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Applied Microbiology and Biotechnology (v.93, #5)

Review of research on Dendrobium, a prized folk medicine by Tzi Bun Ng; Jingyi Liu; Jack Ho Wong; Xiujuan Ye; Stephen Cho Wing Sze; Yao Tong; Kalin Yanbo Zhang (pp. 1795-1803).

Medicinal plants of the Dendrobium genus are highly prized, and hence, methodologies have been developed to authenticate Dendrobium drugs from its adulterants. Many bioactive constituents of Dendrobium species have been identified. The macromolecules included lectins; the enzymes chalcone synthase, sucrose synthase, and cytokinin oxidase; and polysaccharides. The polysaccharides display immunomodulatory and hepatoprotective activities. Alkaloids exhibit antioxidant, anticancer, and neuroprotective activities. Other compounds manifest antioxidant, anticancer, and immunomodulatory.

Keywords: Dendrobium ; Constituents; Bioactivity; Medicinal plants

Pressure to kill or pressure to boost: a review on the various effects and applications of hydrostatic pressure in bacterial biotechnology by Stéphanie Follonier; Sven Panke; Manfred Zinn (pp. 1805-1815).

Much knowledge has been gained for the last 30 years about the effects of pressure on bacteria, and various pressure-based technologies have been designed. The development of modern molecular biology techniques (e.g., DNA microarrays) as well as the technological advances realized in the manufacturing of robust sampling and high-pressure devices has allowed these advances. Not only the direct effects on cell components (membranes, proteins, and nucleic acids) have been unraveled, but also the cellular response to pressure has been investigated by means of transcriptome and proteome analyses. Initially, research was performed by marine biologists who studied the microorganisms living in the deep sea at pressures of 1,000 bar. In parallel, food technologists developed pressure-based methods for inactivating microorganisms without altering the food properties as much as with temperature treatment. The preservation of specific product properties is also the rationale for pressure-based methods for the disinfection of biomaterials and for vaccine production. Therefore, attention was first focused on the “killing” potential of high pressure. On the other hand, there has been a growing interest in using elevated pressures (up to ~10 bar) for enhancing the productivity of bioprocesses. In this case, no killing effect was sought, but pressure was applied to “boost” the process by enhancing the oxygen transfer to the cell culture. This paper gives an overview on the effects of pressures in the range of 1 bar to 10 kbar on bacteria and presents the major and most recent achievements realized in the development of pressure-based biotechnological applications.

Keywords: Pressure; High-pressure bioreactor; Bioprocesses; Food processing; Biomaterial disinfection; Protein refolding

Mannanases: microbial sources, production, properties and potential biotechnological applications by Prakram Singh Chauhan; Neena Puri; Prince Sharma; Naveen Gupta (pp. 1817-1830).

Mannans are the major constituents of the hemicellulose fraction in softwoods and show widespread distribution in plant tissues. The major mannan-degrading enzymes are β-mannanases, β-mannosidases and β-glucosidases. In addition to these, other enzymes such as α-galactosidases and acetyl mannan esterases, are required to remove the side chain substituents. The mannanases are known to be produced by a variety of bacteria, fungi, actinomycetes, plants and animals. Microbial mannanases are mainly extracellular and can act in wide range of pH and temperature because of which they have found applications in pulp and paper, pharmaceutical, food, feed, oil and textile industries. This review summarizes the studies on mannanases reported in recent years in terms of important microbial sources, production conditions, enzyme properties, heterologous expression and potential industrial applications.

Keywords: Hemicellulose; Mannan; β-Mannanase; Biotechnological applications

Monascus purpureus-fermented products and oral cancer: a review by Wei-Hsuan Hsu; Tzu-Ming Pan (pp. 1831-1842).

Tobacco and alcohol consumption have been reported as major factors for the development of oral cancer. Edible fungi of the Monascus species have been used as traditional Chinese medicine in eastern Asia for several centuries. Monascus-fermented products have many functional secondary metabolites, including monacolin K, citrinin, ankaflavin, and monascin. In several recent studies performed in our laboratory, these secondary metabolites have shown anti-inflammatory, anti-oxidative, and anti-tumor activities. Many published studies have shown the efficacy of Monascus-fermented products in the prevention of numerous types of cancer. The current article discusses and provides evidence to support that Monascus-fermented metabolites may be developed as painting drugs for the mouth to prevent or cure oral carcinogenesis. This is a novel therapeutic approach focusing on tumor growth attenuation to improve patient survival and quality of life.

Keywords: Oral cancer; Monascus purpureus ; Red mold rice; Red mold dioscorea; Metabolite

Biodiscovery from rare actinomycetes: an eco-taxonomical perspective by D. İ. Kurtböke (pp. 1843-1852).

Microbial natural products, in particular, the ones produced by the members of the order Actinomycetales, will continue to represent an important route to the discovery of novel classes of bioactive compounds. As a result, the search for and discovery of lesser-known and/or novel actinomycetes is of significant interest to the industry due to a growing need for the development of new and potent therapeutic agents, mainly against drug resistant bacteria. Current advancements in genomics and metagenomics are adding strength to the target-directed search for detection and isolation of bioactive actinomycetes. New discoveries, however, will only stem from a sound understanding and interpretation of knowledge derived from conventional studies conducted since the discovery of streptomycin, on the ecology, taxonomy, physiology and metabolism of actinomycetes, and from a combination of this knowledge with currently available and continuously advancing molecular tools. Such a powerful information platform will then inevitably reveal the whereabouts, taxonomical and chemical identities of previously undetected bioactive actinomycetes including novel species of streptomycetes as potential producers of novel drug candidates.

Keywords: Biodiscovery; Microbial natural products; Streptomyces; Rare actinomycetes; Metagenomics; Genome mining

Available methods for assembling expression cassettes for synthetic biology by Tianwen Wang; Xingyuan Ma; Hu Zhu; Aitao Li; Guocheng Du; Jian Chen (pp. 1853-1863).

Studies in the structural biology of the multicomponent protein complex, metabolic engineering, and synthetic biology frequently rely on the efficient over-expression of these subunits or enzymes in the same cell. As a first step, constructing the multiple expression cassettes will be a complicated and time-consuming job if the classic and conventional digestion and ligation based cloning method is used. Some more efficient methods have been developed, including (1) the employment of a multiple compatible plasmid expression system, (2) the rare-cutter-based design of vectors, (3) in vitro recombination (sequence and ligation independent cloning, the isothermally enzymatic assembly of DNA molecules in a single reaction), and (4) in vivo recombination using recombination-efficient yeast (in vivo assembly of overlapping fragments, reiterative recombination for the chromosome integration of foreign expression cassettes). In this review, we systematically introduce these available methods.

Keywords: Synthetic biology; Simultaneous expression; Pathway construction; Yeast recombination; Cre-loxP site-specific recombination; Acembl system

Bioconversion of crude glycerol by fungi by R. W. Nicol; K. Marchand; W. D. Lubitz (pp. 1865-1875).

The production of synthetic glycerol from petrochemical feedstocks has been decreasing in recent years. This is largely due to increasing supplies of crude glycerol derived as a co-product from the oleochemical industry, especially biodiesel production. The price of glycerol is at historic lows, and the supply of crude glycerol is projected to grow faster than its industrial uses. This oversupply is driving the transition from glycerol as a product to glycerol as a precursor for new industrial applications, including its use as a substrate for bioconversion. This article reviews the use of fungi for the bioconversion of crude glycerol to the value-added products 1,2-propanediol, ethanol, single cell oil, specialty polyunsaturated fatty acids, biosurfactants, and organic acids. Information on the impurities of crude glycerol from different industrial processes is also included.

