| 1. |
- Almstrand, Robert, et al.
(författare)
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Dynamics of specific ammonia-oxidizing bacterial populations and nitrification in response to controlled shifts of ammonium concentrations in wastewater
- 2013
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Ingår i: Applied Microbiology and Biotechnology. - : Springer Verlag (Germany). - 0175-7598 .- 1432-0614. ; 97:5, s. 2183-2191
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Tidskriftsartikel (refereegranskat)abstract
- Ammonia-oxidizing bacteria (AOB) are essential for the nitrification process in wastewater treatment. To retain these slow-growing bacteria in wastewater treatment plants (WWTPs), they are often grown as biofilms, e.g., on nitrifying trickling filters (NTFs) or on carriers in moving bed biofilm reactors (MBBRs). On NTFs, a decreasing ammonium gradient is formed because of the AOB activity, resulting in low ammonium concentrations at the bottom and reduced biomass with depth. To optimize the NTF process, different ammonium feed strategies may be designed. This, however, requires knowledge about AOB population dynamics. Using fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy, we followed biomass changes during 6 months, of three AOB populations on biofilm carriers. These were immersed in aerated MBBR tanks in a pilot plant receiving full-scale wastewater. Tanks were arranged in series, forming a wastewater ammonium gradient mimicking an NTF ammonium gradient. The biomass of one of the dominating Nitrosomonas oligotropha-like populations increased after an ammonium upshift, reaching levels comparable to the high ammonium control in 28 days, whereas a Nitrosomonas europaea-like population increased relatively slowly. The MBBR results, together with competition studies in NTF systems fed with wastewater under controlled ammonium regimes, suggest a differentiation between the two N. oligotropha populations, which may be important for WWTP nitrification.
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| 2. |
- Begerow, D., et al.
(författare)
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Current state and perspectives of fungal DNA barcoding and rapid identification procedures
- 2010
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Ingår i: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 0175-7598 .- 1432-0614. ; 87:1, s. 99-108
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Forskningsöversikt (refereegranskat)abstract
- Fungal research is experiencing a new wave of methodological improvements that most probably will boost mycology as profoundly as molecular phylogeny has done during the last 15 years. Especially the next generation sequencing technologies can be expected to have a tremendous effect on fungal biodiversity and ecology research. In order to realise the full potential of these exciting techniques by accelerating biodiversity assessments, identification procedures of fungi need to be adapted to the emerging demands of modern large-scale ecological studies. But how should fungal species be identified in the near future? While the answer might seem trivial to most microbiologists, taxonomists working with fungi may have other views. In the present review, we will analyse the state of the art of the so-called barcoding initiatives in the light of fungi, and we will seek to evaluate emerging trends in the field. We will furthermore demonstrate that the usability of DNA barcoding as a major tool for identification of fungi largely depends on the development of high-quality sequence databases that are thoroughly curated by taxonomists and systematists.
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| 3. |
- Blomqvist, Johanna, et al.
(författare)
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Fermentation characteristics of Dekkera bruxellensis strains
- 2010
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Ingår i: Applied Microbiology and Biotechnology. - New York, USA : Springer. - 0175-7598 .- 1432-0614. ; 87:4, s. 1487-1497
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Tidskriftsartikel (refereegranskat)abstract
- The influence of pH, temperature and carbon source (glucose and maltose) on growth rate and ethanol yield of Dekkera bruxellensis was investigated using a full-factorial design. Growth rate and ethanol yield were lower on maltose than on glucose. In controlled oxygen-limited batch cultivations, the ethanol yield of the different combinations varied from 0.42 to 0.45 g (g glucose)(-1) and growth rates varied from 0.037 to 0.050 h(-1). The effect of temperature on growth rate and ethanol yield was negligible. It was not possible to model neither growth rate nor ethanol yield from the full-factorial design, as only marginal differences were observed in the conditions tested. When comparing three D. bruxellensis strains and two industrial isolates of Saccharomyces cerevisiae, S. cerevisiae grew five times faster, but the ethanol yields were 0-13% lower. The glycerol yields of S. cerevisiae strains were up to six-fold higher compared to D. bruxellensis, and the biomass yields reached only 72-84% of D. bruxellensis. Our results demonstrate that D. bruxellensis is robust to large changes in pH and temperature and may have a more energy-efficient metabolism under oxygen limitation than S. cerevisiae.
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| 4. |
- Dimarogona, Maria, et al.
(författare)
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Recalcitrant polysaccharide degradation by novel oxidative biocatalysts
- 2013
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Ingår i: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 0175-7598 .- 1432-0614. ; 97:19, s. 8455-8465
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Tidskriftsartikel (refereegranskat)abstract
- The classical hydrolytic mechanism for the degradation of plant polysaccharides by saprophytic microorganisms has been reconsidered after the recent landmark discovery of a new class of oxidases termed lytic polysaccharide monooxygenases (LPMOs). LPMOs are of increased biotechnological interest due to their implication in lignocellulosic biomass decomposition for the production of biofuels and high-value chemicals. They act on recalcitrant polysaccharides by a combination of hydrolytic and oxidative function, generating oxidized and non-oxidized chain ends. They are copper-dependent and require molecular oxygen and an external electron donor for their proper function. In this review, we present the recent findings concerning the mechanism of action of these oxidative enzymes and identify issues and questions to be addressed in the future
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| 5. |
- Doan Van, Thuoc, et al.
