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Applied Microbiology and Biotechnology (v.97, #1)

Interactions of microorganisms with rare earth ions and their utilization for separation and environmental technology by Hiroshi Moriwaki; Hiroki Yamamoto (pp. 1-8).

In recent years, rare earth elements (REEs) have been widely used in various modern technological devices and the global demand for REE has been increasing. The increased demand for REEs has led to environmental exposure or water pollution from rare earth metal mines and various commercial products. Therefore, the development of a safe technology for the separation and adsorption of REEs is very important from the perspective of green chemistry and environmental pollution. In this review, the application and mechanisms of microorganisms for the removal and extraction of REEs from aqueous solutions are described. In addition, the advantages in using microorganisms for REE adsorption and future studies on this topic are discussed.

Keywords: Rare earth elements; Adsorption; Microorganisms; Mechanism; Teichoic acid

Properties and biotechnological applications of halohydrin dehalogenases: current state and future perspectives by Zhong-Yu You; Zhi-Qiang Liu; Yu-Guo Zheng (pp. 9-21).

Halohydrin dehalogenases (HHDHs) are lyases that catalyze the cleavage of carbon–halogen bond of halohydrins. They also can catalyze the reverse reaction in the presence of nucleophiles such as cyanide, azide, and nitrite ions. HHDHs have been recognized as the ideal tools for the degradation of various halogenated environmental pollutants. Moreover, they can be used as biocatalysts for the kinetic resolution of halohydrins and epoxides, and for the preparation of various substituted alcohols. This review is mainly focused on the current status of research on HHDHs, highlighting the production, characterization, structures and mechanism, protein engineering, and biotechnological applications of HHDHs.

Keywords: Halogenated organic compounds; Halohydrin dehalogenases; Properties; Biotechnological applications

Nanobiotechnology as a novel paradigm for enzyme immobilisation and stabilisation with potential applications in biodiesel production by Madan Lal Verma; Colin J. Barrow; Munish Puri (pp. 23-39).

Nanobiotechnology is emerging as a new frontier of biotechnology. The potential applications of nanobiotechnology in bioenergy and biosensors have encouraged researchers in recent years to investigate new novel nanoscaffolds to build robust nanobiocatalytic systems. Enzymes, mainly hydrolytic class of enzyme, have been extensively immobilised on nanoscaffold support for long-term stabilisation by enhancing thermal, operational and storage catalytic potential. In the present report, novel nanoscaffold variants employed in the recent past for enzyme immobilisation, namely nanoparticles, nanofibres, nanotubes, nanopores, nanosheets and nanocomposites, are discussed in the context of lipase-mediated nanobiocatalysis. These nanocarriers have an inherently large surface area that leads to high enzyme loading and consequently high volumetric enzyme activity. Due to their high tensile strengths, nanoscale materials are often robust and resistant to breakage through mechanical shear in the running reactor making them suitable for multiple reuses. The optimisation of various nanosupports process parameters, such as the enzyme type and selection of suitable immobilisation method may help lead to the development of an efficient enzyme reactor. This might in turn offer a potential platform for exploring other enzymes for the development of stable nanobiocatalytic systems, which could help to address global environmental issues by facilitating the production of green energy. The successful validation of the feasibility of nanobiocatalysis for biodiesel production represents the beginning of a new field of research. The economic hurdles inherent in viably scaling nanobiocatalysts from a lab-scale to industrial biodiesel production are also discussed.

Keywords: Nanoparticle; Nanofibre; Nanotube; Nanosheet; Nanoscaffold; Enzyme; Stabilisation; Analytical techniques; Biodiesel; Reactor

Progress in the research of S-adenosyl-l-methionine production by Ju Chu; Jiangchao Qian; Yingping Zhuang; Siliang Zhang; Yourong Li (pp. 41-49).

This minireview mainly aims at the study of S-adenosyl-l-methionine (SAM) production by microbial fermentation. A brief introduction of the biological role and application of SAM was presented. In general, SAM production can be improved by breeding of the producing strain through the conventional mutation or genetic engineering approach in the molecular or cellular scale, by optimization of culture conditions in the cellular scale or bioreactor engineering scale, or by multiscale approach. The productivity of SAM fermentation has been improved greatly through the efforts of many researchers using the methods previously mentioned. The SAM-producing strains used extensively are Pichia pastoris and Saccharomyces cerevisiae. The effect of SAM on antibiotic production was also exemplified. The skill and scheme beneficial to the improvement of SAM production involves the enhancement of SAM synthetase (methionine adenosyltransferase) activity and selection of engineered constitutive promoters with appropriate strength; seeking for and eliminating the rate-limiting factors in SAM synthesis, namely, knocking off the genes that transform SAM and l-methionine (L-Met) to cysteine; release the feedback inhibition of SAM to methylenetetrahydrofolate reductase; blocking the transsulfuration pathway by interfering the responsible enzymes; enhancing ATP level through pulsed feeding of glycerol; and optimizing the L-Met feeding strategy. Precise control of gene expression and quantitative assessment of physiological parameters in engineered P. pastoris were highlighted. Finally, a discussion of the prospect of SAM production was presented.

Keywords: S-adenosyl-l-methionine; l-Methionine; ATP; l-Methionine adenosyltransferase; Pichia pastoris

Microbial cultivation and the role of microbial resource centers in the omics era by Om Prakash; Yogesh Shouche; Kamlesh Jangid; Joel E. Kostka (pp. 51-62).

Despite tremendous advances in microbial ecology over the past two decades, traditional cultivation methods have failed to grow ecologically more relevant microorganisms in the laboratory, leading to a predominance of weed-like species in the world’s culture collections. In this review, we highlight the gap between culture-based and culture-independent methods of microbial diversity analysis, especially in investigations of slow growers, oligotrophs, and fastidious and recalcitrant microorganisms. Furthermore, we emphasize the importance of microbial cultivation and the acquisition of the cultivation-based phenotypic data for the testing of hypotheses arising from genomics and proteomics approaches. Technical difficulties in cultivating novel microorganisms and how modern approaches have helped to overcome these limitations are highlighted. After cultivation, adequate preservation without changes in genotypic and phenotypic features of these microorganisms is necessary for future research and training. Hence, the contribution of microbial resource centers in the handling, preservation, and distribution of this novel diversity is discussed. Finally, we explore the concept of microbial patenting and requisite guidelines of the “Budapest Treaty” for establishment of an International Depositary Authority.

Keywords: Cultivation; Preservation; Microbial resource centers; Budapest Treaty

Extrachromosomal genetic elements in Micrococcus by Julián Rafael Dib; Wolfgang Liebl; Martin Wagenknecht; María Eugenia Farías; Friedhelm Meinhardt (pp. 63-75).

Micrococci are Gram-positive G + C-rich, nonmotile, nonspore-forming actinomycetous bacteria. Micrococcus comprises ten members, with Micrococcus luteus being the type species. Representatives of the genus play important roles in the biodegradation of xenobiotics, bioremediation processes, production of biotechnologically important enzymes or bioactive compounds, as test strains in biological assays for lysozyme and antibiotics, and as infective agents in immunocompromised humans. The first description of plasmids dates back approximately 28 years, when several extrachromosomal elements ranging in size from 1.5 to 30.2 kb were found in Micrococcus luteus. Up to the present, a number of circular plasmids conferring antibiotic resistance, the ability to degrade aromatic compounds, and osmotolerance are known, as well as cryptic elements with unidentified functions. Here, we review the Micrococcus extrachromosomal traits reported thus far including phages and the only quite recently described large linear extrachromosomal genetic elements, termed linear plasmids, which range in size from 75 kb (pJD12) to 110 kb (pLMA1) and which confer putative advantageous capabilities, such as antibiotic or heavy metal resistances (inferred from sequence analyses and curing experiments). The role of the extrachromosomal elements for the frequently proven ecological and biotechnological versatility of the genus will be addressed as well as their potential for the development and use as genetic tools.