Keywords: Fungi; Crude glycerol; Single cell oil; Polyunsaturated fatty acids; Glycolipids; Citric acid

Extracellular production of cycloisomaltooligosaccharide glucanotransferase and cyclodextran by a protease-deficient Bacillus subtilis host–vector system by Yasuyuki Kawabata; Keitarou Kimura; Kazumi Funane (pp. 1877-1884).

A cycloisomaltooligosaccharide (CI; cyclodextran) production system was developed using a Bacillus subtilis expression system for the cycloisomaltooligosaccharide glucanotransferase (CITase) gene. The CITase gene of Bacillus circulans T-3040, along with the α-amylase promoter (PamyQ) and amyQ signal sequence of Bacillus amyloliquefaciens, was cloned into the Bacillus expression vector pUB110 and subsequently expressed in B. subtilis strain 168 and its alkaline (aprE) and neutral (nprE) protease-deficient strains. The recombinant CITase produced by the protease-deficient strains reached 1 U/mL in the culture supernatant within 48 h of cultivation, which was approximately 7.5 times more than that produced by the industrial CITase-producing strain B. circulans G22-10 derived from B. circulans T-3040. When aprE- and nprE-deficient B. subtilis 168 harboring the CITase gene was cultured with 10% dextran 40 for 48 h, 17% of the dextran in the culture was converted to CIs (CI-7 to CI-12), which was approximately three times more than that converted by B. circulans G22-10 under the same dextran concentration. The B. subtilis host–vector system enabled us to produce CIs by direct fermentation of dextran along with high CITase production, which was not possible in B. circulans G22-10 due to growth inhibition by dextran at high concentrations and limited production of CITase.

Keywords: Cyclodextran; Cycloisomaltooligosaccharide; Cycloisomaltooligosaccharide glucanotransferase; Bacillus circulans ; Bacillus subtilis

Physiological conditions conducive to high cell density and high cyanophycin content in Ralstonia eutropha strain H16 possessing a KDPG aldolase gene-dependent addiction system by Kaichien Lin; Yasser Elbahloul; Alexander Steinbüchel (pp. 1885-1894).

The recombinant strain of Ralstonia eutropha H16-PHB⁻4-∆eda (pBBR1MCS-2::cphA ₆₃₀₈/eda _H16) presenting a 2-keto-3-desoxy-phosphogluconate (KDPG) aldolase (eda) gene-dependent catabolic addiction system for plasmid maintenance when using gluconate or fructose as sole carbon source was used in this study. The effects of the initial pH, the nitrogen-to-carbon ratio, the inorganic components of medium, the oxygen supply, and the different carbon and nitrogen sources on the cell dry matter (CDM) and the cyanophycin granule polypeptide (CGP) content of the cells were studied in a mineral salts medium (MSM) without any additional amino acids or CGP precursor substrates. The experiments were designed to systematically find out the optimal conditions for growth of cells to high densities and for high CGP contents of the cells. Maximum contents of water-insoluble CGP and water-soluble CGP, contributing to 47.5% and 5.8% (w/w) of CDM, respectively, were obtained at the 30-L scale cultivation when cells were cultivated in MSM medium containing sufficient supplements of fructose, NH₃, K₂SO₄, MgSO₄⋅7H₂O, Fe(Ш)NH₄-citrate, CaCl₂⋅2H₂O, and trace elements (SL6). The molecular masses of water-insoluble and water-soluble CGP ranged from 25 to 31 kDa and from 15 to 21 kDa, respectively. High cell densities of up to 82.8 g CDM/L containing up to 37.8% (w/w) water-insoluble CGP at the 30-L scale cultivation were also obtained. This is by far the best combination of high cell density and high cellular CGP contents ever reported, and it showed that efficient production of CGP at the industrial scale in white biotechnology could be achieved.

Keywords: Ralstonia eutropha H16-PHB⁻4-∆eda (pBBR1MCS-2::cphA ₆₃₀₈/eda _H16); CGP; High cell density; eda

Agarose-gel-immobilized recombinant bacterial biosensors for simple and disposable on-site detection of phenolic compounds by Hae Ja Shin (pp. 1895-1904).

In this study, recombinant bacterial biosensors were immobilized in an agarose matrix and used for the simple and disposable field monitoring of phenolic compounds. In brief, Escherichia coli cells harboring the pLZCapR plasmid, which was previously designed to express the β-galactosidase reporter gene in the presence of phenolic compounds, were immobilized in agarose gel with or without a substrate [chlorophenol red β-galactopyranoside (CPRG)] and dispensed to the wells of a 96-well plate. Analytes were added to the wells, and color development was monitored either directly from wells containing intact cells co-immobilized with CPRG (SYS I), or using cells that were lysed prior to the addition of CPRG (SYS L). SYS L showed relatively higher intensities and faster color development than SYS I. However, both systems developed a red color (representing hydrolysis of CPRG) in the presence of 10 μM to 10~100 mM phenol, with maximum responses seen at 1~5 and 50 mM phenol for SYS I and SYS L, respectively. Other phenolic compounds (2-chlorophenol, 2-methylphenol, 3-methylphenol, 4-chlorophenol, 2-nitrophenol, resorcinol, catechol, and 2,5-dimethylphenol) were also detected by the systems, with varied detection ranges and responses. The agarose-immobilized biosensors were stable for 28 days, retaining 39~69% of their activities when stored at 4°C without nutrients or additives. The immobilized biosensors described herein do not require the on-site addition of a substrate (in the case of SYS I), the pretreatment of samples, or the use of unwieldy instruments for the on-site monitoring of phenolic compounds from environmental samples.

Keywords: Immobilization; Agarose; Recombinant bacterial biosensor; Phenolic compounds

Caleosin-assembled oil bodies as a potential delivery nanocarrier by Chung-Jen Chiang; Shen-Chuan Lin; Li-Jen Lin; Chih-Jung Chen; Yun-Peng Chao (pp. 1905-1915).

Encapsulation of hydrophobic agents with nanocarriers is challenging. Therefore, we have sought to use nanoscale artificial oil bodies (NOBs) as an alternative delivery carrier. To constitute NOBs, caleosin (Cal), a structural protein of plant seed oil bodies, was first fused with ZH2 (Cal-ZH2). ZH2 is a bivalent anti-HER2/neu affibody with a high affinity towards the HER2/neu receptor. After overproduction in Escherichia coli, insoluble Cal-ZH2 was isolated and used to assemble NOBs in one step. Consequently, resulting NOBs had a zeta potential around −49 mV and ranged in size from 150 to 200 nm. Upon loading with a hydrophobic fluorescence dye, NOBs were found to be selectively internalized into HER2/neu-positive tumor cells. Further analyses showed that more than 90% cells were invaded by dye-loaded NOBs and the cargo dye was released in cells with time. In addition, the in vitro assay revealed the release of the dye from NOBs in a slow and prolong manner. Overall, these results indicate the potential of Cal-based NOBs as a delivery vehicle.

Keywords: Artificial oil body; Caleosin; Targeted delivery; HER2/neu

Engineered Corynebacterium glutamicum as an endotoxin-free platform strain for lactate-based polyester production by Yuyang Song; Ken’ichiro Matsumoto; Miwa Yamada; Aoi Gohda; Christopher J. Brigham; Anthony J. Sinskey; Seiichi Taguchi (pp. 1917-1925).

