Increased product formation induced by a directed secondary substrate limitation in a batch Hansenula polymorpha culture

By the use of directed limitations of secondary substrates, the metabolic flux should be deflected from biomass production to product formation. In order to study the impact of directed limitations caused by various secondary substrates on the growth and product formation of the methylotrophic yeast Hansenula polymorpha, the cultivation systems respiration activity monitoring system (RAMOS) and BioLector were used in parallel. While the RAMOS device allows the online monitoring of the oxygen transfer rate in shake flasks, the BioLector enables in microtiter plates the monitoring of scattered light and the fluorescence intensity of the green fluorescent protein (GFP). Secondary substrate limitations of phosphate, potassium, and magnesium were analyzed in batch fermentations. The sole carbon source was either 10 g/L glucose or 10 g/L glycerol. The expression of the GFP gene is controlled by the FMD promoter (formate dehydrogenase). In batch cultures with glucose as carbon source, a directed limitation of phosphate increased the GFP production 1.87-fold, compared to phosphate unlimited conditions. Under potassium-limited conditions with glycerol as sole carbon source, the GFP production was 1.41-fold higher compared to unlimited conditions. A limitation of the substrate magnesium resulted in a 1.22-fold increase GFP formation in the case of glycerol as carbon source.     

Respiration activity monitoring system for any individual well of a 48-well microtiter plate

Background

Small-scale micro-bioreactors have become the cultivation vessel of choice during the first steps of bioprocess development. They combine high cultivation throughput with enhanced cost efficiency per cultivation. To gain the most possible information in the early phases of process development, online monitoring of important process parameters is highly advantageous. One of these important process parameters is the oxygen transfer rate (OTR). Measurement of the OTR, however, is only available for small-scale fermentations in shake flasks via the established RAMOS technology until now. A microtiter plate-based (MTP) μRAMOS device would enable significantly increased cultivation throughput and reduced resource consumption. Still, the requirements of miniaturization for valve and sensor solutions have prevented this transfer so far. This study reports the successful transfer of the established RAMOS technology from shake flasks to 48-well microtiter plates. The introduced μRAMOS device was validated by means of one bacterial, one plant cell suspension culture and two yeast cultures.

Results

A technical solution for the required miniaturized valve and sensor implementation for an MTP-based μRAMOS device is presented. A microfluidic cover contains in total 96 pneumatic valves and 48 optical fibers, providing two valves and one optical fiber for each well. To reduce costs, an optical multiplexer for eight oxygen measuring instruments and 48 optical fibers is introduced. This configuration still provides a reasonable number of measurements per time and well. The well-to-well deviation is investigated by 48 identical Escherichia coli cultivations showing standard deviations comparable to those of the shake flask RAMOS system. The yeast Hansenula polymorpha and parsley suspension culture were also investigated.

Conclusions

The introduced MTP-based μRAMOS device enables a sound and well resolved OTR monitoring for fast- and slow-growing organisms. It offers a quality similar to standard RAMOS in OTR determination combined with an easier handling. The experimental throughput is increased 6-fold and the media consumption per cultivation is decreased roughly 12.5-fold compared to the established eight shake flask RAMOS device.

     

The oxygen transfer rate as key parameter for the characterization of<Emphasis Type="Italic"> Hansenula polymorpha</Emphasis> screening cultures

Screening cultures are usually non-monitored and non-controlled due to a lack of appropriate measuring techniques. A new device for online measurement of oxygen transfer rate (OTR) in shaking-flask cultures was used for monitoring the screening of Hansenula polymorpha. A shaking frequency of 300 rpm and a filling volume of 20 ml in 250-ml flasks ensured a sufficient oxygen transfer capacity of 0.032 mol (l h)^–1 and thus a respiration not limited by oxygen. Medium buffered with 0.01 mol phosphate l^–1 (pH 6.0) resulted in pH-inhibited respiration, whereas buffering with 0.12 mol phosphate l^–1 (pH 4.1) resulted in respiration that was not inhibited by pH. The ammonium demand was balanced by establishing fixed relations between oxygen, ammonium, and glycerol consumption with 0.245±0.015 mol ammonium per mol glycerol. Plate precultures with complex glucose medium reduced the specific growth rate coefficient to 0.18 h^–1 in subsequent cultures with minimal glycerol medium. The specific growth rate coefficient increased to 0.26 h^–1 when exponentially growing precultures with minimal glycerol medium were used for inoculation. Changes in biomass, glycerol, ammonium, and pH over time were simulated on the basis of oxygen consumption.     