Keywords: Micrococcus ; Extrachromosomal elements; Plasmid; Linear plasmid; Phage

Biochemical mutagens affect the preservation of fungi and biodiversity estimations by R. Russell M. Paterson; Nelson Lima (pp. 77-85).

Many fungi have significant industrial applications or biosafety concerns and maintaining the original characteristics is essential. The preserved fungi have to represent the situation in nature for posterity, biodiversity estimations, and taxonomic research. However, spontaneous fungal mutations and secondary metabolites affecting producing fungi are well known. There is increasing interest in the preservation of microbes in Biological Resource Centers (BRC) to ensure that the organisms remain viable and stable genetically. It would be anathema if they contacted mutagens routinely. However, for the purpose of this discussion, there are three potential sources of biochemical mutagens when obtaining individual fungi from the environment: (a) mixtures of microorganisms are plated routinely onto growth media containing mutagenic antibiotics to control overgrowth by contaminants, (b) the microbial mixtures may contain microorganisms capable of producing mutagenic secondary metabolites, and (c) target fungi for isolation may produce “self” mutagens in pure culture. The probability that these compounds could interact with fungi undermines confidence in the preservation process and the potential effects of these biochemical mutagens are considered for the first time on strains held in BRC in this review.

Keywords: Fungi; Preservation; Secondary metabolites; Biochemical mutagens; Self mutagens

New strategies for drug discovery: activation of silent or weakly expressed microbial gene clusters by Kozo Ochi; Takeshi Hosaka (pp. 87-98).

Genome sequencing of Streptomyces, myxobacteria, and fungi showed that although each strain contains genes that encode the enzymes to synthesize a plethora of potential secondary metabolites, only a fraction are expressed during fermentation. Interest has therefore grown in the activation of these cryptic pathways. We review current progress on this topic, describing concepts for activating silent genes, utilization of “natural” mutant-type RNA polymerases and rare earth elements, and the applicability of ribosome engineering to myxobacteria and fungi, the microbial groups known as excellent searching sources, as well as actinomycetes, for secondary metabolites.

Keywords: Silent gene activation; Strain improvement; Ribosome engineering; Rare earth elements

Combining in the melt physical and biological properties of poly(caprolactone) and chlorhexidine to obtain antimicrobial surgical monofilaments by R. Scaffaro; L. Botta; M. Sanfilippo; G. Gallo; G. Palazzolo; A. M. Puglia (pp. 99-109).

Bacterial infections on a sutured wound represent a critical problem, and the preparation of suture threads possessing antimicrobial properties is valuable. In this work, poly(caprolactone) (PCL) monofilaments were compounded at the concentration of 1, 2 and 4 % (w/w), respectively, to the antiseptic chlorhexidine diacetate (CHX). The incorporation was carried out in the melt by a single-step methodology, i.e. “online” approach. Mechanical tests revealed that the incorporation of CHX does not significantly change tensile properties of PCL fibres as the thermal profile adopted to prepare the compounded fibres does not compromise the antibacterial activity of CHX. In fact, CHX confers to compounded PCL fibres’ antimicrobial property even at the lowest CHX concentration as revealed by microbiological assays performed on Escherichia coli, Micrococcus luteus and Bacillus subtilis strains. The scanning electron microscope micrographs and energy-dispersive X-ray analysis of compounded threads revealed that CHX is uniformly distributed on fibre surface and that the overall amount of superficial CHX increases by increasing compounded CHX concentration. This distribution determines a biphasic CHX release kinetics characterized by an initial rapid solubilisation of superficial CHX micro-crystals, followed by a slow and gradual release of CHX incorporated in the bulk. Interestingly, the compounded threads did not show any toxic effect compromising cell viability of human fibroblasts in vitro, differently from that observed using an equal amount of pure CHX. Thus, this study originally demonstrated the effectiveness of an “online” approach to confer antimicrobial properties to an organic thermoplastic polymeric material commonly used for medical devices.

Keywords: Antimicrobial filaments; Chlorhexidine; Melt processing; Poly(caprolactone)

CAP, a new human suspension cell line for influenza virus production by Yvonne Genzel; Ilona Behrendt; Jana Rödig; Erdmann Rapp; Claudia Kueppers; Stefan Kochanek; Gudrun Schiedner; Udo Reichl (pp. 111-122).

Forced by major drawbacks of egg-based influenza virus production, several studies focused on the establishment and optimization of cell-based production systems. Among numerous possible host cell lines from duck, monkey, canine, chicken, mouse, and human origin, only a few will meet regulatory requirements, accomplish industrial standards, and result in high virus titers. From primary virus isolation up to large-scale manufacturing of human vaccines, however, the most logical choice seems to be the use of human cell lines. For this reason, we evaluated the recently established CAP cell line derived from human amniocytes for its potential in influenza virus production in suspension culture in small scale shaker flask and stirred tank bioreactor experiments. Different human and animal influenza viruses could be adapted to produce hemagglutination (HA) titers of at least 2.0 log₁₀ HA units/100 μL without further process optimization. Adjusting trypsin activity as well as infection conditions (multiplicity of infection, infection medium) resulted in HA titers of up to 3.2 log₁₀ HA units/100 μL and maximum cell-specific virus productivities of 6,400 virions/cell (for human influenza A/PR/8/34 as a reference). Surface membrane expression of sialyloligosaccharides as well as HA N-glycosylation patterns were characterized. Overall, experimental results clearly demonstrate the potential of CAP cells for achieving high virus yields for different influenza strains and the option to introduce a highly attractive fully characterized human cell line compliant with regulatory and industrial requirements as an alternative for influenza virus vaccine production.

Keywords: Human cell line; Amniocytes; Influenza virus; Vaccine production; Suspension growth; Trypsin; Glycosylation; Bioreactor

Production of polysaccharide from Agaricus subrufescens Peck on solid-state fermentation by C. M. Camelini; A. Gomes; F. T. G. S. Cardozo; C. M. O. Simões; M. J. Rossi; A. J. Giachini; J. C. C. Petrus; M. M. de Mendonça (pp. 123-133).

The interest upon products obtained from fungi has increased during the recent years. Among the most noticeable, nutraceuticals, enzymes, and natural drugs occupy a privileged position. Fungal biomass for the obtainment of those products can be produced either by solid-state fermentation (SSF) or submersed fermentation. SSF has been employed for the production of spawn on pretreated wheat grains with the objective of increasing the fungal polysaccharide (glucomannans) contents. Among the important factors for the production of spawn, time of cooking, time of resting after grain cooking, consequently grain moisture, substrate pH, temperature of incubation, and initial inoculum amount are among the most significant. For wheat grains, cooking time of 21 min followed by a 24-min resting time has been shown as optimal for the production of glucomannans by the fungus Agaricus subrufescens (=Agaricus brasiliensis). Amendments of CaSO₄ (up to 3 %) and CaCO₃ (up to 1 %) had an important influence on the substrate pH. In general, better results for glucomannan production were obtained when no supplement was added or when up to 0.25 % CaCO₃ (pH 6.6) has been added to the mix. Our results demonstrate that the inoculum amount necessary for the best polysaccharide levels is around 10.3 %, while the best temperature is around 27.2 °C. Besides using the spawn for its main purpose, it could potentially and alternatively be used as nutraceutical due to the high levels of glucomannan observed (6.89 %), a compound technically proven to be a potent immunostimulatory and antitumoral agent.

Keywords: Agaricus subrufescens ; Mycelial biomass; Polysaccharide; Solid-state fermentation

Controlling autonomous underwater floating platforms using bacterial fermentation by Justin C. Biffinger; Lisa A. Fitzgerald; Erinn C. Howard; Emily R. Petersen; Preston A. Fulmer; Peter K. Wu; Bradley R. Ringeisen (pp. 135-142).