The first biosynthetic system for lactate (LA)-based polyesters was previously created in recombinant Escherichia coli (Taguchi et al. 2008). Here, we have begun efforts to upgrade the prototype polymer production system to a practical stage by using metabolically engineered Gram-positive bacterium Corynebacterium glutamicum as an endotoxin-free platform. We designed metabolic pathways in C. glutamicum to generate monomer substrates, lactyl-CoA (LA-CoA), and 3-hydroxybutyryl-CoA (3HB-CoA), for the copolymerization catalyzed by the LA-polymerizing enzyme (LPE). LA-CoA was synthesized by D-lactate dehydrogenase and propionyl-CoA transferase, while 3HB-CoA was supplied by β-ketothiolase (PhaA) and NADPH-dependent acetoacetyl-CoA reductase (PhaB). The functional expression of these enzymes led to a production of P(LA-co-3HB) with high LA fractions (96.8 mol%). The omission of PhaA and PhaB from this pathway led to a further increase in LA fraction up to 99.3 mol%. The newly engineered C. glutamicum potentially serves as a food-grade and biomedically applicable platform for the production of poly(lactic acid)-like polyester.

Keywords: Polylactide; Biobased plastic; PHA synthase; Polyhydroxyalkanoate; Polyhydroxybutyrate

Energetics of growth of Aspergillus tamarii in a biological real-time reaction calorimeter by Balaji Dhandapani; Surianarayanan Mahadevan; Asit Baran Mandal (pp. 1927-1936).

Fungal cultivation in a biological real-time reaction calorimeter (BioRTCal) is arduous due to the heterogeneous nature of the system and difficulty in optimizing the process variables. The aim of this investigation is to monitor the growth of fungi Aspergillus tamarii MTCC 5152 in a calorimeter. Experiments carried out with a spore concentration of 10⁵ spores/mL indicate that the growth based on biomass and heat generation profiles was comparable to those obtained hitherto. Heat yield due to biomass growth, substrate uptake, and oxygen uptake rate was estimated from calorimetric experiments. The results would be useful in fermenter design and scale-up. Heat of combustion of fungal biomass was determined experimentally and compared to the four models reported so far. The substrate concentration had significant effects on pellet formation with variation in pellet porosity and apparent density. Metabolic heat generation is an online process variable portraying the instantaneous activity of monitoring fungal growth and BioRTCal is employed to measure the exothermic heat in a noninvasive way.

Keywords: Metabolic heat; Yield coefficient; Fungal morphology; BioRTCal; Heat of combustion

Immunological features and the ability of inhibitory effects on enzymatic activity of an epitope vaccine composed of cholera toxin B subunit and B cell epitope from Helicobacter pylori urease A subunit by Le Guo; Xiaokang Li; Feng Tang; Yunmian He; Yingying Xing; Xuepeng Deng; Tao Xi (pp. 1937-1945).

Epitope vaccine based on urease of Helicobacter pylori is a promising option for prophylactic and therapeutic vaccination against H. pylori infection. In this study, we constructed an epitope vaccine with mucosal adjuvant cholera toxin B subunit (CTB) and an epitope (UreA_183-203) of H. pylori urease A subunit named CTB-UA. The CTB-UA fusion protein was expressed in Escherichia coli, and the purified protein was used for intraperitoneal immunization experiments in BALB/c mice. The experimental results indicated that anti-CTB-UA antibody could recognize both H. pylori urease A subunit (UreA) and urease B subunit (UreB). Besides, the CTB-UA epitope vaccine had good immunogenicity and immunoreactivity and could induce specific neutralizing antibodies which showed effectively inhibitory effect on the enzymatic activity of H. pylori urease. CTB-UA is a promising molecule to be investigated as H. pylori vaccine antigen candidate.

Keywords: Epitope vaccine; Helicobacter pylori ; Cholera toxin B subunit; Urease A subunit; Neutralizing antibody

A novel thermostable and glucose-tolerant β-glucosidase from Fervidobacterium islandicum by Dina Jabbour; Barbara Klippel; Garabed Antranikian (pp. 1947-1956).

An open reading frame (ORF) encoding the enzyme β-glucosidase from the extremely thermophilic bacterium Fervidobacterium islandicum has been identified, cloned and sequenced. The bgl1A gene was cloned in a pET-Blue1 vector and transformed in Escherichia coli, resulting in high-level expression of β-glucosidase FiBgl1A that was purified to homogeneity in a two-step purification. FiBgl1A is composed of 459 amino acid residues and showed high homology to glycoside hydrolase family 1 proteins. It exhibited highest activity towards p-nitrophenyl-β-d-glucopyranoside with an optimum activity at pH 6.0 and 7.0 and at 90 °C. The enzyme is resistant to glucose inhibition. Furthermore, it did not require divalent cations for activity, nor was it affected by the addition of p-chloromercuribenzoate (10 mM), EDTA (10 mM), urea (10 mM) or dithiothreitol (10 mM). Addition of surfactants (with the exception of SDS) and a number of solvents enhanced the activity of FiBgl1A. It also displayed remarkable activity across a broad temperature range (80–100 °C). The thermoactivity and thermostability of FiBgl1A and its resistance to denaturing and reducing agents make this enzyme a potential candidate for industrial applications.

Keywords: β-Glucosidase; Glycoside hydrolase family 1; Fervidobacterium islandicum ; Thermoactive enzyme

Expression of CYP107Z13 in Streptomyces lividans TK54 catalyzes the oxidation of avermectin to 4″-oxo-avermectin by Xiliang Jiang; Weide Liu; Ying Ji; Jing Niu; Mei Li (pp. 1957-1963).

Streptomyces ahygroscopicus ZB01 has strong catalytic activity for the regiospecific oxidation of 4″-OH of avermectin to form 4″-oxo-avermectin. A cytochrome P450 gene from S. ahygroscopicus ZB01, cyp107z13, was cloned into pKC1139 to generate pKCZ1 and was transformed into Streptomyces lividans TK54, which does not have the ability to catalyze the conversion of avermectin. CYP107Z13, under the control of an ermE* promoter, was actively expressed in the TK54 recombinant strain as determined by a reduced CO difference spectrum analysis of the crude protein. Analysis of whole-cell biocatalytic activity by high-performance liquid chromatography revealed the recombinant to be able to oxidize avermectin regiospecifically to 4″-oxo-avermectin and CYP107Z13 to be a regioselective oxidase of avermectin. In addition, the whole-cell reaction conditions of the recombinant were optimized. Growth on medium ISP-2 at pH 6 was more conducive for the expression of CYP107Z13 than on medium PYG1 or at pH 7, and active cells of the recombinant strain had higher biocatalytic activity than resting cells.

Keywords: Expression; CYP107Z13; Oxidation; Avermectin; Streptomyces lividans TK54

Exceptional thermal stability and organic solvent tolerance of an esterase expressed from a thermophilic host by Yuxia Mei; Nan Peng; Shumiao Zhao; Yongmei Hu; Huacai Wang; Yunxiang Liang; Qunxin She (pp. 1965-1974).

A protein expression system recently developed for the thermophilic crenarchaeon Sulfolobus islandicus was employed to produce recombinant protein for EstA, a thermophilic esterase encoded in the same organism. Large amounts of protein were readily obtained by an affinity protein purification, giving SisEstA. Upon Escherichia coli expression, only the thioredoxin-tagged EstA recombinant protein was soluble. The fusion protein was then purified, and removing the protein tag yielded EcSisEstA. Both forms of the thermophilic EstA enzyme were characterized. We found that SisEstA formed dimer exclusively in solution, whereas EcSisEstA appeared solely as monomer. The former exhibited a stronger resistance to organic solvents than the latter in general, having a much higher temperature optimum (90°C vs. 65°C). More strikingly, SisEstA exhibited a half-life that was more than 32-fold longer than that of EcSisEstA at 90°C. This indicated that thermophilic enzymes yielded from homologous expression should be better biocatalysts than those obtained from mesophilic expression.

Keywords: Protein stability; Recombinant protein; Esterase; E. coli ; Sulfolobus islandicus

Extracellular production of Streptomyces exfoliatus poly(3-hydroxybutyrate) depolymerase in Rhodococcus sp. T104: determination of optimal biocatalyst conditions by Javier García-Hidalgo; Daniel Hormigo; María Auxiliadora Prieto; Miguel Arroyo; Isabel de la Mata (pp. 1975-1988).

