Ambruticin S production in amino acid rich media

Summary The antimycoticum ambruticin was produced by cultivating the myxobacterium Sorangium cellulosum in shake flasks and stirred tank reactors with 10- and 30-1 working volumes. During growth and product formation amino acid concentrations in the complex media were measured by HPLC. In the logarithmic growth phase free aspartate and glutamate were assimilated without product formation. After consumption of aspartate and glutamate, growth was limited and ambruticin production set in. The effects of biological parameters such as age, amount of inoculum, pretreatment of cells before inoculation and time of precultivation were also investigated.Offprint requests to: W.-D. Deckwer     

Two‐compartment processing as a tool to boost recombinant protein production

Pichia pastoris is used extensively as a production platform for many recombinant proteins. The dissolved oxygen (DO) is one of the most important factors influencing protein production. The influence of the DO on productivity has not been studied independent from the feed rate. In this work, various DO levels were investigated independent from the feed rate. The model system was recombinant P. pastoris under the control of methanol‐induced alcohol oxidase promoter, which expressed HRP as the target protein. No significant effect was observed in terms of titer and specific productivity, which is a confirmation of the fact that the DO in a one‐compartment system cannot boost productivity for the model system under study. Hence, a two‐compartment system (a single reactor coupled with a plug flow reactor) was designed and implemented in order to apply oxygen‐related stress in the plug flow reactor and allow the cells to be recovered in the main reactor. Doing so, more than two‐fold increase in the titer and productivity and three‐fold increase in protein‐specific activity were achieved. Hence, partial application of oxygen‐related stress in the two‐compartment system was proposed as a process technology to enhance protein production.     

Estimation of nitrifier abundances in a partial nitrification reactor treating ammonium-rich saline wastewater using DGGE, T-RFLP and mathematical modeling

The bacterial community in a partial nitrification reactor was analyzed on the basis of 16S rRNA gene by cloning–sequencing method, and the percentages of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in the activated sludge were quantified by three independent methods, namely, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP) and Double Monod modeling. The clone library results suggested that there were only a dominant AOB and a dominant NOB species in the reactor, belonging to Nitrosomonas genus and Nitrospira genus, respectively. The percentages of NOB in total bacterial community increased from almost 0% to 30% when dissolved oxygen (DO) levels were changed from 0.15 mg/L to 0.5 mg/L, coinciding with the accumulation and conversion of nitrite, while the percentages of AOB changed little in the two phases. The results confirmed the importance of low DO level for inhibiting NOB to achieve partial nitrification. Furthermore, the percentages of AOB and NOB in the total bacteria community were estimated based on the results of batch experiments using Double Monod model, and the results were comparable with those determined according to profiles of DGGE and T-RFLP.     

Role of oxygen in the utilization of phenol by Pseudomonas CF600 in continuous culture

The dissolved oxygen (DO) level is the key factor which decides the rate of degradation of the organic load in aerobic growth conditions. In this study the role of DO levels on the utilization of phenols has been reported using the continuous culture system. A phenol-utilizing strain, Pseudomonas CF600 has been used as a model. Its phenol-degrading capacity was studied using continuous cultivation for a period of 60 days. The bioreactor was kept at a dilution rate of 0.006 h^–1 with DO levels maintained at 2, 3, and 4 ppm keeping all the other cultivation conditions constant. Physiological variations under the cultivation conditions were studied by monitoring off-line phenol utilization and respirometric analysis of harvested culture against different substrates. It was observed that the accumulation of 2-hydroxymuconate semialdehyde (HMS), an intermediate in the phenol degradation pathway, depends on the DO level. The maximum level of HMS in the medium observed was 3.92 M when DO was maintained at 2 ppm whereas with 3 ppm of DO, HMS level was below 0.4 M. Oxygen uptake data of the cells harvested from cultures grown at different DO levels showed that the uptake was highest at 3 ppm DO for all the substrates tried. When phenol was used as substrate, the oxygen uptake rate was 42.66, 66.36 and 35.55 nM/min/mg dry weight of cells at 4, 3 and 2 ppm DO respectively. Results show that DO levels influence the rate of phenol utilization in Pseudomonas CF600.     