Biogenic gas has a wide range of energy applications from being used as a source for crude bio-oil components to direct ignition for heating. The current study describes the use of biogenic gases from Clostridium acetobutylicum for a new application—renewable ballast regeneration for autonomous underwater devices. Uninterrupted (continuous) and blocked flow (pressurization) experiments were performed to determine the overall biogas composition and total volume generated from a semirigid gelatinous matrix. For stopped flow experiments, C. acetobutylicum generated a maximum pressure of 55 psi over 48 h composed of 60 % hydrogen gas when inoculated in a 5 % agar (w/v) support with 5 % glucose (w/v) in the matrix. Typical pressures over 24 h at 318 K ranged from 10 to 33 psi. These blocked flow experiments show for the first time the use of microbial gas production as a way to repressurize gas cylinders. Continuous flow experiments successfully demonstrated how to deliver biogas to an open ballast control configuration for deployable underwater platforms. This study is a starting point for engineering and microbiology investigations of biogas which will advance the integration of biology within autonomous systems.

Keywords: Clostridium acetobutylicum ; Hydrogen; Pressure; Ballast; Fermentation

Reductive whole-cell biotransformation with Corynebacterium glutamicum: improvement of NADPH generation from glucose by a cyclized pentose phosphate pathway using pfkA and gapA deletion mutants by Solvej Siedler; Steffen N. Lindner; Stephanie Bringer; Volker F. Wendisch; Michael Bott (pp. 143-152).

In this study, the potential of Corynebacterium glutamicum for reductive whole-cell biotransformation is shown. The NADPH-dependent reduction of the prochiral methyl acetoacetate (MAA) to the chiral (R)-methyl 3-hydroxybutyrate (MHB) by an alcohol dehydrogenase from Lactobacillus brevis (Lbadh) was used as model reaction and glucose served as substrate for the regeneration of NADPH. Since NADPH is mainly formed in the oxidative branch of the pentose phosphate pathway (PPP), C. glutamicum was engineered to redirect carbon flux towards the PPP. Mutants lacking the genes for 6-phosphofructokinase (pfkA) or glyceraldehyde 3-phosphate dehydrogenase (gapA) were constructed and analyzed with respect to growth, enzyme activities, and biotransformation performance. Both mutants showed strong growth defects in glucose minimal medium. For biotransformation of MAA to MHB using glucose as reductant, strains were transformed with an Lbadh expression plasmid. The wild type showed a specific MHB production rate of 3.1 mmol_MHB h⁻¹ g _cdw ⁻¹ and a yield of 2.7 mol_MHB mol _glucose ⁻¹ . The ∆pfkA mutant showed a similar MHB production rate, but reached a yield of 4.8 mol_MHB mol _glucose ⁻¹ , approaching the maximal value of 6 mol_NADPH mol _glucose ⁻¹ expected for a partially cyclized PPP. The specific biotransformation rate of the ΔgapA mutant was decreased by 62 % compared to the other strains, but the yield was increased to 7.9 mol_MHB mol _glucose ⁻¹ , which to our knowledge is the highest one reported so far for this mode of NADPH regeneration. As one fourth of the glucose was converted to glycerol, the experimental yield was close to the theoretically maximal yield of 9 mol_NADPH mol _glucose ⁻¹ .

Keywords: Corynebacterium glutamicum ; Pathway engineering; NADPH yield; Pentose phosphate pathway; Resting cells; Reductive whole-cell biotransformation; Phosphofructokinase; Glyceraldehyde 3-phosphate dehydrogenase; pfk ; gap

Comparative characterization of recombinant ZZ protein–alkaline phosphatase and its application in enzyme immunoassays by Jin-Bao Tang; Hong-Ming Yang; Shu-Juan Liang; Yong Chen; Qing-Jie Mu; Jin-Bao Zhang (pp. 153-158).

A functional fusion protein, which consists of an antibody and an enzyme that can be used in enzyme immunoassays, has been constructed. However, a quantitative comparison of the characteristics of fusion proteins and chemical conjugates of the parents, which are functionally produced in a uniform microbial system, has not been adequately achieved. In this study, a fusion protein between the ZZ protein and Escherichia coli alkaline phosphatase (AP) and the parental ZZ protein and AP for chemical conjugate was functionally produced in the same bacterial system. A detailed examination of the ZZ–AP fusion protein and the effect of the ZZ–AP chemical conjugate on IgG affinity and enzymatic activity were performed. Compared with the parents, the equilibrium dissociation constant of ZZ–AP conjugate decreased by 32 % and catalytic activity decreased by 24 %, whereas the ZZ–AP fusion retained full parental activities and exhibited an approximately tenfold higher sensitivity than that of ZZ–AP conjugate in enzyme-linked immunosorbent assay. Thus, ZZ–AP fusion is a promising immunoreagent for IgG detection and a potential biolinker between antibodies and reporter enzymes (i.e., IgG–ZZ–AP fusion complex) in immunoassays.

Keywords: Alkaline phosphatase; Chemical conjugate; Enzyme immunoassay; Fusion protein; IgG; ZZ protein

A comparative study of hydrolysis and transglycosylation activities of fungal β-glucosidases by Christina Bohlin; Eigil Praestgaard; Martin J. Baumann; Kim Borch; Jens Praestgaard; Rune N. Monrad; Peter Westh (pp. 159-169).

β-glucosidases (BGs) from Aspergillus fumigatus, Aspergillus niger, Aspergillus oryzae, Magnaporthe grisea, Neurospora crassa, and Penicillium brasilianum were purified to homogeneity, and investigated for their (simultaneous) hydrolytic and transglycosylation activity in samples with high concentrations of either cellobiose or glucose. The rate of the hydrolytic process (which converts one cellobiose to two glucose molecules) shows a maximum around 10–15 mM cellobiose and decreases with further increase in the concentration of substrate. At the highest investigated concentration (100 mM cellobiose), the hydrolytic activity for the different enzymes ranged from 10% to 55% of the maximum value. This decline in hydrolysis was essentially compensated by increased transglycosylation (which converts two cellobiose to one glucose and one trisaccharide). Hence, it was concluded that the hydrolytic slowdown at high substrate concentrations solely relies on an increased flow through the transglycosylation pathway and not an inhibition that delays the catalytic cycle. Transglycosylation was also detected at high product (glucose) concentrations, but in this case, it was not a major cause for the slowdown in hydrolysis. The experimental data was modeled to obtain kinetic parameters for both hydrolysis and transglycosylation. These parameters were subsequently used in calculations that quantified the negative effects on BG activity of respectively transglycosylation and product inhibition. The kinetic parameters and the mathematical method presented here allow estimation of these effects, and we suggest that this may be useful for the evaluation of BGs for industrial use.

Keywords: β-glucosidase; Hydrolytic activity; Transglycosylation activity; Substrate inhibition

Mitsuaria chitosanase with unrevealed important amino acid residues: characterization and enhanced production in Pichia pastoris by Nan Peng; Weiling Xu; Fan Wang; Jinlong Hu; Minhui Ma; Yuanliang Hu; Shumiao Zhao; Yunxiang Liang; Xiangyang Ge (pp. 171-179).

A chitosan plate assay was employed to screen for chitosanase-producing bacterial strains and isolate 141 was found to exhibit high activity. Characterization of this isolate revealed that it belonged to Mitsuaria (designated as Mitsuaria sp. 141). The encoded chitosanase (choA) gene was then cloned by PCR and the deduced amino acid sequence showed 98% identity to a formerly described Mitsuaria chitosanitabida 3001 ChoA (McChoA). Surprisingly, the ChoA encoded by Mitsuaria sp. 141 (MsChoA) appeared to have a much higher optimum temperature compared to McChoA. Site-directed mutagenesis was then employed to generate five MschoA mutant genes encoding MsChoA K204Q, R216K, T222N, R216K/T222N, or K204Q/R216K/T222N. All the ChoA mutants exhibited a much lower specific activity and a lower optimum temperature. The results confirmed that the substitution of three non-conserved amino acids accounts for the major reduction of the enzyme activity in MsChoA. Furthermore, the MschoA gene was cloned for over-expression in Pichia pastoris after coding sequence optimization. One of the P. pastoris transformants with Mut^S phenotype was found to produce 1,480.2 ± 340.9 U ChoA mL⁻¹ of cell culture by high-cell-density fermentation. This represents the highest yield of recombinant ChoA production that has ever been reported thus far. The recombinant P. pastoris strain should therefore be well suited for industrial-scale production of chitosanase.