The phaZ Sex gene encoding poly(3-hydroxybutyrate) depolymerase from Streptomyces exfoliatus has been successfully cloned and expressed in Rhodococcus sp. T104 for the first time. Likewise, the recombinant enzyme was efficiently produced as an extracellular active form and purified to homogeneity by two hydrophobic chromatographic steps. MALDI-TOF analysis showed that the native enzyme is a monomer. Circular dichroism studies have revealed a secondary structure showing 25.6% α-helix, 21.4% β-sheet, 17.1% β-turns, and 35.2% random coil, with a midpoint transition temperature (T _m) of 55.8 °C. Magnesium and calcium ions enhanced the enzyme activity, whereas manganese inhibited it. EDTA moderately decreased the activity, and the enzyme was completely deactivated at 3 M NaCl. Chemical modification studies indicated the presence of the catalytic triad serine–histidine–carboxylic acid in the active site. High-performance liquid chromatography (HPLC)–mass spectrometry (MS) analysis of PHB products of enzymatic hydrolysis showed monomers and dimers of 3-hydroxybutyric acid, demonstrating that PHB depolymerase is an exo-hydrolase. Addition of methyl-β-cyclodextrin simultaneously increased the activity as well as preserved the enzyme during lyophilization. Finally, thermoinactivation studies showed that the enzyme is highly stable at 40 °C. All these features support the potential industrial application of this recombinant enzyme in the production of (R)-3-hydroxyalkanoic acid derivatives as well as in the degradation of bioplastics.

Keywords: Extracellular PHB depolymerase; Streptomyces exfoliatus ; Rhodococcus sp. T104; Cloning

Identification, cloning, and characterization of β-glucosidase from Ustilago esculenta by Masahiro Nakajima; Tetsuro Yamashita; Machiko Takahashi; Yuki Nakano; Takumi Takeda (pp. 1989-1998).

Hydrolytic enzymes responsible for laminarin degradation were found to be secreted during growth of Ustilago esculenta on laminarin. An enzyme involved in laminarin degradation was purified by assaying release of glucose from laminaribiose. Ion-exchange chromatography of the culture filtrate followed by size-exclusion chromatography yielded a 110-kDa protein associated with laminaribiose hydrolysis. LC/MS/MS analysis of the 110-kDa protein identified three peptide sequences that shared significant similarity with a putative glucoside hydrolase family (GH) 3 β-glucosidase in Ustilago maydis. Based on the DNA sequence of the U. maydis GH3 β-glucosidase, a gene encoding a putative GH3 β-glucosidase in U. esculenta (Uebgl3A) was cloned by PCR. Based on the deduced amino acid sequence, the protein encoded by Uebgl3A has a molecular mass of 91 kDa and shares 90% identity with U. maydis GH3 β-glucosidase. Recombinant UeBgl3A expressed in Aspergillus oryzae released glucose from β-1,3-, β-1,4-, and β-1,6-linked oligosaccharides, and from 1,3-1,4-β-glucan and laminarin polysaccharides, indicating that UeBgl3A is a β-glucosidase. Kinetic analysis showed that UeBgl3A preferentially hydrolyzed laminaritriose and laminaritetraose. These results suggest that UeBgl3A is a key enzyme that produces glucose from laminarioligosaccharides during growth of U. esculenta on laminarin.

Keywords: Ustilago esculenta ; GH 3 β-glucosidase; Laminarioligosaccharides; Saccharification; Plant cell wall

Gene cloning, expression, and characterization of a novel acetaldehyde dehydrogenase from Issatchenkia terricola strain XJ-2 by Zhengying Yao; Chong Zhang; Fengxia Lu; Xiaomei Bie; Zhaoxin Lu (pp. 1999-2009).

Acetaldehyde is a known mutagen and carcinogen. Active aldehyde dehydrogenase (ALDH) represents an important mechanism for acetaldehyde detoxification. A yeast strain XJ-2 isolated from grape samples was found to produce acetaldehyde dehydrogenase with a high activity of 2.28 U/mg and identified as Issatchenkia terricola. The enzyme activity was validated by oxidizing acetaldehyde to acetate with NAD⁺ as coenzyme based on the headspace gas chromatography analysis. A novel acetaldehyde dehydrogenase gene (ist-ALD) was cloned by combining SiteFinding-PCR and self-formed adaptor PCR. The ist-ALD gene comprised an open reading frame of 1,578 bp and encoded a protein of 525 amino acids. The predicted protein of ist-ALD showed the highest identity (73%) to ALDH from Pichia angusta. The ist-ALD gene was expressed in Escherichia coli, and the gene product (ist-ALDH) presented a productivity of 442.3 U/mL cells. The purified ist-ALDH was a homotetramer of 232 kDa consisting of 57 kDa-subunit according to the SDS-PAGE and native PAGE analysis. Ist-ALDH exhibited the optimal activity at pH 9.0 and 40°C, respectively. The activity of ist-ALDH was enhanced by K⁺, NH4⁺, dithiothreitol, and 2-mercaptoethanol but strongly inhibited by Ag⁺, Hg²⁺, Cu²⁺, and phenylmethyl sulfonylfluoride. In the presence of NAD⁺, ist-ALDH could oxidize many aliphatic, aromatic, and heterocyclic aldehydes, preferably acetaldehyde. Kinetic study revealed that ist-ALDH had a k _cat value of 27.71/s and a k _cat/K _m value of 26.80 × 10³/(mol s) on acetaldehyde, demonstrating ist-ALDH, a catalytically active enzyme by comparing with other ALDHs. These studies indicated that ist-ALDH was a potential enzymatic product for acetaldehyde detoxification.

Keywords: Acetaldehyde; Acetaldehyde dehydrogenase; Issatchenkia terricola ; Gene cloning; Productivity; Enzyme characterization

Heterologous expression system in Aspergillus oryzae for fungal biosynthetic gene clusters of secondary metabolites by Kanae Sakai; Hiroshi Kinoshita; Takuya Nihira (pp. 2011-2022).

Fungal secondary metabolites have been considered promising resources in the search for novel bioactive compounds. Given the high potential of fungi as genetic resources, it is essential to find an efficient way to link biosynthetic genes to the product in a heterologous system, because many genes for the secondary metabolite in the original strain are silent under standard laboratory conditions. In a previous study, we constructed a heterologous expression system for a biosynthetic gene cluster using Aspergillus oryzae as the host. To make the host more versatile for the expression of secondary metabolism genes, the expression levels of a global regulator, laeA, were increased by placing the A. oryzae laeA gene under the control of the constitutive active pgk promoter. In the A. oryzae overexpressing laeA, two clusters of heterologous biosynthetic genes [the monacolin K (MK) gene cluster from Monascus pilosus and the terrequinone A (TQ) gene cluster from Aspergillus nidulans] were successfully overexpressed, resulting in the production of the corresponding metabolite, MK or TQ. The successful production of secondary metabolites belonging to different structural groups, namely MK as a polyketide and TQ as a hybrid of amino acid and isoprenoid, indicated that the laeA-enriched A. oryzae was a versatile host for the heterologous expression of the biosynthetic gene cluster.

Keywords: Aspergillus oryzae ; Secondary metabolite; Heterologous expression; laeA

Wild-type and feedback-resistant phosphoribosyl pyrophosphate synthetases from Bacillus amyloliquefaciens: purification, characterization, and application to increase purine nucleoside production by Natalia P. Zakataeva; Dmitriy V. Romanenkov; Victoria S. Skripnikova; Maria V. Vitushkina; Vitaliy A. Livshits; Alexandr D. Kivero; Anna E. Novikova (pp. 2023-2033).

