A heat shock following electroporation induces highly efficient transformation of Corynebacterium glutamicum with xenogeneic plasmid DNA

An improved method for the electrotransformation of wild-type Corynebacterium glutamicum (ATCC 13032) is described. The two crucial alterations to previously developed methods are: cultivation of cells used for electrotransformation at 18 °C instead of 30 °C, and application of a heat shock immediately following electrotransformation. Cells cultivated at sub optimal temperature have a 100-fold improved transformation efficiency (10⁸ cfu μg⁻¹) for syngeneic DNA (DNA isolated from the same species). A heat shock applied to these cells following electroporation improved the transformation efficiency for xenogeneic DNA (DNA isolated from a different species). In combination, low cultivation temperature and heat shock act synergistically and increased the transformation efficiency by four orders of magnitude to 2.5 × 10⁶ cfu μg⁻¹ xenogeneic DNA. The method was used to generate gene disruptions in C. glutamicum. Received: 26 March 1999 / Received revision: 9 June 1999 / Accepted: 11 June 1999     

Scaling food chains in aquatic mesocosms: do the effects of depth override the effects of planktivory?

To assess the effects of physical dimension and planktivorous fish on phytoplankton standing crop, we repeated an experiment at different scales in plastic enclosures during summer 1995 in Lake Créteil, France. Enclosures were scaled for a constant surface (1.5 × 1.5 m) as depth was increased from 2.5 to 4.5 m. Even-link (zooplankton and phytoplankton) and odd-link (planktivorous fish, zooplankton and phytoplankton) food webs were established in both shallow and deep enclosures. Fish densities in the deep enclosures were scaled to allow comparisons with shallow ones for both in individuals m⁻² or individuals m⁻³. We explicitly designed this experiment to examine the scale-dependent behavior of the top-down mechanism of algal biomass control in lakes, and in particular to test the hypothesis of stronger cascading effects of fish on lower trophic levels at reduced depth. Both fish and enclosure size had highly significant effects on phytoplankton biomass over the duration of the experiment. No depth × fish interaction effects were observed. The presence of planktivorous fish enhanced phytoplankton biomass in both shallow and deep enclosures, although the reduction in depth generally produced a stronger effect. The mean concentration of chlorophyll a in the deep odd-link systems (ca 5 mg m⁻³) was lower than in the shallow even-link systems (ca 17 mg m⁻³). Statistical interpretation did not change when data were expressed as phytoplankton biomass per unit of surface area. Light limitation and zooplankton grazing are the most probable mechanisms explaining our results in these nutrient-enriched systems. Moreover, we found that the strength of the cascading effect of fish on plankton was not a function of depth. We believe that further studies on scaling effects should be conducted in order to improve our understanding of ecological patterns and to extrapolate results from micro/mesocosms to natural ecosystems. Received: 18 January 1999 / Accepted: 7 June 1999     

Helix-helix transitions in DNA: fibre X-ray study of the particular cases poly(dG-dC) · poly(dG-dC) and poly(dA) · 2poly(dT)

The helix-helix transitions which occur in poly(dG-dC) · poly(dG-dC) and in poly (dG-m⁵dC) · poly(dG-m⁵dC) are commonly assumed to be changes between the right-handed A- or B-DNA double helices and the left-handed Z-DNA structure. The mechanisms for such transconformations are highly improbable, especially when they are supposed to be active in long polynucleotide chains organised in semicrystalline fibres. The present alternative possibility assumes that rather than the Z-DNA it is a right-handed double helix (S-DNA) which actually takes part in these form transitions. Two molecular models of this S form, in good agreement with X-ray measurements, are proposed. They present alternating C(2′)-endo and C(3′)-endo sugar puckering like the “alternating B-DNA” put forward some years ago. Dihedral angles, sets of atomic coordinates and stereo views of the two S-DNA structures are given, together with curves of calculated diffracted intensities. Furthermore, we question the possibility of obtaining semicrystalline fibres with triple helices of poly(dA) · 2poly(dT) in a way which renders X-ray diffraction efficient. It is suggested that, up to now, only double helices of poly(dA) · poly(dT) can actually be observed by fibre X-ray diffraction measurements. Received: 30 March 1999 / Revised version: 30 June 1999 / Accepted: 30 June 1999     

On the comparative static properties of the expected population density in the presence of stochastic fluctuations