Optical device for parallel online measurement of dissolved oxygen and pH in shake flask cultures

We describe a new device with parallel optical measurement of dissolved oxygen (DO) and pH in up to nine shake flasks applicable in any conventional shaking incubator. Measurement ranges are 0–500% of air saturation for oxygen and 5.5–8.5 for pH. It was used to characterize growth profiles of different l-lysine producing strains of Corynebacterium glutamicum, of Saccharomyces cerevisiae and of Escherichia coli. Cultures in unbaffled flasks were highly reproducible. Oxygen limitation was indicated online which is particularly important when cultivating fast growing cells as E. coli. C. glutamicum strains showed distinct characteristic patterns of DO and pH indicating biological events. During the cultivation of S. cerevisiae on glucose, fructose and galactose, oxygen uptake rate was determined using the predetermined value of k _L a. pH measurement was used to determine the minimum buffer requirement for a culture of C. glutamicum.     

Enhanced heme protein expression by ammonia-oxidizing communities acclimated to low dissolved oxygen conditions

This study has investigated the acclimation of ammonia-oxidizing communities (AOC) to low dissolved oxygen (DO) concentrations. Under controlled laboratory conditions, two sequencing batch reactors seeded with activated sludge from the same source were operated at high DO (near saturation) and low DO (0.1 mg O₂/L) concentrations for a period of 220 days. The results demonstrated stable and complete nitrification at low DO conditions after an acclimation period of approximately 140 days. Acclimation brought about increased specific oxygen uptake rates and enhanced expression of a particular heme protein in the soluble fraction of the cells in the low DO reactor as compared to the high DO reactor. The induced protein was determined not to be any of the enzymes or electron carriers present in the conventional account of ammonia oxidation in ammonia-oxidizing bacteria (AOB). Further research is required to determine the specific nature of the heme protein detected; a preliminary assessment suggests either a type of hemoglobin protein or a lesser-known component of the energy-transducing pathways of AOB. The effect of DO on AOC dynamics was evaluated using the 16S rRNA gene as the basis for phylogenetic comparisons and organism quantification. Ammonium consumption by ammonia-oxidizing archaea and anaerobic ammonia-oxidizing bacteria was ruled out by fluorescent in situ hybridization in both reactors. Even though Nitrosomonas europaea was the dominant AOB lineage in both high and low DO sequencing batch reactors at the end of operation, this enrichment could not be linked in the low DO reactor to acclimation to oxygen-limited conditions.     

The Phosphatomes of the Multicellular Myxobacteria Myxococcus xanthus and Sorangium cellulosum in Comparison with Other Prokaryotic Genomes

Background

Analysis of the complete genomes from the multicellular myxobacteria Myxococcus xanthus and Sorangium cellulosum identified the highest number of eukaryotic-like protein kinases (ELKs) compared to all other genomes analyzed. High numbers of protein phosphatases (PPs) could therefore be anticipated, as reversible protein phosphorylation is a major regulation mechanism of fundamental biological processes.

Methodology

Here we report an intensive analysis of the phosphatomes of M. xanthus and S. cellulosum in which we constructed phylogenetic trees to position these sequences relative to PPs from other prokaryotic organisms.

Principal Findings

Predominant observations were: (i) M. xanthus and S. cellulosum possess predominantly Ser/Thr PPs; (ii) S. cellulosum encodes the highest number of PP2c-type phosphatases so far reported for a prokaryotic organism; (iii) in contrast to M. xanthus only S. cellulosum encodes high numbers of SpoIIE-like PPs; (iv) there is a significant lack of synteny among M. xanthus and S. cellulosum, and (v) the degree of co-organization between kinase and phosphatase genes is extremely low in these myxobacterial genomes.

Conclusions

We conclude that there has been a greater expansion of ELKs than PPs in multicellular myxobacteria.     