Bacillus strains are used for the industrial production of the purine nucleosides inosine and guanosine, which are raw materials for the synthesis of the flavor enhancers disodium inosinate and disodium guanylate. An important precursor of purine nucleosides is 5-phospho-α-d-ribosyl-1-pyrophosphate, which is synthesized by phosphoribosyl pyrophosphate synthetase (PRS, EC 2.7.6.1). Class I PRSs are widespread in bacteria and mammals, are highly conserved among different organisms, and are negatively regulated by two end products of purine biosynthesis, adenosine 5′-diphosphate (ADP) and guanosine 5′-diphosphate (GDP). The D52H, N114S, and L129I mutations in the human PRS isozyme I (PRS1) have been reported to cause uric acid overproduction and gout due to allosteric deregulation and enzyme superactivity. In this study, to find feedback-resistant Bacillus amyloliquefaciens PRS, the influence of the D58H, N120S, and L135I mutations (corresponding to the D52H, N114S, and L129I mutations in PRS1, respectively) on PRS enzymatic properties has been studied. Recombinant histidine-tagged wild-type PRS and three mutant PRSs were expressed in Escherichia coli, purified, and characterized. The N120S and L135I mutations were found to release the enzyme from ADP and GDP inhibition and significantly increase its sensitivity to inorganic phosphate (P_i) activation. In contrast, PRS with the D58H mutation exhibited nearly identical sensitivity to ADP and GDP as the wild-type protein and had a notably greater P_i requirement for activation. The N120S and L135I mutations improved B. amyloliquefaciens and Bacillus subtilis purine nucleoside-producing strains.

Keywords: Bacillus amyloliquefaciens ; Bacillus subtilis ; Feedback resistance; Phosphoribosyl pyrophosphate synthetase; Purine nucleoside-producing strains

Polyphasic approach for the characterization of rhizobial symbionts effective in fixing N₂ with common bean (Phaseolus vulgaris L.) by Juscélio Donizete Cardoso; Mariangela Hungria; Diva S. Andrade (pp. 2035-2049).

Common bean (Phaseolus vulgaris L.) is a legume that has been reported as highly promiscuous in nodulating with a variety of rhizobial strains, often with low effectiveness in fixing nitrogen. The aim of this work was to assess the symbiotic efficiency of rhizobial strains isolated from common bean seeds, nodules of Arachis hypogaea, Mucuna pruriens, and soils from various Brazilian agroecosystems, followed by the characterization of elite strains identified in the first screening. Forty-five elite strains were analyzed for symbiotic properties (nodulation, plant-growth, and nitrogen-fixation parameters) under greenhouse conditions in pots containing non-sterile soil, and variation in symbiotic performance was observed. Elite strains were also characterized in relation to morpho-physiological properties, genetic profiles of rep-polymerase chain reaction (PCR; BOX), and restriction fragment length polymorphism (RFLP)-PCR of the 16S rRNA. Sequence analyses of the 16S rRNA were obtained for 17 strains representative of the main groups resulting from all previous analyses. One of the most effective strains, IPR-Pv 2604, was clustered with Rhizobium tropici, whereas strain IPR-Pv 583, showing lower effectiveness in fixing N₂, was clustered with Herbaspirillum lusitanum. Surprisingly, effective strains were clustered with unusual symbiotic genera/species, including Leifsonia xyli, Stenotrophomonas maltophilia, Burkholderia, and Enterobacter. Some strains recognized in this study were outstanding in their nitrogen-fixing capacity and therefore, show high biotechnological potential for use in commercial inoculants.

Keywords: Biological nitrogen fixation; BOX-PCR; RFLP-PCR; 16S rRNA; Phaseolus vulgaris ; Principal component analysis (PCA)

Identification of genes involved in Listeria monocytogenes biofilm formation by mariner-based transposon mutagenesis by Yuhua Chang; Weimin Gu; Nils Fischer; Lynne McLandsborough (pp. 2051-2062).

Listeria monocytogenes is a ubiquitous food-borne pathogen, whose distribution and survival in food-processing environments are associated with the ability to form biofilms. The process of biofilm formation is complex and its molecular mechanism is relatively poorly understood in L. monocytogenes. To better understand the genetics of this process, a mariner-based transposon mutagenesis strategy was used to identify genes involved in biofilm formation of L. monocytogenes. A library of 6,500 mutant colonies was screened for reduced biofilm formation using a microtiter plate biofilm assay. Forty biofilm-deficient mutants of L. monocytogenes were identified based on DNA sequences of the transposon-flanking regions and Southern hybridization with a transposon-based probe. The insertions harbored by these mutants led to the identification of 24 distinct loci, 18 of which, to our knowledge, have not been previously reported to function in the biofilm formation in L. monocytogenes. Genetic complementation confirmed the importance of lmo1386, a gene encoding a putative DNA translocase, for biofilm formation. Molecular analyses of mutants indicated that the majority of the 24 identified genes are related to flagella motility, gene regulation, and cell surface structures.

Keywords: Listeria monocytogenes ; Biofilm; Transposon mutagenesis; Genetics

Computational identification of gene over-expression targets for metabolic engineering of taxadiene production by Brett A. Boghigian; John Armando; Daniel Salas; Blaine A. Pfeifer (pp. 2063-2073).

Taxadiene is the first dedicated intermediate in the biosynthetic pathway of the anticancer compound Taxol. Recent studies have taken advantage of heterologous hosts to produce taxadiene and other isoprenoid compounds, and such ventures now offer research opportunities that take advantage of the engineering tools associated with the surrogate host. In this study, metabolic engineering was applied in the context of over-expression targets predicted to improve taxadiene production. Identified targets included genes both within and outside of the isoprenoid precursor pathway. These targets were then tested for experimental over-expression in a heterologous Escherichia coli host designed to support isoprenoid biosynthesis. Results confirmed the computationally predicted improvements and indicated a synergy between targets within the expected isoprenoid precursor pathway and those outside this pathway. The presented algorithm is broadly applicable to other host systems and/or product choices.

Keywords: Taxol; Taxadiene; Taxadiene synthase; Over-expression; E. coli ; Heterologous biosynthesis; Metabolic engineering

Phanerochaete chrysosporium produces a diverse array of extracellular enzymes when grown on sorghum by Anamika Ray; Sayali Saykhedkar; Patricia Ayoubi-Canaan; Steven D. Hartson; Rolf Prade; Andrew J. Mort (pp. 2075-2089).

In an effort to understand how fungi degrade biomass, we grew Phanerochaete chrysosporium on sorghum stover and chronicled the growth of the fungus over the course of 14 days. The fungal mass grew steadily until the fifth day, reaching 0.06 mg of cells per milligram of dry mass, which fell by the seventh day and stayed at nearly the same level until day 14. After 1 day, hemicellulases, cellulases, and polygalacturonases were detected in the extracellular fluid at 1.06, 0.34, and 0.20 U/ml, respectively. Proteomic studies performed with the extracellular fluid using liquid chromatography–tandem mass spectrometry identified 57, 116, and 102 degradative enzymes targeting cellulose, hemicellulose, pectin, lignin, proteins, and lipids on days 1, 7, and 14, respectively. Significant concentrations of breakdown products of the sorghum polysaccharides were detected in the extracellular fluid indicating that the enzymes were breaking the polysaccharides, and after 14 days, almost 39% of the sorghum sugars had been used by the fungus. Our results suggest that P. chrysosporium produces a set of enzymes to degrade the components of lignocellulose from the beginning of its growth, but modifies the complement of enzymes it secretes over time to adapt to the particular substrate available.

Keywords: Phanerochaete chrysosporium ; Proteomics; Sorghum; Lignocellulose

Virulence factor prediction in Streptococcus pyogenes using classification and clustering based on microarray data by Liliana López-Kleine; Francisco Torres-Avilés; Fabio H. Tejedor; Luz A. Gordillo (pp. 2091-2098).