Keywords: Chitosanase; Mitsuaria ; Site-directed mutagenesis; Coding sequence optimization; High-cell-density fermentation

4,6-α-Glucanotransferase activity occurs more widespread in Lactobacillus strains and constitutes a separate GH70 subfamily by Hans Leemhuis; Willem P. Dijkman; Justyna M. Dobruchowska; Tjaard Pijning; Pieter Grijpstra; Slavko Kralj; Johannis P. Kamerling; Lubbert Dijkhuizen (pp. 181-193).

Family 70 glycoside hydrolase glucansucrase enzymes exclusively occur in lactic acid bacteria and synthesize a wide range of α-d-glucan (abbreviated as α-glucan) oligo- and polysaccharides. Of the 47 characterized GH70 enzymes, 46 use sucrose as glucose donor. A single GH70 enzyme was recently found to be inactive with sucrose and to utilize maltooligosaccharides [(1→4)-α-d-glucooligosaccharides] as glucose donor substrates for α-glucan synthesis, acting as a 4,6-α-glucanotransferase (4,6-αGT) enzyme. Here, we report the characterization of two further GH70 4,6-αGT enzymes, i.e., from Lactobacillus reuteri strains DSM 20016 and ML1, which use maltooligosaccharides as glucose donor. Both enzymes cleave α1→4 glycosidic linkages and add the released glucose moieties one by one to the non-reducing end of growing linear α-glucan chains via α1→6 glycosidic linkages (α1→4 to α1→6 transfer activity). In this way, they convert pure maltooligosaccharide substrates into linear α-glucan product mixtures with about 50% α1→6 glycosidic bonds (isomalto/maltooligosaccharides). These new α-glucan products may provide an exciting type of carbohydrate for the food industry. The results show that 4,6-αGTs occur more widespread in family GH70 and can be considered as a GH70 subfamily. Sequence analysis allowed identification of amino acid residues in acceptor substrate binding subsites +1 and +2, differing between GH70 GTF and 4,6-αGT enzymes.

Keywords: α-Glucan; Fiber; Glucansucrase; Glycoside hydrolase; 4,6-α-Glucanotransferase; Isomaltooligosaccharide; Starch

A comparison of two novel alcohol dehydrogenase enzymes (ADH1 and ADH2) from the extreme halophile Haloferax volcanii by Leanne M. Timpson; Ann-Kathrin Liliensiek; Diya Alsafadi; Jennifer Cassidy; Michael A. Sharkey; Susan Liddell; Thorsten Allers; Francesca Paradisi (pp. 195-203).

Haloarchaeal alcohol dehydrogenases are exciting biocatalysts with potential industrial applications. In this study, two alcohol dehydrogenase enzymes from the extremely halophilic archaeon Haloferax volcanii (HvADH1 and HvADH2) were homologously expressed and subsequently purified by immobilized metal-affinity chromatography. The proteins appeared to copurify with endogenous alcohol dehydrogenases, and a double Δadh2 Δadh1 gene deletion strain was constructed to prevent this occurrence. Purified HvADH1 and HvADH2 were compared in terms of stability and enzymatic activity over a range of pH values, salt concentrations, and temperatures. Both enzymes were haloalkaliphilic and thermoactive for the oxidative reaction and catalyzed the reductive reaction at a slightly acidic pH. While the NAD⁺-dependent HvADH1 showed a preference for short-chain alcohols and was inherently unstable, HvADH2 exhibited dual cofactor specificity, accepted a broad range of substrates, and, with respect to HvADH1, was remarkably stable. Furthermore, HvADH2 exhibited tolerance to organic solvents. HvADH2 therefore displays much greater potential as an industrially useful biocatalyst than HvADH1.

Keywords: Alcohol dehydrogenase; Biocatalyst discovery; Protein characterization; Extremophile; Haloferax volcanii ; Organic solvents

Efficient (R)-3-hydroxybutyrate production using acetyl CoA-regenerating pathway catalyzed by coenzyme A transferase by Ken’ichiro Matsumoto; Takehiro Okei; Inori Honma; Toshihiko Ooi; Hirobumi Aoki; Seiichi Taguchi (pp. 205-210).

(R)-3-hydroxybutyrate [(R)-3HB] is a useful precursor in the synthesis of value-added chiral compounds such as antibiotics and vitamins. Typically, (R)-3HB has been microbially produced from sugars via modified (R)-3HB-polymer-synthesizing pathways in which acetyl CoA is converted into (R)-3-hydroxybutyryl-coenzyme A [(R)-3HB-CoA] by β-ketothiolase (PhaA) and acetoacetyl CoA reductase (PhaB). (R)-3HB-CoA is hydrolyzed into (R)-3HB by modifying enzymes or undergoes degradation of the polymerized product. In the present study, we constructed a new (R)-3HB-generating pathway from glucose by using propionyl CoA transferase (PCT). This pathway was designed to excrete (R)-3HB by means of a PCT-catalyzed reaction coupled with regeneration of acetyl CoA, the starting substance for synthesizing (R)-3HB-CoA. Considering the equilibrium reaction of PCT, the PCT-catalyzed (R)-3HB production would be expected to be facilitated by the addition of acetate since it acts as an acceptor of CoA. As expected, the engineered Escherichia coli harboring the phaAB and pct genes produced 1.0 g L⁻¹ (R)-3HB from glucose, and with the addition of acetate into the medium, the concentration was increased up to 5.2 g L⁻¹, with a productivity of 0.22 g L⁻¹ h⁻¹. The effectiveness of the extracellularly added acetate was evaluated by monitoring the conversion of ¹³C carbonyl carbon-labeled acetate into (R)-3HB using gas chromatography/mass spectrometry. The enantiopurity of (R)-3HB was determined to be 99.2% using chiral liquid chromatography. These results demonstrate that the PCT pathway achieved a rapid co-conversion of glucose and acetate into (R)-3HB.

Keywords: Chiral synthesis; Enantioselective; Production rate; Polyhydroxybutyrate; Polyhydroxyalkanoate

Polyester hydrolytic and synthetic activity catalyzed by the medium-chain-length poly(3-hydroxyalkanoate) depolymerase from Streptomyces venezuelae SO1 by Marta Santos; Joana Gangoiti; Helmut Keul; Martin Möller; Juan L. Serra; María J. Llama (pp. 211-222).

The extracellular medium-chain-length polyhydroxyalkanote (MCL-PHA) depolymerase from an isolate identified as Streptomyces venezuelae SO1 was purified to electrophoretic homogeneity and characterized. The molecular mass and pI of the purified enzyme were approximately 27 kDa and 5.9, respectively. The depolymerase showed its maximum activity in the alkaline pH range and 50 °C and retained more than 70 % of its initial activity after 8 h at 40 °C. The MCL-PHA depolymerase hydrolyzes various p-nitrophenyl-alkanoates and polycaprolactone but not polylactide, poly-3-hydroxybutyrate, and polyethylene succinate. The enzymatic activity was markedly enhanced by the presence of low concentrations of detergents and organic solvents, being inhibited by dithiothreitol and EDTA. The potential of using the enzyme to produce (R)-3-hydroxyoctanoate in aqueous media or to catalyze ester-forming reactions in anhydrous media was investigated. In this sense, the MCL-PHA depolymerase catalyzes the hydrolysis of poly-3-hydroxyoctanoate to monomeric units and the ring-opening polymerization of β-butyrolactone and lactides, while ε-caprolactone and pentadecalactone were hardly polymerized.