We consider the impact of increased stochastic fluctuations on the expected density of an unstructured population evolving according to a regular diffusion process subject to a concave expected growth rate. By relying on the flow nature of the solutions of stochastic differential equations and Girsanovs theorem, we demonstrate that typically increased volatility decreases the expected future population density. As a consequence, we are able to characterize the sensitivity of the expected population density with respect to changes in the diffusion coefficient measuring the size of the stochastic fluctuations. We provide both qualitative and quantitative information about the consequences of a mis-specified volatility structure and, especially, of a deterministic approximation to stochastic population growth. We also consider the effect of uncertainty in the initial density and demonstrate that the sign of the relationship between the expected population density and initial uncertainty is unambiguosly negative. Received: 15 February 1999 / Revised version: 29 September 1999 / Published online: 5 May 2000     

Quantification of bacterial polyhydroxyalkanoic acids by Nile red staining

The fluorescence properties of one chemically and seven biologically produced polyhydroxyalkanoic acids were investigated as film castings and in living cells respectively after staining with Nile red. All these polyesters show a similar fluorescence behaviour, revealing a clear fluorescence maximum at an excitation wavelength between 540 nm and 560 nm and an emission wavelength between 570 nm and 605 nm. This could be shown by the use of two-dimensional fluorescence spectroscopy and flow cytometry. The examination of native poly(3-hydroxybutyric acid), poly(3HB), granules isolated from cells of Ralstonia eutropha H16 showed that the addition of 6.0 μg Nile red is necessary for total staining of 1.0 mg granules. The fluorescence intensity at an excitation wavelength of 550 nm and an emission wavelength of 600 nm showed high correlation to the poly(3HB) concentration of grana suspensions at different grana concentrations. These results and the staining of cell suspensions during cultivation experiments revealed that Nile red has a high potential for the quantitative determination of hydrophobic bacterial polyhydroxyalkanoic acids. Received: 13 November 1998 / Received revision: 4 February 1999 / Accepted: 12 February 1999     

Immobilization of pancreatic islet cells with preserved secretory potential

Dispersed pancreatic islet cells from rats were cultured overnight in the presence of macroporous gelatin microcarriers. The cells attached to the microcarriers were then incubated for 90 min in the absence or presence of 15.0 mM d-glucose and/or 1.25 mM theophylline. The release of insulin during incubation was about three times higher in the simultaneous presence of these two secretagogues than in their absence. This procedure could thus be used for the immobilization of pancreatic islet cells with preserved secretory potential. Received: 9 April 1999 / Received revision: 12 July 1999 / Accepted: 13 July 1999     

Biodegradation of azo dyes in a sequential anaerobic–aerobic system

A sequential anaerobic–aerobic treatment process based on mixed culture of bacteria isolated from textile dye effluent-contaminated soil was used to degrade sulfonated azo dyes Orange G (OG), Amido black 10B (AB), Direct red 4BS (DR) and Congo red (CR). Under anaerobic conditions in a fixed-bed column using glucose as co-substrate, the azo dyes were reduced and amines were released by the bacterial biomass. The amines were completely mineralized in a subsequent aerobic treatment using the same isolates. The maximum degradation rate observed in the treatment system for OG was 60.9 mg/l per day (16.99 mg/g glucose utilized), for AB 571.3 mg/l per day (14.46 mg/g glucose utilized), for DR 112.5 mg/l per day (32.02 mg/g glucose utilized) and for CR 134.9 mg/l per day (38.9 mg/g glucose utilized). Received: 6 August 1999 / Received revision: 20 December 1999 / Accepted: 24 December 1999     

Bioconversion of alpha pinene to verbenone by resting cells of Aspergillus niger

Resting cells of a locally isolated strain of Aspergillus niger caused the bioconversion of alpha pinene to verbenone. The formation of verbenone was raised from trace amounts (under screening conditions) to 3.28 mg/100 ml (equivalent to a molar yield of 16.5% conversion of the substrate) by amending the cultivation medium for the fungus. The optimal conditions were: 6 g/100 ml for the glucose concentration, a pH of 7.0, an alpha pinene concentration of 20 mg/100 ml, and a 6-h incubation period for the reaction. Received: 9 August 1999 / Received revision: 24 September 1999 / Accepted: 24 September 1999     