Characterization of photosynthetically active duckweed (<Emphasis Type="Italic">Wolffia australiana</Emphasis>) in vitro culture by Respiration Activity Monitoring System (RAMOS)

The feasibility of oxygen transfer rate (OTR) measurement to non-destructively monitor plant propagation and vitality of photosynthetically active plant in vitro culture of duckweed (Wolffia australiana, Lemnaceae) was tested using Respiration Activity Monitoring System (RAMOS). As a result, OTR proofed to be a sensitive indicator for plant vitality. The culture characterization under day/night light conditions, however, revealed a complex interaction between oxygen production and consumption, rendering OTR measurement an unsuitable tool to track plant propagation. However, RAMOS was found to be a useful tool in preliminary studies for process development of photosynthetically active plant in vitro cultures.     

The influence of cultivation methods on Shewanella oneidensis physiology and proteome expression

High-throughput analyses that are central to microbial systems biology and ecophysiology research benefit from highly homogeneous and physiologically well-defined cell cultures. While attention has focused on the technical variation associated with high-throughput technologies, biological variation introduced as a function of cell cultivation methods has been largely overlooked. This study evaluated the impact of cultivation methods, controlled batch or continuous culture in bioreactors versus shake flasks, on the reproducibility of global proteome measurements in Shewanella oneidensis MR-1. Variability in dissolved oxygen concentration and consumption rate, metabolite profiles, and proteome was greater in shake flask than controlled batch or chemostat cultures. Proteins indicative of suboxic and anaerobic growth (e.g., fumarate reductase and decaheme c-type cytochromes) were more abundant in cells from shake flasks compared to bioreactor cultures, a finding consistent with data demonstrating that “aerobic” flask cultures were O₂ deficient due to poor mass transfer kinetics. The work described herein establishes the necessity of controlled cultivation for ensuring highly reproducible and homogenous microbial cultures. By decreasing cell to cell variability, higher quality samples will allow for the interpretive accuracy necessary for drawing conclusions relevant to microbial systems biology research.     

Efficacy of commercial products in enhancing oil biodegradation in closed laboratory reactors

Summary A laboratory screening protocol was designed and conducted to test the efficacy of eight commercial bacterial cultures and two non-bacterial products in enhancing the biodegradation of weathered Alaska North Slope crude oil in closed flasks. Three lines of evidence were used to support the decision to progress to field testing in Prince William Sound: rapid onset and high rate of oxygen uptake, substantial growth of oil degraders, and significant degradation of the aliphatic and aromatic hydrocarbon fractions of the weathered Alaska North Slope crude oil. A product had to enhance biodegradation greater than that achieved with excess mineral nutrients. Experiments were conducted in closed respirometer flasks and shake flasks, using seawater from Prince William Sound and weathered crude oil from a contaminated beach. Analysis of the data resulted in selection of two of the ten products for field testing. Both were bacterial products. Findings suggested that the indigenous Alaskan microorganisms were primarily responsible for the biodegradation in the closed flasks and respirometer vessels.     

Bioleaching of chalcopyrite by pure and mixed cultures of Acidithiobacillus spp. and Leptospirillum ferriphilum

Bioleaching is an economical method for the recovery of metals that requires low investment and operation costs. Furthermore, it is generally more environmentally friendly than many physicochemical metal extraction processes. The bioleaching of chalcopyrite in shake flasks was investigated with pure and mixed cultures of Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans, Acidithiobacillus caldus, and Leptospirillum ferriphilum. The mixed cultures containing both iron- and sulfur-oxidizing bacteria were more efficient than the pure culture alone. The presence of sulfur-oxidizing bacteria positively increased the dissolution rate and the percentage recovery of copper from chalcopyrite. Mixed cultures consisting of moderately thermophilic L. ferriphilum and A. caldus leached chalcopyrite more effectively than mesophilic A. ferrooxidans pure and mixed cultures. The decrease of the chalcopyrite dissolution rate in leaching systems containing A. ferrooxidans after 12–16 days coincided with the formation of jarosite precipitation as a passivation layer on the mineral surface during bioleaching. Low pH significantly reduces jarosite formation in pure and mixed cultures of L. ferriphilum and A. caldus.     