Keywords: Screening; MCL-PHA depolymerase; Streptomyces ; Enzymatic ring-opening polymerization; (R)-3-hydroxyoctanoic acid

Yeast genes involved in sulfur and nitrogen metabolism affect the production of volatile thiols from Sauvignon Blanc musts by Michael J. Harsch; Richard C. Gardner (pp. 223-235).

Two volatile thiols, 3-mercaptohexan-1-ol (3MH), and 3-mercaptohexyl-acetate (3MHA), reminiscent of grapefruit and passion fruit respectively, are critical varietal aroma compounds in Sauvignon Blanc (SB) wines. These aromatic thiols are not present in the grape juice but are synthesized and released by the yeast during alcoholic fermentation. Single deletion mutants of 67 candidate genes in a laboratory strain of Saccharomyces cerevisiae were screened using gas chromatography mass spectrometry for their thiol production after fermentation of SB grape juice. None of the deletions abolished production of the two volatile thiols. However, deletion of 17 genes caused increases or decreases in production by as much as twofold. These 17 genes, mostly related to sulfur and nitrogen metabolism in yeast, may act by altering the regulation of the pathway(s) of thiol production or altering substrate supply. Deleting subsets of these genes in a wine yeast strain gave similar results to the laboratory strain for sulfur pathway genes but showed strain differences for genes involved in nitrogen metabolism. The addition of two nitrogen sources, urea and di-ammonium phosphate, as well as two sulfur compounds, cysteine and S-ethyl-L-cysteine, increased 3MH and 3MHA concentrations in the final wines. Collectively these results suggest that sulfur and nitrogen metabolism are important in regulating the synthesis of 3MH and 3MHA during yeast fermentation of grape juice.

Keywords: Saccharomyces cerevisiae ; Sauvignon Blanc; Single-gene deletion; Aroma compounds; Wine; Varietal thiols

Characterization of putative class II bacteriocins identified from a non-bacteriocin-producing strain Lactobacillus casei ATCC 334 by Yang-Cheng Kuo; Cheng-Feng Liu; Jhao-Fen Lin; An-Chieh Li; Ta-Chun Lo; Thy-Hou Lin (pp. 237-246).

Several putative class II bacteriocin-like genes were identified in Lactobacillus casei ATCC 334, all of which might encode peptides with a double-glycine leader. Six peptides encoded by these genes were heterologously expressed in Escherichia coli and then partially purified in order to test their bacteriocin activity. The results revealed that the mature LSEI_2163 peptide was a class IId bacteriocin that exhibited antimicrobial activity against some lactobacilli and several Listeria species. Similarly, mature LSEI_2386 was a putative pheromone peptide that also had significant bacteriocin activity against several Listeria species. The activities of both peptides tolerated 121°C for 30 min but not treatment with proteinase K or trypsin. The two Cys residues located at positions 4 and 24 in the mature LSEI_2163 peptide were shown by mass spectrometry to form a disulfide bridge, which was required for optimal antibacterial activity. However, replacement of one or both Cys with Ser would cause significant reduction of the antibacterial activity, the reduction being greater when only one of the Cys residues (C4S) was replaced than when both (C4S/C24S) were replaced.

Keywords: Class II bacteriocin; Lactobacillus casei ; Double-glycine leader peptide; Heterologous expression

Microbial production of N-acetyl cis-4-hydroxy-l-proline by coexpression of the Rhizobium l-proline cis-4-hydroxylase and the yeast N-acetyltransferase Mpr1 by Thi Mai Hoa Bach; Ryotaro Hara; Kuniki Kino; Iwao Ohtsu; Nobuyuki Yoshida; Hiroshi Takagi (pp. 247-257).

The proline analogue cis-4-hydroxy-l-proline (CHOP), which inhibits the biosynthesis of collagen, has been clinically evaluated as an anticancer drug, but its water solubility and low molecular weight limits its therapeutic potential since it is rapidly excreted. In addition, CHOP is too toxic to be practical as an anticancer drug, due primarily to its systematic effects on noncollagen proteins. To promote CHOP’s retention in blood and/or to decrease its toxicity, N-acetylation of CHOP might be a novel approach as a prodrug. The present study was designed to achieve the microbial production of N-acetyl CHOP from l-proline by coexpression of l-proline cis-4-hydroxylases converting l-proline into CHOP (SmP4H) from the Rhizobium Sinorhizobium meliloti and N-acetyltransferase converting CHOP into N-acetyl CHOP (Mpr1) from the yeast Saccharomyces cerevisiae. We constructed a coexpression plasmid harboring both the SmP4H and Mpr1 genes and introduced it into Escherichia coli BL21(DE3) or its l-proline oxidase gene-disrupted (ΔputA) strain. M9 medium containing l-proline produced more N-acetyl CHOP than LB medium containing l-proline. E. coli ΔputA cells accumulated l-proline (by approximately 2-fold) compared to that in wild-type cells, but there was no significant difference in CHOP production between wild-type and ΔputA cells. The addition of NaCl and l-ascorbate resulted in a 2-fold increase in N-acetyl CHOP production in the l-proline-containing M9 medium. The highest yield of N-acetyl CHOP was achieved at 42 h cultivation in the optimized medium. Five unknown compounds were detected in the total protein reaction, probably due to the degradation of N-acetyl CHOP. Our results suggest that weakening of the degradation or deacetylation pathway improves the productivity of N-acetyl CHOP.

Keywords: l-Proline; cis-4-Hydroxy-l-proline; N-Acetyl cis-4-hydroxy-l-proline; l-Proline cis-4-hydroxylase; N-Acetyltransferase Mpr1

Six novel constitutive promoters for metabolic engineering of Aspergillus niger by Marzena Blumhoff; Matthias G. Steiger; Hans Marx; Diethard Mattanovich; Michael Sauer (pp. 259-267).

Genetic tools for the fine-tuning of gene expression levels are a prerequisite for rational strain optimization through metabolic engineering. While Aspergillus niger is an industrially important fungus, widely used for production of organic acids and heterologous proteins, the available genetic tool box for this organism is still rather limited. Here, we characterize six novel constitutive promoters of A. niger providing different expression levels. The selection of the promoters was based on published transcription data of A. niger. The promoter strength was determined with the β-glucuronidase (gusA) reporter gene of Escherichia coli. The six promoters covered a GUS activity range of two to three orders of magnitude depending on the strain background. In order to demonstrate the power of the newly characterized promoters for metabolic engineering, they were used for heterologous expression of the cis-aconitate decarboxylase (cad1) gene of Aspergillus terreus, allowing the production of the building block chemical itaconic acid with A. niger. The CAD activity, dependent on the choice of promoter, showed a positive correlation with the specific productivity of itaconic acid. Product titers from the detection limit to up to 570 mg/L proved that the set of constitutive promoters is a powerful tool for the fine-tuning of metabolic pathways for the improvement of industrial production processes.

Keywords: Promoter study; Aspergillus niger ; Metabolic engineering; Genetic engineering; Heterologous protein expression; Itaconic acid

Increased production of fatty acids and triglycerides in Aspergillus oryzae by enhancing expressions of fatty acid synthesis-related genes by Koichi Tamano; Kenneth S. Bruno; Sue A. Karagiosis; David E. Culley; Shuang Deng; James R. Collett; Myco Umemura; Hideaki Koike; Scott E. Baker; Masayuki Machida (pp. 269-281).