(författare)
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Ectoine-mediated protection of enzyme from the effect of pH and temperature stress: a study using Bacillus halodurans xylanase as a model.
- 2013
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Ingår i: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 1432-0614 .- 0175-7598. ; 97:14, s. 6271-6278
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Tidskriftsartikel (refereegranskat)abstract
- Compatible solutes are small, soluble organic compounds that have the ability to stabilise proteins against various stress conditions. In this study, the protective effect of ectoines against pH stress is examined using a recombinant xylanase from Bacillus halodurans as a model. Ectoines improved the enzyme stability at low (4.5 and 5.0) and high pH (11 and 12); stabilisation effect of hydroxyectoine was superior to that of ectoine and trehalose. In the presence of hydroxyectoine, residual activity (after 10 h heating at 50 °C) increased from about 45 to 86 % at pH 5 and from 33 to 89 % at pH 12. When the xylanase was incubated at 65 °C for 5 h with 50 mM hydroxyectoine at pH 10, about 40 % of the original activity was retained while no residual activity was detected in the absence of additives or in the presence of ectoine or trehalose. The xylanase activity was slightly stimulated in the presence of 25 mM ectoines and then gradually decreased with increase in ectoines concentration. The thermal unfolding of the enzyme in the presence of the compatible solutes showed a modest increase in denaturation temperature but a larger increase in calorimetric enthalpy.
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| 6. |
- Dopson, Mark, et al.
(författare)
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Metal resistance in acidophilic microorganisms and its significance for biotechnologies.
- 2014
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Ingår i: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 0175-7598 .- 1432-0614. ; 98:19, s. 8133-8144
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Tidskriftsartikel (refereegranskat)abstract
- Extremely acidophilic microorganisms have an optimal pH of <3 and are found in all three domains of life. As metals are more soluble at acid pH, acidophiles are often challenged by very high metal concentrations. Acidophiles are metal-tolerant by both intrinsic, passive mechanisms as well as active systems. Passive mechanisms include an internal positive membrane potential that creates a chemiosmotic gradient against which metal cations must move, as well as the formation of metal sulfate complexes reducing the concentration of the free metal ion. Active systems include efflux proteins that pump metals out of the cytoplasm and conversion of the metal to a less toxic form. Acidophiles are exploited in a number of biotechnologies including biomining for sulfide mineral dissolution, biosulfidogenesis to produce sulfide that can selectively precipitate metals from process streams, treatment of acid mine drainage, and bioremediation of acidic metal-contaminated milieux. This review describes how acidophilic microorganisms tolerate extremely high metal concentrations in biotechnological processes and identifies areas of future work that hold promise for improving the efficiency of these applications.
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| 7. |
- Ganachaud, C., et al.
(författare)
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An anomalous behavior of trypsin immobilized in alginate network
- 2013
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Ingår i: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 1432-0614 .- 0175-7598. ; 97:10, s. 4403-4414
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Tidskriftsartikel (refereegranskat)abstract
- Alginate is a biopolymer used in drug formulations and for surgical purposes. In the presence of divalent cations, it forms solid gels, and such gels are of interest for immobilization of cells and enzymes. In this work, we entrapped trypsin in an alginate gel together with a known substrate, N (alpha)-benzoyl-l-arginine-4-nitroanilide hydrochloride (l-BAPNA), and in the presence or absence of d-BAPNA, which is known to be a competitive inhibitor. Interactions between alginate and the substrate as well as the enzyme were characterized with transmission electron microscopy, rheology, and nuclear magnetic resonance spectroscopy. The biocatalysis was monitored by spectrophotometry at temperatures ranging from 10 to 42 A degrees C. It was found that at 37 and 42 A degrees C a strong acceleration of the reaction was obtained, whereas at 10 A degrees C and at room temperature, the presence of d-BAPNA leads to a retardation of the reaction rate. The same effect was found when the reaction was performed in a non-cross-linked alginate solution. In alginate-free buffer solution, as well as in a solution of carboxymethylcellulose, a biopolymer that resembles alginate, the normal behavior was obtained; however, with d-BAPNA acting as an inhibitor at all temperatures. A more detailed investigation of the reaction kinetics showed that at higher temperature and in the presence of alginate, the curve of initial reaction rate versus l-BAPNA concentration had a sigmoidal shape, indicating an allosteric behavior. We believe that the anomalous behavior of trypsin in the presence of alginate is due to conformational changes caused by interactions between the positively charged trypsin and the strongly negatively charged alginate.