Combined dissolved oxygen tension and online viscosity measurements in shake flask cultivations via infrared fluorescent oxygen-sensitive nanoparticles

Oxygen supply is one of the most critical process parameters in aerobic cultivations. To assure sufficient oxygen supply, shake flasks are usually used in combination with orbital shaking machines. In this study, a measurement technique for the dissolved oxygen tension (DOT) in shake flask cultures with viscosity changes is presented. The movement of the shaker table is monitored by means of a Hall effect sensor. For DOT measurements, infrared fluorescent oxygen-sensitive nanoparticles are added to the culture broth. The position of the rotating bulk liquid needs to be determined to assure measurements inside the liquid. The leading edge of the bulk liquid is detected based on the fluorescence signal intensity of the oxygen-sensitive nanoparticles. Furthermore, online information about the viscosity of the culture broth is acquired due to the detection of the position of the leading edge of the bulk liquid relative to the direction of the centrifugal force, as described by Sieben et al. (2019. Sci. Rep., 9, 8335). The DOT measurement is combined with a respiration activity monitoring system which allows for the determination of the oxygen transfer rate (OTR) in eight parallel shake flasks. Based on DOT and OTR, the volumetric oxygen transfer coefficient (k_La) is calculated during cultivation. The new system was successfully applied in cultivations of Escherichia coli, Bacillus licheniformis, and Xanthomonas campestris.     

Cellulolytic activity of four Fusarium spp.

Fusarium lini, F. lycopersici, F. pallidoroseum and F. semitectum grown in shake flasks produced, respectively, 0.19, 0.33, 0.13 and 0.09 units filter-paper cellulase/ml. Trichoderma reesei, in comparison, produced 0.8 U/ml.The authors are with Defence Food Research Laboratory, Mysore-570 011, India.     

Non-invasive methods for determination of cellular growth inPodophyllum hexandrum suspension cultures

Culture conductivity and on-line NADH fluorescence were used to measure cellular growth in plant cell suspension cultures ofPodophyllum hexandrum. An inverse correlation between dry cell weight and medium conductivity was observed during shake flask cultivation. A linear relationship between dry cell weight and culture NADH fluorescence was obtained during the exponential phase of batch cultivation in a bioreactor under the pH stat (pH 6) conditions. It was observed that conductivity measurement were suitable for biomass characterisation under highly dynamic uncontrolled shake flask cultivation conditions. However, if the acid/alkali feeding is done for pH control the conductivity measurement could not be applied. On the other hand the NADH fluorescence measurement allowed online-in situ biomass monitoring of rather heterogenous plant cell suspension cultures in bioreactor even under the most desirable pH stat conditions.     

Development of a nontoxic acoustic window nutrient-mist bioreactor and relevant growth data

Summary A nutrient-mist bioreactor was designed that separates the nutrient medium from the electronic components via an acoustic window. This eliminates compromising culture sterility when repairing mechanical failures common with commercially available mist reactors. The experimental mist bioreactor is low cost and can be assembled in any laboratory. Toxicity tests of several potential acoustically transparent materials are included. Details of the construction procedures include methods for casting the window. Growth data using the newly designed nutrient mist bioreactor are compared to data from a commercial mist reactor, shake flasks, and Gelrite cultures.Artemisia annua hairy roots andNephrolepis exaltata shoot cultures showed growth comparable to the conventional tissue culture methods.     

Improved paclitaxel production in a two-phase suspension culture ofTaxus cuspidata using silicone cubes

Two-phase cultures ofTaxus cuspidata were performed using silicone cubes as a second phase in shake flasks for paclitaxel production. Among various taxanes, paclitaxel was selectively adsorbed on the silicon cubes. When silicone cubes were added to suspension culture ofTaxus cuspidata, paclitaxel production increased about 45 folds. The maximum paclitaxel production was 3.95 mg/L when 10% of silicone cubes were added to the culture at the 7th day from inoculation.     

