iron hydroxide was dominated by Methanosarcina ssp. The reactor without iron additives was characterized by propionate and acetate accumulation and high hydrogen sulfide content and was dominated by hydrogenotrophic methanogens of the genus Methanoculleus.

Keywords: Biogas; DDGS; T-RFLP; Methanogenic archaea; Porphyromonadaceae ; Actinomycetales

Performance of a pilot-scale continuous flow microbial electrolysis cell fed winery wastewater by Roland D. Cusick; Bill Bryan; Denny S. Parker; Matthew D. Merrill; Maha Mehanna; Patrick D. Kiely; Guangli Liu; Bruce E. Logan (pp. 2053-2063).

A pilot-scale (1,000 L) continuous flow microbial electrolysis cell was constructed and tested for current generation and COD removal with winery wastewater. The reactor contained 144 electrode pairs in 24 modules. Enrichment of an exoelectrogenic biofilm required ~60 days, which is longer than typically needed for laboratory reactors. Current generation was enhanced by ensuring adequate organic volatile fatty acid content (VFA/SCOD ≥ 0.5) and by raising the wastewater temperature (31 ± 1°C). Once enriched, SCOD removal (62 ± 20%) was consistent at a hydraulic retention time of 1 day (applied voltage of 0.9 V). Current generation reached a maximum of 7.4 A/m³ by the planned end of the test (after 100 days). Gas production reached a maximum of 0.19 ± 0.04 L/L/day, although most of the product gas was converted to methane (86 ± 6%). In order to increase hydrogen recovery in future tests, better methods will be needed to isolate hydrogen gas produced at the cathode. These results show that inoculation and enrichment procedures are critical to the initial success of larger-scale systems. Acetate amendments, warmer temperatures, and pH control during startup were found to be critical for proper enrichment of exoelectrogenic biofilms and improved reactor performance.

Keywords: Biohydrogen; Biomethane; Bioelectricity; Microbial electrolysis cell; Bioenergy

Erratum to: Metabolism of glucose and xylose as single and mixed feed in Debaryomyces nepalensis NCYC 3413: production of industrially important metabolites by Sawan Kumar; Sathyanarayana N. Gummadi (pp. 2065-2065).

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Applied Microbiology and Biotechnology (v.89, #6)