A simple and rapid method to gain high amounts of manganese peroxidase with immobilized mycelium of the agaric white-rot fungus Clitocybula dusenii

The agaric basidiomycete Clitocybula dusenii was used for the production of the extracellular ligninolytic enzyme, manganese (Mn) peroxidase. An immobilization technique is described using cellulose and polypropylene as carrier for the fungal mycelium. High amounts of Mn peroxidase were obtained with agitated cultures of immobilized fungus (up to 3,000 U l⁻¹) while the biomass was recovered and used for further production cycles. Purification of Mn peroxidase revealed the existence of two forms: MnP1 (molecular mass 43 kDa, pI 4.5) and MnP2 (42 kDa, pI 3.8). Received: 30 July 1999 / Received revision: 1 December 1999 / Accepted: 3 December 1999     

Topography of cell traces studied by atomic force microscopy

Migrating adherent cells release material onto artificial substrates like glass and silicon while moving. Traces of mouse fibroblasts (L929) have been visualised by atomic force microscopy (AFM). “Non-contact” mode AFM in a liquid environment can extract topographic information from these traces. This dynamic mode allows the study of these soft structures without damage or compression. The AFM images show crossing and branching networks (with specific angles of branching), structured patches, nodular elements, linear elements with irregular height and other features. Fourier analysis of segment spacing in the strands is presented. These spatial features of fibroblast traces are strong indications that actin linked to structural proteins is involved in the formation of cell traces. We also give methods for trace preparation and undistorted imaging and discuss further perspectives. Received: 11 January 1999 / Revised version: 1 April 1999 / Accepted: 8 April 1999     

Production of (R)-3-pentyn-2-ol through stereoinversion of racemic 3-pentyn-2-ol by Nocardia fusca AKU 2123

Wet cells of Nocardia fusca AKU 2123 are good catalysts for the production of (R)-3-pentyn-2-ol (PYOH) from (RS)-PYOH through a stereoinversion reaction. Under optimal conditions (350 mM potassium phosphate buffer, pH 8.0, 30% (w/v) wet cells, 0.12% NADPH, 10% glucose, and 30 U/ml glucose dehydrogenase) (R)-PYOH of high optical purity (98.7% e.e.) was produced from 2% (v/v) (RS)-PYOH with a yield of 70.4% by 140 h incubation. Received: 22 January 1999 / Received revision: 23 April 1999 / Accepted: 1 May 1999     

Preparation of stearoyl lactic acid ester catalyzed by lipases from Rhizomucor miehei and porcine pancreas optimization using response surface methodology

The esterification reaction between stearic acid and lactic acid using Rhizomucor miehei lipase and porcine pancreas lipase was optimized for maximum esterification using response surface methodology. The formation of the ester was found to depend on three parameters namely enzyme/substrate ratio, lactic acid (stearic acid) concentration and incubation period. The maximum esterification predicted by theoretical equations for both lipases matched well with the observed experimental values. In the case of R. miehei lipase, stearoyl lactic acid ester formation was found to increase with incubation period and lactic acid (stearic acid) concentrations with maximum esterification of 26.9% at an enzyme/substrate (E/S) ratio of 125 g mol⁻¹. In the case of porcine pancreas lipase, esterification showed a steady increase with increase in incubation period and lactic acid (stearic acid) concentration independent of the E/S ratios employed. In the case of PPL, a maximum esterification of 18.9% was observed at an E/S ratio of 25 g mol⁻¹ at a lactic acid (stearic acid) concentration of 0.09 M after an incubation period of 72 h. Received: 12 February 1999 / Received revision: 31 May 1999 / Accepted: 4 June 1999     

Batch and continuous cultivation of Anaerobiospirillum succiniciproducens for the production of succinic acid from whey

Batch and continuous cultivation of Anaerobiospirillum succiniciproducens were systematically studied for the production of succinic acid from whey. Addition of 2.5 g l⁻¹ yeast extract and 2.5 g l⁻¹ polypeptone per 10 g l⁻¹ whey was most effective for succinic acid production from both treated and nontreated whey. When 20 g l⁻¹ nontreated whey and 7 g l⁻¹ glucose were used as cosubstrates, the yield and productivity of succinic acid reached at the end of fermentation were 95% and 0.46 g (l h)⁻¹, respectively. These values were higher than those obtained using nontreated whey alone [93% and 0.24 g (l h)⁻¹ for 20 g l⁻¹ whey]. Continuous fermentation of A. succiniciproducens at an optimal dilution rate resulted in the production of succinic acid with high productivity [1.35 g (l h)⁻¹], high conversion yield (93%), and higher ratio of succinic acid to acetic acid (5.1:1) from nontreated whey. Received: 23 July 1999 / Received revision: 17 November 1999 / Accepted: 24 December 1999     