Interesting biological information as, for example, gene expression data (microarrays), can be extracted from publicly available genomic data. As a starting point in order to narrow down the great possibilities of wet lab experiments, global high throughput data and available knowledge should be used to infer biological knowledge and emit biological hypothesis. Here, based on microarray data, we propose the use of cluster and classification methods that have become very popular and are implemented in freely available software in order to predict the participation in virulence mechanisms of different proteins coded by genes of the pathogen Streptococcus pyogenes. Confidence of predictions is based on classification errors of known genes and repetitive prediction by more than three methods. A special emphasis is done on the nonlinear kernel classification methods used. We propose a list of interesting candidates that could be virulence factors or that participate in the virulence process of S. pyogenes. Biological validations should start using this list of candidates as they show similar behavior to known virulence factors.

Keywords: Classification; Microarray data; Protein function; Statistical genomics; Support vector machines; Virulence factor

Detection of invasive Candida albicans infection using a specific ^99mTc-labeled monoclonal antibody for the C. albicans germ tube by Lan Ge; Li Wang; Qiu-He Song; Ming-Fu Yang; Ren-Mei Sun; Bai-Yu Zhong; Yan Xu; Ding-de Huang; Fei Hao (pp. 2099-2108).

Accurate diagnosis is critical for effective treatment of the invasive infection by Candida albicans. Here, we investigated whether a ^99m technetium (Tc)-labeled Fab’ fragment of the monoclonal antibody specific for the C. albicans germ tube could specifically identify an invasive C. albicans infection. The germ tube of C. albicans was used as an immunogen to obtain monoclonal antibodies and the Fab’ fragment of MAb03.2 C1–C2 with highest affinity and specificity was labeled with ^99mTc. In vitro binding assays showed that the labeled Fab’ preferentially bound to the germ tubes of C. albicans (4.23 ± 0.17 × 10² Bq per 1 × 10⁷ cells). These values were significantly higher than those for blastospores of C. albicans, blastospores of heat-killed C. albicans, Aspergillus fumigatus, Staphylococcus aureus, and Escherichia coli (P < 0.05). By using in vivo biodistribution and planar imaging with single photon emission computed tomography, we demonstrated a significant specific accumulation of radioactivity in C. albicans-infected tissues. In summary, ^99mTc-MAb03.2 C1–C2 Fab’ is able to specifically accumulate in C. albicans-infected tissues, but not in tissue infected with A. fumigatus or bacteria or in a sterile inflammation. This study provides a new and specific radiopharmaceutical for the diagnosis of invasive C. albicans infections.

Keywords: Infection imaging; Technetium-^99m labeling; C. albicans ; Diagnosis; Invasive fungal infections

Acetate scavenging activity in Escherichia coli: interplay of acetyl–CoA synthetase and the PEP–glyoxylate cycle in chemostat cultures by Sergio Renilla; Vicente Bernal; Tobias Fuhrer; Sara Castaño-Cerezo; José M. Pastor; José L. Iborra; Uwe Sauer; Manuel Cánovas (pp. 2109-2124).

Impairment of acetate production in Escherichia coli is crucial for the performance of many biotechnological processes. Aerobic production of acetate (or acetate overflow) results from changes in the expression of central metabolism genes. Acetyl−CoA synthetase scavenges extracellular acetate in glucose-limited cultures. Once converted to acetyl−CoA, it can be catabolized by the tricarboxylic acid cycle or the glyoxylate pathway. In this work, we assessed the significance of these pathways on acetate overflow during glucose excess and limitation. Gene expression, enzyme activities, and metabolic fluxes were studied in E. coli knock-out mutants related to the glyoxylate pathway operon and its regulators. The relevance of post-translational regulation by AceK-mediated phosphorylation of isocitrate dehydrogenase for pathway functionality was underlined. In chemostat cultures performed at increasing dilution rates, acetate overflow occurs when growing over a threshold glucose uptake rate. This threshold was not affected in a glyoxylate-pathway-deficient strain (lacking isocitrate lyase, the first enzyme of the pathway), indicating that it is not relevant for acetate overflow. In carbon-limited chemostat cultures, gluconeogenesis (maeB, sfcA, and pck), the glyoxylate operon and, especially, acetyl−CoA synthetase are upregulated. A mutant in acs (encoding acetyl−CoA synthetase) produced acetate at all dilution rates. This work demonstrates that, in E. coli, acetate production occurs at all dilution rates and that overflow is the result of unbalanced synthesis and scavenging activities. The over-expression of acetyl−CoA synthetase by cAMP−CRP-dependent induction limits this phenomenon in cultures consuming glucose at low rate, ensuring the recycling of the acetyl−CoA and acetyl−phosphate pools, although establishing an energy-dissipating substrate cycle.

Keywords: Acetate overflow; PEP glyoxylate cycle; Acetyl−coenzyme A synthetase; Chemostat; ¹³C fluxes; Catabolite repression

A shift to 50°C provokes death in distinct ways for glucose- and oleate-grown cells of Yarrowia lipolytica by Thi Minh Ngoc Ta; Lan Cao-Hoang; Cynthia Romero-Guido; Morgane Lourdin; Hanh Phan-Thi; Sébastien Goudot; Pierre-André Marechal; Yves Waché (pp. 2125-2134).

Based on the observation that shocks provoked by heat or amphiphilic compounds present some similarities, this work aims at studying whether cells grown on oleate (amphiphilic pre-stress) acquire a tolerance to heat shock. In rich media, changing glucose for oleate significantly enhanced the cell resistance to the shock, however, cells grown on a minimal oleate medium lost their ability to grow on agar with the same kinetic than glucose-grown cells (more than 7-log decrease in 18 min compared with 3-log for oleate-grown cells). Despite this difference in kinetics, the sequence of events was similar for oleate-grown cells maintained at 50°C with a (1) loss of ability to form colonies at 27°C, (2) loss of membrane integrity and (3) lysis (observed only for some minimal-oleate-grown cells). Glucose-grown cells underwent different changes. Their membranes, which were less fluid, lost their integrity as well and cells were rapidly inactivated. But, surprisingly, their nuclear DNA was not stained by propidium iodide and other cationic fluorescent DNA-specific probes but became stainable by hydrophobic ones. Moreover, they underwent a dramatic increase in membrane viscosity. The evolution of lipid bodies during the heat shock depended also on the growth medium. In glucose-grown cells, they seemed to coalesce with the nuclear membrane whereas for oleate-grown cells, they coalesced together forming big droplets which could be released in the medium. In some rare cases of oleate-grown cells, lipid bodies were fragmented and occupied all the cell volume. These results show that heat triggers programmed cell death with uncommon hallmarks for glucose-grown cells and necrosis for methyl-oleate-grown cells.

Keywords: Heat; Membrane integrity; Membrane fluidity; Fluorescence; Yarrowia lipolytica ; Programmed cell death; Lipid; Oleate; Chromatin changes

Oxidation of arsenite by two β-proteobacteria isolated from soil by Sachin P. Bachate; Rashmi M. Khapare; Kisan M. Kodam (pp. 2135-2145).