Microbial production of fats and oils is being developed as a means of converting biomass to biofuels. Here we investigate enhancing expression of enzymes involved in the production of fatty acids and triglycerides as a means to increase production of these compounds in Aspergillus oryzae. Examination of the A. oryzae genome demonstrates that it contains two fatty acid synthases and several other genes that are predicted to be part of this biosynthetic pathway. We enhanced the expression of fatty acid synthesis-related genes by replacing their promoters with the promoter from the constitutively highly expressed gene tef1. We demonstrate that by simply increasing the expression of the fatty acid synthase genes we successfully increased the production of fatty acids and triglycerides by more than two-fold. Enhancement of expression of the fatty acid pathway genes ATP-citrate lyase and palmitoyl-ACP thioesterase increased productivity to a lesser extent. Increasing expression of acetyl-CoA carboxylase caused no detectable change in fatty acid levels. Increases in message level for each gene were monitored using quantitative real-time reverse transcription polymerase chain reaction. Our data demonstrate that a simple increase in the abundance of fatty acid synthase genes can increase the detectable amount of fatty acids.

Keywords: Fatty acid; Triglyceride; Biofuel; Productivity; Aspergillus oryzae

Overcoming recalcitrant transformation and gene manipulation in Pucciniomycotina yeasts by Erika P. Abbott; Giuseppe Ianiri; Raffaello Castoria; Alexander Idnurm (pp. 283-295).

The red yeasts of the Pucciniomycotina have rarely been transformed with DNA molecules. Transformation methods were recently developed for a species of Sporobolomyces, based on selection using uracil auxotrophs and plasmids carrying the wild-type copies of the URA3 and URA5 genes. However, these plasmids were ineffective in the transformation of closely related species. Using the genome-sequenced strain of Rhodotorula graminis as a starting point, the URA3 and URA5 genes were cloned and tested for the transformation ability into different Pucciniomycotina species by biolistic and Agrobacterium-mediated transformations. Transformation success depended on the red yeast species and the origin of the URA3 or URA5 genes, which may be related to the high G + C DNA content found in several species. A new vector was generated to confer resistance to nourseothricin, using a native promoter from R. graminis and the naturally high G + C nourseothricin acetyltransferease gene. This provides a second selectable marker in these species. Targeted gene disruption was tested in Sporobolomyces sp. IAM 13481 using different lengths of homologous DNA with biolistic and Agrobacterium transformation methods. Both DNA delivery methods were effective for targeted replacement of a gene required for carotenoid pigment biosynthesis. The constructs also triggered transgene silencing. These developments open the way to identify and manipulate gene functions in a large group of basidiomycete fungi.

Keywords: Basidiomycete; Rhodotorula slooffiae ; Rhodosporidium kratochvilovae ; β-Carotene; RNAi; T-DNA

Novel physiological roles for glutathione in sequestering acetaldehyde to confer acetaldehyde tolerance in Saccharomyces cerevisiae by Yoshimi Matsufuji; Kohei Yamamoto; Kosei Yamauchi; Tohru Mitsunaga; Takashi Hayakawa; Tomoyuki Nakagawa (pp. 297-303).

In this work, we identified novel physiological functions of glutathione in acetaldehyde tolerance in Saccharomyces cerevisiae. Strains deleted in the genes encoding the enzymes involved in glutathione synthesis and reduction, GSH1, GSH2 and GLR1, exhibited severe growth defects compared to wild-type under acetaldehyde stress, although strains deleted in the genes encoding glutathione peroxidases or glutathione transferases did not show any growth defects. On the other hand, intracellular levels of reduced glutathione decreased in the presence of acetaldehyde in response to acetaldehyde concentration. Moreover, we show that glutathione can trap a maximum of four acetaldehyde molecules within its molecule in a non-enzymatic manner. Taken together, these findings suggest that glutathione has an important role in acetaldehyde tolerance, as a direct scavenger of acetaldehyde in the cell.

Keywords: Acetaldehyde; Stress tolerance; Glutathione; Yeast

Cytotoxic metabolites from Perenniporia tephropora, an endophytic fungus from Taxus chinensis var. mairei by Ling-Shang Wu; Chang-Ling Hu; Ting Han; Cheng-Jian Zheng; Xue-Qin Ma; Khalid Rahman; Lu-Ping Qin (pp. 305-315).

Based on bioactivity-oriented isolation, the EtOAc extract of a culture broth of the endophytic fungus Perenniporia tephropora Z41 from Taxus chinensis var. mairei, with strong anti-Pyricularia oryzae activity, afforded a new sesquiterpenoid, perenniporin A (1), together with three known compounds, ergosterol (2), rel-(+)-(2aR,5R,5aR,8S,8aS,8bR)-decahydro-2,2,5,8-tetramethyl-2H-naphtho[1,8-bc]genfuran-5-ol (3), and albicanol (4). Their structures were elucidated by means of spectroscopic methods. All the isolated compounds and the EtOAc extract of P. tephropora Z41 (EPT) were evaluated for their cytotoxic activity against three human cancer cell lines (HeLa, SMMC-7721, and PANC-1). EPT demonstrated significant cytotoxicity with IC₅₀ values ranging from 2 to 15 μg/mL. Compound 2 was the most cytotoxic constituent against the tested cell lines with IC₅₀ values of 1.16, 11.63, and 11.80 μg/mL, respectively, while compounds 1, 3, and 4 exhibited moderate cytotoxicity with IC₅₀ values ranging from 6 to 58 μg/mL. We conclude that the endophytic fungus P. tephropora is a promising source of novel and cytotoxic metabolites.

Keywords: Perenniporia tephropora ; Taxus chinensis var. mairei ; Endophytic fungi; Perenniporin A; Cytotoxic activity

Non-invasive determination of conjugative transfer of plasmids bearing antibiotic-resistance genes in biofilm-bound bacteria: effects of substrate loading and antibiotic selection by Hongyan Ma; James D. Bryers (pp. 317-328).

Biofilms cause much of all human microbial infections. Attempts to eradicate biofilm-based infections rely on disinfectants and antibiotics. Unfortunately, biofilm bacteria are significantly less responsive to antibiotic stressors than their planktonic counterparts. Sublethal doses of antibiotics can actually enhance biofilm formation. Here, we have developed a non-invasive microscopic image analyses to quantify plasmid conjugation within a developing biofilm. Corroborating destructive samples were analyzed by a cultivation-independent flow cytometry analysis and a selective plate count method to cultivate transconjugants. Increases in substrate loading altered biofilm 3-D architecture and subsequently affected the frequency of plasmid conjugation (decreases at least two times) in the absence of any antibiotic selective pressure. More importantly, donor populations in biofilms exposed to a sublethal dose of kanamycin exhibited enhanced transfer efficiency of plasmids containing the kanamycin resistance gene, up to tenfold. However, when stressed with a different antibiotic, imipenem, transfer of plasmids containing the kan^R+ gene was not enhanced. These preliminary results suggest biofilm bacteria “sense” antibiotics to which they are resistant, which enhances the spread of that resistance. Confocal scanning microscopy coupled with our non-invasive image analysis was able to estimate plasmid conjugative transfer efficiency either averaged over the entire biofilm landscape or locally with individual biofilm clusters.

Keywords: Biofilm plasmid transfer; Non-invasive biofilm diagnostics; Antibiotic selection pressure; Confocal microscopy

Diversity and antibiotic resistance of Acinetobacter spp. in water from the source to the tap by Carlos Narciso-da-Rocha; Ivone Vaz-Moreira; Liselott Svensson-Stadler; Edward R. B. Moore; Célia M. Manaia (pp. 329-340).

Acinetobacter spp. are ubiquitous bacteria in the environment. Acinetobacter spp. isolated from a municipal drinking water treatment plant and from connected tap water were identified to the species level on the basis of rpoB gene partial sequence analysis. Intraspecies variation was assessed based on the analysis of partial sequences of housekeeping genes (rpoB, gyrB, and recA). Antibiotic resistance was characterized using the disk diffusion method and isolates were classified as wild or non-wild type (non-WT), according to the observed phenotype. The strains of Acinetobacter spp. were related to 11 different validly published species, although three groups of isolates, presenting low rpoB sequence similarities with previously described species, may represent new species. Most of the isolates were related to the species A. johnsonii and A. lwoffii. These two groups, as well as others related to the species A. parvus and A. tjernbergiae, were detected in the water treatment plant and in tap water. Other strains, related to the species A. pittii and A. beijerinckii, were isolated only from tap water. Most of the isolates (80 %) demonstrated wild type (WT) to all of the 12 antibiotics tested. Non-WT for tetracycline, meropenem, and ceftazidime, among others, were observed in water treatment plant or in tap water samples. Although, in general, this study suggests a low prevalence of acquired antibiotic resistance in water Acinetobacter spp., the potential of some species to acquire and disseminate resistance via drinking water is suggested.