Green krill, the indicator of micro- and nano-size phytoplankton availability to krill

Size-fractionated chlorophyll-a concentrations of surface seawater were measured for pico-, nano-, and micro-size fractions (<2 μm, 2–10 μm, and >10 μm respectively) during commercial krill fishery operations in the waters north of the South Shetland Islands. The proportion of green krill (individuals discoloured due to active feeding on phytoplankton) had significant regressions with chlorophyll-a concentrations in micro- and nano-size fractions. Between these two fractions, chlorophyll-a concentration in the micro-size fraction showed the higher partial regression coefficient. This result shows the importance of phytoplankton larger than nano-phytoplankton, especially micro-phytoplankton, in terms of a phytoplanktonic food source for Antarctic krill in the natural environment. Accepted: 6 February 1999     

Gravitropism in Phycomyces: a role for sedimenting protein crystals and floating lipid globules

To elucidate the graviperception of the unicellular fungus, Phycomycesblakesleeanus, sporangiophores were inspected for intracellular structures which relocate with respect to gravity. Two structures, paracrystalline proteins (so-called octahedral crystals) and an aggregate of lipid globules, were identified which showed redistribution upon reorientation of the sporangiophore. Octahedral crystals occur throughout the sporangiophore, including the apical growing zone, and are localized inside vacuoles in which they reside singly or in clusters of up to 40 loosely associated individuals. Upon a 90° reorientation of sporangiophores, crystal clusters sedimented in approximately 50–200 s from the upper to the lower side, corresponding to a speed of 0.5–2 μm s⁻¹. Stage-4 sporangiophores (with sporangium) of three mutants which lack the crystals displayed anormal kinetics of gravitropism and substantially reduced bending angles in comparison to sporangiophores of the wild type. While horizontally placed wild-type sporangiophores reached the vertical position after 10–12 h, the crystal-lacking mutants bent maximally 40°–50° upward. In stage-1 sporangiophores a conspicuous aggregate of lipid globules is positioned about 50 μm below the apex. The globules floated upwards when the sporangiophore was placed horizontally forming in this way a cap-like aggregate. It is proposed that both the sedimenting protein crystals and the upward-floating globules are involved in gravisensing. Received: 23 March 1999 / Accepted: 27 May 1999     

4-Chlorophenol degradation by a bacterial consortium: development of a granular activated carbon biofilm reactor

A bacterial consortium that can degrade chloro- and nitrophenols has been isolated from the rhizosphere of Phragmitis communis. Degradation of 4-chlorophenol (4-CP) by a consortium attached to granular activated carbon (GAC) in a biofilm reactor was evaluated during both open and closed modes of operation. During the operation of the biofilm reactor, 4-CP was not detected in the column effluent, being either adsorbed to the GAC or biodegraded by the consortium. When 4-CP at 100 mg l⁻¹ was fed to the column in open mode operation (20 mg g⁻¹ GAC total supply), up to 27% was immediately available for biodegradation, the rest being adsorbed to the GAC. Biodegradation continued after the system was returned to closed mode operation, indicating that GAC bound 4-CP became available to the consortium. Biofilm batch cultures supplied with 10–216 mg 4-CP g⁻¹ GAC suggested that a residual fraction of GAC-bound 4-CP was biologically unavailable. The consortium was able to metabolise 4-CP after perturbations by the addition of chromium (Cr VI) at 1–5 mg l⁻¹ and nitrate at concentrations up to 400 mg l⁻¹. The development of the biofilm structure was analysed by scanning electron microscopy and confocal laser scanning microscopy (CLSM) techniques. CLSM revealed a heterogeneous structure with a network of channels throughout the biofilm, partially occupied by microbial exopolymer structures. Received: 17 March 1999 / Received revision: 27 May 1999 / Accepted: 28 May 1999     