Two heterotrophic As(III)-oxidizing bacteria, SPB-24 and SPB-31 were isolated from garden soil. Based on 16S rRNA gene sequence analysis, strain SPB-24 was closely related to genus Bordetella, and strain SPB-31 was most closely related to genus Achromobacter. Both strains exhibited high As(III) (15 mM for SPB-24 and 40 mM for SPB-31) and As(V) (>300 mM for both strains) resistance. Both strains oxidized 5 mM As(III) in minimal medium with oxidation rate of 554 and 558 μM h⁻¹ for SPB-24 and SPB-31, respectively. Washed cells of both strains oxidized As(III) over broad pH and temperature range with optimum pH 6 and temperature 42°C for both strains. The As(III) oxidation kinetic by washed cells showed K _m and V _max values of 41.7 μM and 1,166 μM h⁻¹ for SPB-24, 52 μM and 1,186 μM h⁻¹ for SPB-31. In the presence of minimal amount of carbon source, the strains showed high As(III) oxidation rate and high specific arsenite oxidase activity. The ability of strains to resist high concentration of arsenic and oxidize As(III) with highest rates reported so far makes them potential candidates for bioremediation of arsenic-contaminated environment.

Keywords: Arsenite oxidation; Achromobacter ; Bordetella

Characterization and regulation of the 2,3-butanediol pathway in Serratia marcescens by Ben Rao; Liao Yuan Zhang; Jian’an Sun; Gang Su; Dongzhi Wei; Ju Chu; Jiawen Zhu; Yaling Shen (pp. 2147-2159).

Serratia marcescens has been proved to be a potential strain for industrial 2,3-butanediol production for its high yield, productivity, and other advantages. In this study, the genes slaA, slaB, slaC, and slaR were successfully cloned which were further confirmed to be encoding acetolactate decarboxylase, acetolactate synthase, 2,3-butanediol dehydrogenase, and a LysR-like regulator, respectively. Unlike in Klebsiella sp. or Klebsiella pneumonie and Vibrio sp. or Vibrio cholerae, the gene slaC is separated from other genes. Then it showed that two regulators, SwrR and SlaR, are in charge of this process by exerting effect on the transcription of genes slaA and slaB. By contrast, the expression of gene slaC is unaffected by the two regulators. It means that these two regulators affect the production of 2,3-butanediol by regulating the production of acetoin. Based on these findings, we successfully accelerated the 2,3-butanediol production by inactivation of gene swrR. The obtained results and further investigations should lead to a more suitable fermentation strategy and strain improvement which would be applicable to the industrial production of 2,3-butanediol.

Keywords: Serratia marcescens ; Acetoin; 2,3-Butanediol; Regulation

Improved detection of Rhodococcus coprophilus with a new quantitative PCR assay by Melanie Wicki; Adrian Auckenthaler; Richard Felleisen; Marianne Liniger; Caroline Loutre; Isabel Niederhauser; Marcel Tanner; Andreas Baumgartner (pp. 2161-2169).

Agricultural practices, such as spreading liquid manure or the utilisation of land as animal pastures, can result in faecal contamination of water resources. Rhodococcus coprophilus is used in microbial source tracking to indicate animal faecal contamination in water. Methods previously described for detecting of R. coprophilus in water were neither sensitive nor specific. Therefore, the aim of this study was to design and validate a new quantitative polymerase chain reaction (qPCR) to improve the detection of R. coprophilus in water. The new PCR assay was based on the R. coprophilus 16S rRNA gene. The validation showed that the new approach was specific and sensitive for deoxyribunucleic acid from target host species. Compared with other PCR assays tested in this study, the detection limit of the new qPCR was between 1 and 3 log lower. The method, including a filtration step, was further validated and successfully used in a field investigation in Switzerland. Our work demonstrated that the new detection method is sensitive and robust to detect R. coprophilus in surface and spring water. Compared with PCR assays that are available in the literature or to the culture-dependent method, the new molecular approach improves the detection of R. coprophilus.

Keywords: Contamination; LightCycler; Sewage; Validation; Water quality

Microbial population analysis of nutrient removal-related organisms in membrane bioreactors by Ana F. Silva; Gilda Carvalho; Adrian Oehmen; Maria Lousada-Ferreira; Arjen van Nieuwenhuijzen; Maria A. M. Reis; M. Teresa Barreto Crespo (pp. 2171-2180).

Membrane bioreactors (MBR) are an important and increasingly implemented wastewater treatment technology, which are operated at low food to microorganism ratios (F/M) and retain slow-growing organisms. Enhanced biological phosphorus removal (EBPR)-related organisms grow slower than ordinary heterotrophs, but have never been studied in detail in MBRs. This study presents a comprehensive analysis of the microorganisms involved in EBPR in pilot- and full-scale MBRs, using fluorescence in situ hybridization (FISH), as well as an overall assessment of other relevant microbial groups. The results showed that polyphosphate accumulating organisms (PAOs) were present at similar levels in all studied MBRs (10% ± 6%), even those without a defined anaerobic zone. Glycogen accumulating organisms were also detected, although rarely. The FISH results correlated well with the observed P removal performance of each plant. The results from this study suggest that a defined anaerobic zone is not necessarily required for putative PAO growth in MBRs, since polyphosphate storage may provide a selective advantage in fulfilling cell maintenance requirements in substrate-limited conditions (low F/M).

Keywords: Membrane bioreactor (MBR); Biological nutrient removal (BNR); Fluorescence in situ hybridization (FISH); Polyphosphate accumulating organisms (PAO); Glycogen accumulating organisms (GAO)

Molecular analysis of the biomass of a fluidized bed reactor treating synthetic vinasse at anaerobic and micro-aerobic conditions by Elisa Rodríguez; Alexandre Lopes; María Fdz.-Polanco; Alfons J. M. Stams; Pedro A. García-Encina (pp. 2181-2191).

The microbial communities (Bacteria and Archaea) established in an anaerobic fluidized bed reactor used to treat synthetic vinasse (betaine, glucose, acetate, propionate, and butyrate) were characterized by denaturing gradient gel electrophoresis (DGGE) and phylogenetic analysis. This study was focused on the competitive and syntrophic interactions between the different microbial groups at varying influent substrate to sulfate ratios of 8, 4, and 2 and anaerobic or micro-aerobic conditions. Acetogens detected along the anaerobic phases at substrate to sulfate ratios of 8 and 4 seemed to be mainly involved in the fermentation of glucose and betaine, but they were substituted by other sugar or betaine degraders after oxygen application. Typical fatty acid degraders that grow in syntrophy with methanogens were not detected during the entire reactor run. Likely, sugar and betaine degraders outnumbered them in the DGGE analysis. The detected sulfate-reducing bacteria (SRB) belonged to the hydrogen-utilizing Desulfovibrio. The introduction of oxygen led to the formation of elemental sulfur (S⁰) and probably other sulfur compounds by sulfide-oxidizing bacteria (γ-Proteobacteria). It is likely that the sulfur intermediates produced from sulfide oxidation were used by SRB and other microorganisms as electron acceptors, as was supported by the detection of the sulfur respiring Wolinella succinogenes. Within the Archaea population, members of Methanomethylovorans and Methanosaeta were detected throughout the entire reactor operation. Hydrogenotrophic methanogens mainly belonging to the genus Methanobacterium were detected at the highest substrate to sulfate ratio but rapidly disappeared by increasing the sulfate concentration.

Keywords: Sulfate-reducing bacteria; DGGE; Micro-aerobic; Sulfur-oxidizing bacteria; Methanogenesis

Methanotrophic community structure and activity under warming and grazing of alpine meadow on the Tibetan Plateau by Yong Zheng; Wei Yang; Xiang Sun; Shi-Ping Wang; Yi-Chao Rui; Cai-Yun Luo; Liang-Dong Guo (pp. 2193-2203).