Keywords: Drinking water; Antibiotic resistance; ECOFF; gyrB; recA; rpoB

Viable quantitative PCR for assessing the response of Candida albicans to antifungal treatment by Gemma Agustí; Mariana Fittipaldi; Jordi Morató; Francesc Codony (pp. 341-349).

Propidium monoazide (PMA) or ethidium bromide monoazide (EMA) treatment has been used before nucleic acid detection methods, such as PCR, to distinguish between live and dead cells using membrane integrity as viability criterion. The performance of these DNA intercalating dyes was compared in many studies utilizing different microorganisms. These studies demonstrated that EMA and PMA differ in their abilities to identify nonviable cells from mixed cell populations, depending on the microorganism and the nature of the sample. Due to this heterogeneity, both dyes were used in the present study to specifically distinguish dead from live Candida albicans cells using viable quantitative PCR (qPCR). The viable qPCR was optimized, and the best results were obtained when pre-treating the cells for 10 min in the dark with 25 μM EMA followed by continuous photoactivation for 15 min. The suitability of this technique to distinguish clotrimazole- and fluconazole-treated C. albicans cells from untreated cells was then assessed. Furthermore, the antifungal properties of two commercial essential oils (Thymus vulgaris and Matricaria chamomilla) were evaluated. The viable qPCR method was determined to be a feasible technique for assessing the viability of C. albicans after drug treatment and may help to provide a rapid diagnostic and susceptibility testing method for fungal infections, especially for patients treated with antifungal therapies.

Keywords: Candida albicans ; Viable quantitative PCR; Ethidium bromide monoazide; Propidium monoazide; Antifungal treatment

In vivo random mutagenesis of streptomycetes using mariner-based transposon Himar1 by Bohdan Bilyk; Stephen Weber; Maksym Myronovskyi; Oksana Bilyk; Lutz Petzke; Andriy Luzhetskyy (pp. 351-359).

We report here the in vivo expression of the synthetic transposase gene himar1(a) in Streptomyces coelicolor M145 and Streptomyces albus. Using the synthetic himar1(a) gene adapted for Streptomyces codon usage, we showed random insertion of the transposon into the streptomycetes genome. The insertion frequency for the Himar1-derived minitransposons is nearly 100 % of transformed Streptomyces cells, and insertions are stably inherited in the absence of an antibiotic selection. The minitransposons contain different antibiotic resistance selection markers (apramycin, hygromycin, and spectinomycin), site-specific recombinase target sites (rox and/or loxP), I-SceI meganuclease target sites, and an R6Kγ origin of replication for transposon rescue. We identified transposon insertion loci by random sequencing of more than 100 rescue plasmids. The majority of insertions were mapped to putative open-reading frames on the S. coelicolor M145 and S. albus chromosomes. These insertions included several new regulatory genes affecting S. coelicolor M145 growth and actinorhodin biosynthesis.

Keywords: Himar1 ; Actinobacteria ; Transposon mutagenesis; Recombinases; Rescue plasmids

Pine cone-mediated green synthesis of silver nanoparticles and their antibacterial activity against agricultural pathogens by Palanivel Velmurugan; Sang-Myung Lee; Mahudunan Iydroose; Kui-Jae Lee; Byung-Taek Oh (pp. 361-368).

The medicinal and physicochemical properties of nanoscale materials are strong functions of the particle size and the materials used in their synthesis. The nanoparticle shape also contributes significantly to their medicinal properties. Several shapes ranging from oval, spherical, rods, to teardrop structures may be obtained by chemical methods. Triangular and hexagonal nanoparticles have been synthesized by using a pine cone extract (PCE). Here, we report the discovery that PCE, when reacted with silver nitrate ions, yields a high percentage of thin, flat, single-crystalline nanohexagonal and nanotriangular silver nanoparticles. The nanohexagonal and nanotriangular nanoparticles appear to grow by a process involving rapid reduction with assembly at room temperature at a high pH. The nanoparticles were characterized by UV–Vis absorption spectroscopy, SEM-EDS, TEM, FTIR, and X-ray diffraction analyses. The anisotropy of the nanoparticle shape results in large near-infrared absorption by the particles. Highly anisotropic particles are applicable in various fields, including agriculture and medicine. The obtained silver nanoparticles (Ag NPs) had significant antibacterial action on both Gram classes of bacteria associated with agriculture. Because the Ag NPs are encapsulated with functional group-rich PCE, they can be easily integrated in various applications.

Keywords: Antibacterial activity; Green synthesis; Silver nanoparticles; Pine cone extract

Bacterial biodiversity from anthropogenic extreme environments: a hyper-alkaline and hyper-saline industrial residue contaminated by chromium and iron by Elcia M. S. Brito; Hilda A. Piñón-Castillo; Rémy Guyoneaud; César A. Caretta; J. Félix Gutiérrez-Corona; Robert Duran; Georgina E. Reyna-López; G. Virginia Nevárez-Moorillón; Anne Fahy; Marisol Goñi-Urriza (pp. 369-378).

Anthropogenic extreme environments are among the most interesting sites for the bioprospection of extremophiles since the selection pressures may favor the presence of microorganisms of great interest for taxonomical and astrobiological research as well as for bioremediation technologies and industrial applications. In this work, T-RFLP and 16S rRNA gene library analyses were carried out to describe the autochthonous bacterial populations from an industrial waste characterized as hyper-alkaline (pH between 9 and 14), hyper-saline (around 100 PSU) and highly contaminated with metals, mainly chromium (from 5 to 18 g kg⁻¹) and iron (from 2 to 108 g kg⁻¹). Due to matrix interference with DNA extraction, a protocol optimization step was required in order to carry out molecular analyses. The most abundant populations, as evaluated by both T-RFLP and 16S rRNA gene library analyses, were affiliated to Bacillus and Lysobacter genera. Lysobacter related sequences were present in the three samples: solid residue and lixiviate sediments from both dry and wet seasons. Sequences related to Thiobacillus were also found; although strains affiliated to this genus are known to have tolerance to metals, they have not previously been detected in alkaline environments. Together with Bacillus (already described as a metal reducer), such organisms could be of use in bioremediation technologies for reducing chromium, as well as for the prospection of enzymes of biotechnological interest.

Keywords: Landfill; Industrial waste; DNA extraction optimization; Chromium hexavalent; T-RFLP

Sulfur bacteria in wastewater stabilization ponds periodically affected by the ‘red-water’ phenomenon by Abdelaziz Belila; Ben Abbas; Imed Fazaa; Neila Saidi; Mejdi Snoussi; Abdennaceur Hassen; Gerard Muyzer (pp. 379-394).

Several wastewater stabilization ponds (WSP) in Tunisia suffer periodically from the ‘red-water’ phenomenon due to blooming of purple sulfur bacteria, indicating that sulfur cycle is one of the main element cycles in these ponds. In this study, we investigated the microbial diversity of the El Menzeh WSP and focused in particular on the different functional groups of sulfur bacteria. For this purpose, we used denaturing gradient gel electrophoresis of PCR-amplified fragments of the 16S rRNA gene and of different functional genes involved in microbial sulfur metabolism (dsrB, aprA, and pufM). Analyses of the 16S rRNA revealed a relatively high microbial diversity where Proteobacteria, Chlorobi, Bacteroidetes, and Cyanobacteria constitute the major bacterial groups. The dsrB and aprA gene analysis revealed the presence of deltaproteobacterial sulfate-reducing bacteria (i.e., Desulfobacter and Desulfobulbus), while the analysis of 16S rRNA, aprA, and pufM genes assigned the sulfur-oxidizing bacteria community to the photosynthetic representatives belonging to the Chlorobi (green sulfur bacteria) and the Proteobacteria (purple sulfur and non sulfur bacteria) phyla. These results point on the diversity of the metabolic processes within this wastewater plant and/or the availability of sulfate and diverse electron donors.