Biotransformation of N-acetylphenothiazine by fungi

Cultures of the fungi Aspergillus niger, Cunninghamella verticillata, and Penicillium simplicissimum, grown in a sucrose/peptone medium, transformed N-acetylphenothiazine to N-acetylphenothiazine sulfoxide (from 13% to 28% of the total) and phenothiazine sulfoxide (from 5% to 27%). Phenothiazin-3-one (4%) and phenothiazine N-glucoside (4%) were also produced by C. verticillata. The probable intermediate, phenothiazine, was detected only in cultures of P. simplicissimum (6%). Received: 15 January 1999 / Received revision: 7 May 1999 / Accepted: 21 May 1999     

Improvement of ferulic acid bioconversion into vanillin by use of high-density cultures of Pycnoporus cinnabarinus

High-density cultures of Pycnoporus cinnabarinus were tested with a view to optimisation of ferulic acid bioconversion into vanillin. The dry weight was increased fourfold by using glucose, fructose or a mixture of glucose and phospholipids as carbon source instead of maltose, the carbon source previously used. 5 mmol l⁻¹ vanillin, i.e. 760 mg l⁻¹, was produced over 15 days with glucose-phospholipid medium. In contrast, formation of vanillin was lower using glucose or fructose compared to the maltose control. A bioreactor (2 l) with a glucose-phospholipid medium gave a molar yield of vanillin of 61% (4 mmol l⁻¹). An alternative strategy was to grow the fungus on a glucose or fructose medium for 3 days, then switch to maltose during the bioconversion phase: this method allowed 3.3 mmol l⁻¹ vanillin to be obtained in 10 days. Many by-products such as methoxyhydroquinone and vanillyl alcohol were also produced. Received: 19 February 1999 / Received revision: 4 June 1999 / Accepted: 4 June 1999     

Production of 2,3-butanediol by newly isolated Enterobacter cloacae

Enterobacter cloacae NRRL B-23289 was isolated from local decaying wood/corn soil samples while screening for microorganisms for conversion of l-arabinose to fuel ethanol. The major product of fermentation by the bacterium was meso-2,3-butanediol (2,3-BD). In a typical fermentation, a BD yield of 0.4 g/g arabinose was obtained with a corresponding productivity of 0.63 g/l per hour at an initial arabinose concentration of 50 g/l. The effects of initial arabinose concentration, temperature, pH, agitation, various monosaccharides, and multiple sugar mixtures on 2,3-BD production were investigated. BD productivity, yield, and byproduct formation were influenced significantly within these parameters. The bacterium utilized sugars from acid plus enzyme saccharified corn fiber and produced BD (0.35 g/g available sugars). It also produced BD from dilute acid pretreated corn fiber by simultaneous saccharification and fermentation (0.34 g/g theoretical sugars). Received: 17 December 1998 / Revision received: 9 March 1999 / Accepted: 20 March 1999     

Bioremediation of atrazine-contaminated soil by repeated applications of atrazine-degrading bacteria

Bioaugmentation has previously been unreliable for the in situ clean-up of contaminated soils because of problems with poor survival and the rapid decline in activity of the bacterial inoculum. In an attempt to solve these problems, a 500-l batch fermenter was investigated for its ability to deliver inoculum repeatedly to contaminated soils via irrigation lines. In a field experiment, mesocosms were filled with 350 kg soil containing 100 mg kg⁻¹ atrazine, and inoculated one, four or eight times with an atrazine-degrading bacterial consortium that was produced in the fermenter. After 12 weeks, no significant degradation of atrazine had occurred in soil that was inoculated only once; whereas, mesocosms inoculated four and eight times mineralized 38% and 72% of the atrazine respectively. Similar results were obtained in a laboratory experiment using soil contaminated with 100 mg kg⁻¹ [¹⁴C]atrazine. After 35 days, soil that was inoculated once with 10⁸ cfu ml⁻¹ of the consortium or with the atrazine-degrading bacterium, Pseudomonas sp. strain ADP, mineralized 17% and 35% of the atrazine respectively. In comparison, microcosms inoculated every 3 days with the consortium or with Pseudomonas sp. (ADP) mineralized 64% or 90% of the atrazine over this same period. Results of these experiments suggest that repeated inoculation from an automated fermenter may provide a strategy for bioaugmentation of contaminated soil with xenobiotic-degrading bacteria. Received: 20 November 1998 / Received revision: 8 February 1999 / Accepted: 12 February 1999