The Effect of Fungal Morphology on Ligninolytic Enzyme Production by a Recently Isolated Wood-Degrading Fungus Trichophyton Rubrum LSK-27

The morphology and ligninolytic enzyme production of a recently isolated wood-degrading fungus Trichophyton rubrum LSK-27 was investigated. In submerged cultures, the organism appeared to be an efficient manganese peroxidase (MnP) producer. When grown in baffled and unbaffled shake flasks with three different working volume/total volume ratios (WV/TV 10, 25 and 50%), the organism displayed notable morphological differences, with variations in pellet shape and size. Cultivation in baffled flasks with 25% WV/TV resulted in higher MnP and also laccase production as well as an earlier appearance of these enzymes in culture broth. However, oxygen limitation conditions inhibited MnP and laccase production and resulted in considerable changes in the morphology of this fungus.     

Scale-up of biopesticide production processes using wastewater sludge as a raw material

Studies were conducted on the production of Bacillus thuringiensis (Bt)-based biopesticides to ascertain the performance of the process in shake flasks, and in two geometrically similar fermentors (15 and 150 l) utilizing wastewater sludge as a raw material. The results showed that it was possible to achieve better oxygen transfer in the larger capacity fermentor. Viable cell counts increased by 38–55% in the bioreactor compared to shake flasks. As for spore counts, an increase of 25% was observed when changing from shake flask to fermentor experiments. Spore counts were unchanged in bench (15 l) and pilot scale (5.3–5.5 e⁺⁰⁸ cfu/ml; 150 l). An improvement of 30% in the entomotoxicity potential was obtained at pilot scale. Protease activity increased by two to four times at bench and pilot scale, respectively, compared to the maximum activity obtained in shake flasks. The maximum protease activity (4.1 IU/ml) was obtained in pilot scale due to better oxygen transfer. The Bt fermentation process using sludge as raw material was successfully scaled up and resulted in high productivity for toxin protein yield and a high protease activity.     

Ensuring constant oxygen supply during inoculation is essential to obtain reproducible results with obligatory aerobic acetic acid bacteria in vinegar production

Since obligatory aerobic acetic acid bacteria in vinegar production suffer even from short oxygen depletion during traditional precultivation steps, the reproducibility of results in the main culture is insufficient. Thus, the aim of this paper is to establish a reproducible small scale cultivation method for obligatory aerobic acetic acid bacteria at industrially relevant high ethanol and acetic acid concentrations by ensuring constant oxygen transfer in the whole inoculation procedure. An acetic acid bacteria preculture was drained off from a laboratory-scale bioreactor into an aerated mobile bubble column and then transferred to an already shaking RAMOS shake flask device. Whereas the respiration curves of the traditionally processed acetic acid bacteria cultures were low and greatly diverged, those of the preculture transferred first into the bubble column and then into the already shaking flasks were high and coincided with one another. Furthermore, shutting off aeration in the mobile bubble column led to a rapid decrease in bacterial activity. In conclusion, traditional precultivation steps are not suitable for obligatory aerobic acetic acid bacteria in vinegar production. Maintaining constant oxygen transfer is necessary to guarantee the reproducibility of main culture experiments with such bacteria.     

Automated determination of critical oxygen concentration for routinely active fish

Synopsis We describe an automated respirometer and control system that determines critical (metabolism-limiting) oxygen concentration for routinely active fish. A microcomputer monitors fish metabolic rate as oxygen concentration in the closed respirometer declines; the critical oxygen concentration is signaled by metabolic-rate change, which is resolved via statistically based rules that consider both magnitude and consistency of rate deviations. After the critical oxygen concentration is found, data are written to disk, the respirometer is reoxygenated and another trial is initiated. This sequence can be repeated indefinitely without human intervention, allowing replicate estimates from a single fish. Ideally, metabolic rate should be calculated frequently during a trial, to minimize exposure of the fish to sub-critical oxygen concentrations. However, precision of measurement is limited by ‘noise’ related to length of time interval over which changes in oxygen concentration are determined, respirometer chamber volume, and fish respiration rate. Short time intervals lead to excessive noise, whereas long time intervals result in insufficient numbers of rate measurements. In a respirometer chamber of calculable optimum volume, measurements made by averaging oxygen readings taken very rapidly over two to three minute intervals provide a good compromise. We present data from experiments with bluegill,Lepomis macrochirus, to illustrate the method and show that critical oxygen concentrations identified by the system are consistent with estimates made by humans viewing graphs of the same experiments     