Keywords: Sulfur bacteria; PCR–DGGE; Functional diversity; Red-water phenomenon; Wastewater stabilization ponds

Functionality of the TOL plasmid under varying environmental conditions following conjugal transfer by Kaoru Ikuma; Claudia K. Gunsch (pp. 395-408).

Conjugation of catabolic plasmids in contaminated environments is a naturally occurring horizontal gene transfer phenomenon, which could be utilized in genetic bioaugmentation. The potentially important parameters for genetic bioaugmentation include gene regulation of transferred catabolic plasmids that may be controlled by the genetic characteristics of transconjugants as well as environmental conditions that may alter the expression of the contaminant-degrading phenotype. This study showed that both genomic guanine–cytosine contents and phylogenetic characteristics of transconjugants were important in controlling the phenotype functionality of the TOL plasmid. These genetic characteristics had no apparent impact on the stability of the TOL plasmid, which was observed to be highly variable among strains. Within the environmental conditions tested, the addition of glucose resulted in the largest enhancement of the activities of enzymes encoded by the TOL plasmid in all transconjugant strains. Glucose (1 g/L) enhanced the phenotype functionality by up to 16.4 (±2.22), 30.8 (±7.03), and 90.8 (±4.56)-fold in toluene degradation rates, catechol 2,3-dioxygenase enzymatic activities, and xylE gene expression, respectively. These results suggest that genetic limitations of the expression of horizontally acquired genes may be overcome by the presence of alternate carbon substrates. Such observations may be utilized in improving the effectiveness of genetic bioaugmentation.

Keywords: Genetic bioaugmentation; Plasmid conjugation; TOL plasmid; Guanine–cytosine content; Carbon amendment

Domestic wastewater treatment using multi-electrode continuous flow MFCs with a separator electrode assembly design by Yongtae Ahn; Bruce E. Logan (pp. 409-416).

Treatment of domestic wastewater using microbial fuel cells (MFCs) will require reactors with multiple electrodes, but this presents unique challenges under continuous flow conditions due to large changes in the chemical oxygen demand (COD) concentration within the reactor. Domestic wastewater treatment was examined using a single-chamber MFC (130 mL) with multiple graphite fiber brush anodes wired together and a single air cathode (cathode specific area of 27 m²/m³). In fed-batch operation, where the COD concentration was spatially uniform in the reactor but changed over time, the maximum current density was 148 ± 8 mA/m² (1,000 Ω), the maximum power density was 120 mW/m², and the overall COD removal was >90 %. However, in continuous flow operation (8 h hydraulic retention time, HRT), there was a 57 % change in the COD concentration across the reactor (influent versus effluent) and the current density was only 20 ± 13 mA/m². Two approaches were used to increase performance under continuous flow conditions. First, the anodes were separately wired to the cathode, which increased the current density to 55 ± 15 mA/m². Second, two MFCs were hydraulically connected in series (each with half the original HRT) to avoid large changes in COD among the anodes in the same reactor. The second approach improved current density to 73 ± 13 mA/m². These results show that current generation from wastewaters in MFCs with multiple anodes, under continuous flow conditions, can be improved using multiple reactors in series, as this minimizes changes in COD in each reactor.

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

Isolation and characterization of novel 1,3-propanediol-producing Lactobacillus panis PM1 from bioethanol thin stillage by Nurul H. Khan; Tae Sun Kang; Douglas A. S. Grahame; Monique C. Haakensen; Kornsulee Ratanapariyanuch; Martin J. Reaney; Darren R. Korber; Takuji Tanaka (pp. 417-428).

Conversion of glycerol to 1,3-propanediol (1,3-PDO) is an attractive option to increase the economic efficiency of the biofuel industry. A bacterial strain that produced 1,3-PDO in the presence of glycerol was isolated from thin stillage, the fermentation residue of bioethanol production. This 1,3-PDO-producing organism was identified as Lactobacillus panis through biochemical characteristics and by 16S rRNA sequencing. Characterization of the L. panis strain hereafter designated as PM1 revealed it was an aerotolerant acidophilic anaerobe able to grow over a wide range of temperatures; tolerant to high concentrations of sodium chloride, ethanol, acetic acid, and lactic acid; and resistant to many common antibiotics. L. panis PM1 could utilize glucose, lactose, galactose, maltose, xylose, and arabinose, but could not grow on sucrose or fructose. Production of 1,3-PDO by L. panis PM1 occurred only when glucose was available as the carbon source in the absence of oxygen. These metabolic characteristics strongly suggested NADH recycling for glucose metabolism is achieved through 1,3-PDO production by this strain. These characteristics classified L. panis PM1 within the group III heterofermentative lactic acid bacteria, which includes the well-characterized 1,3-PDO-producing strain, Lactobacillus reuteri. Metabolite production profiles showed that L. panis PM1 produced considerable amounts of succinic acid (~11–12 mM) from normal MRS medium, which distinguishes this strain from L. reuteri strains.

Keywords: Glycerol; Biofuel waste; Value-added product; Fermentation; Glucose metabolism; NADH recycling

Comparison of power output by rice (Oryza sativa) and an associated weed (Echinochloa glabrescens) in vascular plant bio-photovoltaic (VP-BPV) systems by Paolo Bombelli; Durgaprasad Madras Rajaraman Iyer; Sarah Covshoff; Alistair J. McCormick; Kamran Yunus; Julian M. Hibberd; Adrian C. Fisher; Christopher J. Howe (pp. 429-438).

Vascular plant bio-photovoltaics (VP-BPV) is a recently developed technology that uses higher plants to harvest solar energy and the metabolic activity of heterotrophic microorganisms in the plant rhizosphere to generate electrical power. In the present study, electrical output and maximum power output variations were investigated in a novel VP-BPV configuration using the crop plant rice (Oryza sativa L.) or an associated weed, Echinochloa glabrescens (Munro ex Hook. f.). In order to compare directly the physiological performances of these two species in VP-BPV systems, plants were grown in the same soil and glasshouse conditions, while the bio-electrochemical systems were operated in the absence of additional energy inputs (e.g. bias potential, injection of organic substrate and/or bacterial pre-inoculum). Diurnal oscillations were clearly observed in the electrical outputs of VP-BPV systems containing the two species over an 8-day growth period. During this 8-day period, O. sativa generated charge ∼6 times faster than E. glabrescens. This greater electrogenic activity generated a total charge accumulation of 6.75 ± 0.87 Coulombs for O. sativa compared to 1.12 ± 0.16 for E. glabrescens. The average power output observed over a period of about 30 days for O. sativa was significantly higher (0.980 ± 0.059 GJ ha⁻¹ year⁻¹) than for E. glabrescens (0.088 ± 0.008 GJ ha⁻¹ year⁻¹). This work indicates that electrical power can be generated in both VP-BPV systems (O. sativa and E. glabrescens) when bacterial populations are self-forming. Possible reasons for the differences in power outputs between the two plant species are discussed.

Keywords: Microbial fuel cell; Photosynthesis; Bioelectricity; Electrochemistry; Vascular plant

Erratum to: Efficient (R)-3-hydroxybutyrate production using acetyl CoA-regenerating pathway catalyzed by coenzyme A transferase by Ken’ichiro Matsumoto; Takehiro Okei; Inori Honma; Toshihiko Ooi; Hirobumi Aoki; Seiichi Taguchi (pp. 439-439).

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Applied Microbiology and Biotechnology (v.97, #1)

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Applied Microbiology and Biotechnology (v.97, #1)