Four‐stage dissolved oxygen strategy based on multi‐scale analysis for improving spinosad yield by Saccharopolyspora spinosa ATCC49460

Dissolved oxygen (DO) is an important influencing factor in the process of aerobic microbial fermentation. Spinosad is an aerobic microbial‐derived secondary metabolite. In our study, spinosad was used as an example to establish a DO strategy by multi‐scale analysis, which included a reactor, cell and gene scales. We changed DO conditions that are related to the characteristics of cell metabolism (glucose consumption rate, biomass accumulation and spinosad production). Consequently, cell growth was promoted by maintaining DO at 40% in the first 24 h and subsequently increasing DO to 50% in 24 h to 96 h. In an in‐depth analysis of the key enzyme genes (gtt, spn A, spn K and spn O), expression of spinosad and specific Adenosine Triphosphate (ATP), the spinosad yield was increased by regulating DO to 30% within 96 h to 192 h and then changing it to 25% in 192 h to 240 h. Under the four‐phase DO strategy, spinosad yield increased by 652.1%, 326.1%, 546.8%, and 781.4% compared with the yield obtained under constant DO control at 50%, 40%, 30%, and 20% respectively. The proposed method provides a novel way to develop a precise DO strategy for fermentation.     

A flow injection analysis system with encapsulated high-density <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> cells for rapid determination of biochemical oxygen demand

The biochemical oxygen demand (BOD) determination was studied using a novel flow injection analysis (FIA) system with encapsulated Saccharomyces cerevisiae cells and an oxygen electrode and was compared with conventional 5-day BOD tests. S. cerevisiae cells were packed in a calcium alginate capsule at a dry cell weight of 250 g/l of capsule core. The level of dissolved oxygen (DO) was reduced due to the enhanced respiratory activity of the microbial cells when the injected nutrient passed through the bioreactor. The decrease in DO (ΔDO) was intensified with the amount of microbial cells packed in the bioreactor. However, the specific ΔDO decreased as the amount of cells loaded in the bioreactor increased. The ΔDO value was dependent on the pH and temperature of the mobile phase and reached its maximum value at 35°C and pH 7–8. Also, ΔDO became larger at longer response times as the flow rate of the mobile phase decreased. The measurement of ΔDO was repeated more than six times consecutively using a 20-ppm standard glucose and glutamic acid solution, which confirmed the reproducibility with a standard deviation of 0.95%. A strong linear correlation between ΔDO and BOD was also observed. The 5-day BOD values of actual water and wastewater samples were in accordance with the BOD values obtained by this FIA method using encapsulated S. cerevisiae cells. Unlike the cell-immobilized bead system, there was no contamination of the bioreactor resulting from any leak of yeast cells from the sensor capsules during BOD measurements.     

Characterization of a novel micro-pressure swirl reactor for removal of chemical oxygen demand and total nitrogen from domestic wastewater at low temperature

A novel micro-pressure swirl reactor (MPSR) was designed and applied to treat domestic wastewater at low temperature by acclimating microbial biomass with steadily decreasing temperature from 15 to 3 °C. Chemical oxygen demand (COD) was constantly removed by 85% and maintained below 50 mg L^?1 in the effluent during the process. When the air flow was controlled at 0.2 m³ h^?1, a swirl circulation was formed in the reactor, which created a dissolved oxygen (DO) gradient with a low DO zone in the center and a high DO zone in the periphery for denitrification and nitrification. 81% of total nitrogen was removed by this reactor, in which ammonium was reduced by over 90%. However, denitrification was less effective because of the presence of low levels of oxygen. The progressively decreasing temperature favored acclimation of psychrophilic bacteria in the reactor, which replaced mesophilic bacteria in the process of treatment.     