Knowledge about methanotrophs and their activities is important to understand the microbial mediation of the greenhouse gas CH₄ under climate change and human activities in terrestrial ecosystems. The effects of simulated warming and sheep grazing on methanotrophic abundance, community composition, and activity were studied in an alpine meadow soil on the Tibetan Plateau. There was high abundance of methanotrophs (1.2–3.4 × 10⁸ pmoA gene copies per gram of dry weight soil) assessed by real-time PCR, and warming significantly increased the abundance regardless of grazing. A total of 64 methanotrophic operational taxonomic units (OTUs) were obtained from 1,439 clone sequences, of these OTUs; 63 OTUs (98.4%) belonged to type I methanotrophs, and only one OTU was Methylocystis of type II methanotrophs. The methanotroph community composition and diversity were not apparently affected by the treatments. Warming and grazing significantly enhanced the potential CH₄ oxidation activity. There were significantly negative correlations between methanotrophic abundance and soil moisture and between methanotrophic abundance and NH₄–N content. The study suggests that type I methanotrophs, as the dominance, may play a key role in CH₄ oxidation, and the alpine meadow has great potential to consume more CH₄ under future warmer and grazing conditions on the Tibetan Plateau.

Keywords: Clone library; Grazing; Methanotrophs; pmoA ; Tibetan Plateau; Real-time PCR

Degradation of 2-chlorotoluene by Rhodococcus sp. OCT 10 by Daniel Dobslaw; Karl-Heinrich Engesser (pp. 2205-2214).

A strain Rhodococcus sp. OCT 10 DSM 45596^T, exhibiting 99.9% of 16S rDNA identity with Rhodococcus wratislaviensis NCIMB 13082, was isolated from a soil sample. The strain completely mineralised 2-chlorotoluene, 2-bromotoluene, o-xylene, benzyl alcohol and benzoate. In contrast, 2-fluorotoluene was only partially mineralised. By GC-MS and ¹H-NMR analyses, 4-chloro-3-methylcatechol was identified as the central intermediate in the degradation pathway of 2-chlorotoluene. It was further degraded by enzymes of the meta cleavage pathway. Catechol 1,2-dioxygenase and chlorocatechol 1,2-dioxygenase as the initial enzymes of the ortho cleavage pathways were not detectable under these conditions. Furthermore, neither formation nor oxidation of 2-chlorobenzylic alcohol, 2-chlorobenzaldehyde, or 2-chlorobenzoate was observed, thereby excluding side chain oxidation activity.

Keywords: Degradation; 2-Chlorotoluene; 2-Halotoluene; 4-Chloro-3-methylcatechol; Mineralisation; 2-Chloromethylbenzene

Biodiscovery of new Australian thraustochytrids for production of biodiesel and long-chain omega-3 oils by Kim Jye Lee Chang; Graeme A. Dunstan; Guy C. J. Abell; Lesley A. Clementson; Susan I. Blackburn; Peter D. Nichols; Anthony Koutoulis (pp. 2215-2231).

Heterotrophic growth of thraustochytrids has potential in co-producing a feedstock for biodiesel and long-chain (LC, ≥C₂₀) omega-3 oils. Biodiscovery of thraustochytrids from Tasmania (temperate) and Queensland (tropical), Australia, covered a biogeographic range of habitats including fresh, brackish, and marine waters. A total of 36 thraustochytrid strains were isolated and separated into eight chemotaxonomic groups (A–H) based on fatty acid (FA) and sterol composition which clustered closely with four different genera obtained by 18S rDNA molecular identification. Differences in the relative proportions (%FA) of long-chain C₂₀, C₂₂, omega-3, and omega-6 polyunsaturated fatty acids (PUFA), including docosahexaenoic acid (DHA), docosapentaenoic acid, arachidonic acid, eicosapentaenoic acid (EPA), and saturated FA, as well as the presence of odd-chain PUFA (OC-PUFA) were the major factors influencing the separation of these groups. OC-PUFA were detected in temperate strains of groups A, B, and C (Schizochytrium and Thraustochytrium). Group D (Ulkenia) had high omega-3 LC-PUFA (53% total fatty acids (TFA)) and EPA up to 11.2% TFA. Strains from groups E and F (Aurantiochytrium) contained DHA levels of 50–61% TFA after 7 days of growth in basal medium at 20 °C. Groups G and H (Aurantiochytrium) strains had high levels of 15:0 (20–30% TFA) and the sum of saturated FA was in the range of 32–51%. β,β-Carotene, canthaxanthin, and astaxanthin were identified in selected strains. Phylogenetic and chemotaxonomic groupings demonstrated similar patterns for the majority of strains. Our results demonstrate the potential of these new Australian thraustochytrids for the production of biodiesel in addition to omega-3 LC-PUFA-rich oils.

Keywords: Thraustochytrid; Biodiesel; Polyunsaturated fatty acids; Docosahexaenoic acid

Depolymerization of alginate into a monomeric sugar acid using Alg17C, an exo-oligoalginate lyase cloned from Saccharophagus degradans 2-40 by Hee Taek Kim; Jae Hyuk Chung; Damao Wang; Jieun Lee; Hee Chul Woo; In-Geol Choi; Kyoung Heon Kim (pp. 2233-2239).

Macroalgae are considered to be promising biomass for fuels and chemicals production. To utilize brown macroalgae as biomass, the degradation of alginate, which is the main carbohydrate of brown macroalgae, into monomeric units is a critical prerequisite step. Saccharophagus degradans 2-40 is capable of degrading more than ten different polysaccharides including alginate, and its genome sequence demonstrated that this bacterium contains several putative alginate lyase genes including alg17C. The gene for Alg17C, which is classified into the PL-17 family, was cloned and overexpressed in Escherichia coli. The recombinant Alg17C was found to preferentially act on oligoalginates with degrees of polymerization higher than 2 to produce the alginate monomer, 4-deoxy-l-erythro-5-hexoseulose uronic acid. The optimal pH and temperature for Alg17C were found to be 6 and 40 °C, respectively. The K _M and V _max of Alg17C were 35.2 mg/ml and 41.7 U/mg, respectively. Based on the results of this study, Alg17C could be used as the key enzyme to produce alginate monomers in the process of utilizing alginate for biofuels and chemicals production.

Keywords: Oligoalginate lyase; Alg17C; Polysaccharide lyase-17; Exo-type alginate lyase; Saccharophagus degradans 2-40

A multi-electrode continuous flow microbial fuel cell with separator electrode assembly design by Yongtae Ahn; Bruce E. Logan (pp. 2241-2248).

Scaling up microbial fuel cells (MFCs) requires the development of compact reactors with multiple electrodes. A scalable single chamber MFC (130 mL), with multiple graphite fiber brush anodes and a single air-cathode cathode chamber (27 m²/m³), was designed with a separator electrode assembly (SEA) to minimize electrode spacing. The maximum voltage produced in fed-batch operation was 0.65 V (1,000 Ω) with a textile separator, compared to only 0.18 V with a glass fiber separator due to short-circuiting by anode bristles through this separator with the cathode. The maximum power density was 975 mW/m², with an overall chemical oxygen demand (COD) removal of >90% and a maximum coulombic efficiency (CE) of 53% (50 Ω resistor). When the reactor was switched to continuous flow operation at a hydraulic retention time (HRT) of 8 h, the cell voltage was 0.21 ± 0.04 V, with a very high CE = 85%. Voltage was reduced to 0.13 ± 0.03 V at a longer HRT = 16 h due to a lower average COD concentration, and the CE (80%) decreased slightly with increased oxygen intrusion into the reactor per amount of COD removed. Total internal resistance was 33 Ω, with a solution resistance of 2 Ω. These results show that the SEA type MFC can produce stable power and a high CE, making it useful for future continuous flow treatment using actual wastewaters.

Keywords: Microbial fuel cell; Scaling up; Separator electrode assembly; Continuous flow

Erratum to: Cultivation-independent analysis of archaeal and bacterial communities of the formation water in an Indian coal bed to enhance biotransformation of coal into methane by Durgesh Narain Singh; Ashok Kumar; Munish Prasad Sarbhai; Anil Kumar Tripathi (pp. 2249-2250).

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Applied Microbiology and Biotechnology (v.93, #5)