Noninvasive online biomass detector system for cultivation in shake flasks

A novel online sensor system for noninvasive and continuous monitoring of cell growth in shake flasks is described. The measurement principle is based on turbidity measurement by detecting 180°‐scattered light and correlation to OD by nonlinear calibration models. The sensor system was integrated into a commercial shaking tablar to read out turbidity from below the shake flasks bottom. The system was evaluated with two model microorganisms, Escherichia coli K12 as prokaryotic and Saccharomyces cerevisiae as eukaryotic model. The sensor allowed an accurate monitoring of turbidity and correlation with OD₆₀₀ ≤ 30. The determination of online OD showed relative errors of about 7.5% for E. coli K12 and 12% for S. cerevisiae. This matches the errors of the laborious offline OD and thus facilitates to overcome the drawbacks of the classical method as risk of contamination and decreasing volumes through sampling. One major challenge was to ensure a defined, nonvarying measurement zone as the rotating suspension in the shake flask forms a liquid sickle which circulates round the flasks inner bottom wall. The resulting alteration of liquid height above the sensor could be compensated by integration of an acceleration sensor into the tablar to synchronize the sensor triggering.     

Metabolic costs of the predation strategy of the spider Pardosa amentata (Clerck) (Lycosidae)

Summary Pardosa amentata adopts a sit-and-wait predation strategy with periodic changes of site. The metabolic costs of this strategy were evaluated using a Gilson respirometer. The respirometer was run at the mean temperatures prevailing month by month in the litter layer from which the experimental animals were collected and equations relating standard respiration rate to spider weight were established for each temperature. The mean value of b, the exponent relating weight to respiration rate, was 0.8011. Active respiration rate was determined at each temperature by using larger experimental flasks containing small glass beads which, in conjunction with the shaker mechanism on the respirometer, ensured that the spiders in the respirometer flasks maintained a fairly consistent level of locomotory activity. It was found that the measured active respiration rate was on average 3.17 times the standard rate. The two respiration rates were combined in the appropriate proportions to calculate the daily energy expenditure of an adult spider exhibiting its normal pattern of activity at different temperatures. It is shown that as locomotory activity is very limited in duration in P. amentata, the associated active respiration rate accounts for only a small proportion of daily respiratory energy losses, 0.36% at 5°C, 0.69% at 10°C, and 1.01% at 15°C.     

The biological response of hairy roots to O2 levels in bioreactors

Summary The efficient exchange of gases between roots and their environment is one of the biggest challenges in bioreactor design for transformed root cultures. Gas-phase reactors can alleviate this problem as well as provide a new tool for studying the biological response of roots and other differentiated tissues to changes in the gas phase composition. In our comparison of liquid- and gas-phase reactors, roots grown in liquid (shake flasks or bubble column reactors) are shown to be under hypoxic stress. Roots grown in a gas-phase reactor (nutrient mist), while not hypoxic, produced 50% less biomass. These results suggest that the response of the tissues to gas phase composition are complex and need further study.     

Analysis of morphological characteristics of Solanum chrysotrichum cell suspension cultures

Cell size distribution of Solanum chrysotrichum cell suspension cultures was determined using mechanical sieving and an image analysis system. The results were compared using the sieve size (<0.25, 0.25–0.50, 0.5–1.0 and >1.00 mm) as the criterion. Mechanical sieving as well as image analysis showed that S. chrysotrichum cultures developed in shake flasks present a similar tendency to increase in aggregate size as growth persists. However, there are considerable differences in the values of each fraction. Fractions obtained by mechanical sieving were characterized by image analysis demonstrating that an inefficient separation of the cell population exists. The results demonstrate that digital image analysis was more precise than mechanical sieving to describe the cell size distribution changes occurring during cell growth. It was also possible to achieve a total characterization of S. chrysotrichum morphology.