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| 8. |
- Geladi, Paul
(författare)
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Growth characteristics of three Fusarium species evaluated by near-infrared hyperspectral imaging and multivariate image analysis
- 2012
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Ingår i: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 0175-7598 .- 1432-0614. ; 96, s. 803-813
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Tidskriftsartikel (refereegranskat)abstract
- Colony growth of three Fusarium spp. on potato dextrose agar was followed by collecting near-infrared (NIR) hyperspectral images of the colonies at regular intervals after inoculation up to 55 h. After principal component analysis (PCA), two clusters were apparent in the score plot along principal component 1. Using the brushing technique, these clusters were divided into four groups of pixels with similar score values. These could be visualised as growth zones within the colonies in the corresponding score image. Three spectral bands, i.e. 1,166, 1,380 and 1,918 nm, were prominent in the multiplicative scatter corrected and Savitzky-Golay second derivative spectra. These indicated chemical changes, associated with carbohydrates (1,166 and 1,380 nm) and protein (1,918 nm), that occurred as the mycelium grew and matured. The protein band was more prominent in the mature fungal material while the carbohydrate band was less pronounced. The younger material and the agar were characterised by the carbohydrate spectral band. Integrating whole mycelium colonies as the sum of pixels over time made it possible to construct curves that resembled growth curves; this included the lag phase, active growth phase, deceleration phase and phase of constant growth. Growth profiles constructed from individual growth zones indicated more detailed growth characteristics. The use of NIR hyperspectral imaging and multivariate image analysis (MIA) allowed one to visualise radial growth rings in the PCA score images. This would not have been possible with bulk spectroscopy. Interpreting spectral data enabled better understanding of microbial growth characteristics on agar medium. NIR hyperspectral imaging combined with MIA is a powerful tool for the evaluation of growth characteristics of fungi.
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| 9. |
- Hjort, Karin, et al.
(författare)
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Bacterial chitinase with phytopathogen control capacity from suppressive soil revealed by functional metagenomics
- 2014
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Ingår i: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 0175-7598 .- 1432-0614. ; 98:6, s. 2819-2828
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Tidskriftsartikel (refereegranskat)abstract
- Plant disease caused by fungal pathogens results in vast crop damage globally. Microbial communities of soil that is suppressive to fungal crop disease provide a source for the identification of novel enzymes functioning as bioshields against plant pathogens. In this study, we targeted chitin-degrading enzymes of the uncultured bacterial community through a functional metagenomics approach, using a fosmid library of a suppressive soil metagenome. We identified a novel bacterial chitinase, Chi18H8, with antifungal activity against several important crop pathogens. Sequence analyses show that the chi18H8 gene encodes a 425-amino acid protein of 46 kDa with an N-terminal signal peptide, a catalytic domain with the conserved active site F175DGIDIDWE183, and a chitinase insertion domain. Chi18H8 was expressed (pGEX-6P-3 vector) in Escherichia coli and purified. Enzyme characterization shows that Chi18H8 has a prevalent chitobiosidase activity with a maximum activity at 35 °C at pH lower than 6, suggesting a role as exochitinase on native chitin. To our knowledge, Chi18H8 is the first chitinase isolated from a metagenome library obtained in pure form and which has the potential to be used as a candidate agent for controlling fungal crop diseases. Furthermore, Chi18H8 may also answer to the demand for novel chitin-degrading enzymes for a broad range of other industrial processes and medical purposes.
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| 10. |
- Hou, Jin, 1982, et al.
(författare)
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Heat shock response improves heterologous protein secretion in Saccharomyces cerevisiae
- 2013
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Ingår i: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 1432-0614 .- 0175-7598. ; 97:8, s. 3559-3568
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Tidskriftsartikel (refereegranskat)abstract
- The yeast Saccharomyces cerevisiae is a widely used platform for the production of heterologous proteins of medical or industrial interest. However, heterologous protein productivity is often low due to limitations of the host strain. Heat shock response (HSR) is an inducible, global, cellular stress response, which facilitates the cell recovery from many forms of stress, e.g., heat stress. In S. cerevisiae, HSR is regulated mainly by the transcription factor heat shock factor (Hsf1p) and many of its targets are genes coding for molecular chaperones that promote protein folding and prevent the accumulation of mis-folded or aggregated proteins. In this work, we over-expressed a mutant HSF1 gene HSF1-R206S which can constitutively activate HSR, so the heat shock response was induced at different levels, and we studied the impact of HSR on heterologous protein secretion. We found that moderate and high level over-expression of HSF1-R206S increased heterologous alpha-amylase yield 25 and 70 % when glucose was fully consumed, and 37 and 62 % at the end of the ethanol phase, respectively. Moderate and high level over-expression also improved endogenous invertase yield 118 and 94 %, respectively. However, human insulin precursor was only improved slightly and this only by high level over-expression of HSF1-R206S, supporting our previous findings that the production of this protein in S. cerevisiae is not limited by secretion. Our results provide an effective strategy to improve protein secretion and demonstrated an approach that can induce ER and cytosolic chaperones simultaneously.
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