Comparison of oxygen consumption in freshwater mussels (Unionidae) from different habitats during declining dissolved oxygen concentration

The rate of oxygen consumption (OC) of 9 species of freshwater mussels was measured under declining dissolved oxygen (DO) concentrations. The effects of temperature for some species also was investigated. The pattern of the OC vs. DO curve for each species was used in a hyperbolic model to compare abilities to regulate OC under low oxygen conditions. At 24.5 °C, Pyganodon grandis (from lakes), Amblema plicata and Quadrula pustulosa (from mud or sand in large rivers), Elliptio complanata (from pool areas in rivers), and Elliptio fisheriana and Elliptio lanceolata (from bank margins of rivers) were better able to maintain OC under low DO than were Villosa iris and Villosa constricta (which inhabit riffles) and Pleurobema cordatum (found in rivers with moderate flow). Villosa iris was especially sensitive to low oxygen conditions. The ability to maintain normal OC at low DO was improved considerably at 16.5 °C for V. iris, P. grandis and E. complanata. It is concluded that oxygen regulation ability appears to be related to the degree of hypoxia a species normally experiences in its habitat type, and it is enhanced at low temperature. The measurement of OC vs. DO may be a useful technique for estimating DO water quality criteria for endangered species because it is noninvasive.     

Production of rosmarinic acid by<Emphasis Type="Italic">Lavandula vera</Emphasis> MM cell suspension in bioreactor: effect of dissolved oxygen concentration and agitation

The relationship between dissolved oxygen (DO) concentration, agitation rate and growth of Lavandula vera MM and rosmarinic acid biosynthesis was investigated in 3 l laboratory bioreactor. Lavandula vera MM cell suspension accumulated the highest amounts of biomass (34.8 g/l) and rosmarinic acid (1870.6 mg/l) on day 12 of cultivation at 50% dissolved oxygen and agitation speed 100 rpm and at 30% dissolved oxygen and agitation speed 300 rpm, respectively.     

Impact of Oxygen Availability on Microbially Induced Calcite Precipitation (MICP) Treatment

Most microbially induced calcite precipitation (MICP) processes are induced by aerobic bacteria; thus, oxygen availability plays an important role in MICP treatment. To determine the effects of oxygen supply on MICP treatment catalyzed by Sporosarcina pasteurii, contrast tests under an aerated condition, air-restricted condition, and open air condition were conducted. The results showed that dissolved oxygen (DO) in the air-restricted reactor decreased with time and was almost exhausted within 7 days; DO in the open box decreased by 50% after 7 days of treatment because of the superficial air supply; and DO in the aerated box maintained an initial high level because the consumed oxygen was supplied immediately by adequate air bubbles in the treatment solution. Unconfined compressive strength (UCS) and CaCO₃ content are high under the aerated condition, moderate under the open condition, and poor under the air-restricted condition. The UCS can be 100 times different depending on the different oxygen supply conditions. The overall influence process is as follows: oxygen is dissolved to supply DO for life and activity of the aerobic urea hydrolysis bacteria; then, urea is hydrolyzed to carbonate anions for CaCO₃ precipitation in the presence of Ca²⁺; and finally, CaCO₃ precipitation results in the strengthening of sand. The results indicate that a sufficient air supply is essential to improve MICP processes catalyzed by aerobic bacteria.     

Behavioural responses of different blackfly species to short-term oxygen depletion

Behavioural changes of four larval blackflies (Simulium noelleri, S. ornatum (complex), S. trifasciatum [syn. S. spinosum] and S. variegatum) to experimental reduction of dissolved oxygen were investigated with videotechniques. Since these species are characterised by different habitat preferences, they were expected to respond differently to oxygen depletion. During experiments lasting 120–140 min., dissolved oxygen (DO) was reduced to 0.3–0.6 mg/1 within the first hour and kept constant for another hour. Water velocity in the laboratory channel was 135 cm/s. Transparent plastic walls allowed video-recording of larval behavioural responses to oxygen depletion. Blackflies did not engage in undulative or other ventilation movements, and they did not increase locomotory activity, nor did they actively drift. Oxygen depletion mainly altered filter-feeding activity and non-locomotory movements (bending and sweeping). With decreasing DO concentrations larvae of all four species reduced and finally ceased filter-feeding. Non-locomotory movements first temporarily increased and then also ceased, except in S. variegatum, where these movements were immediately suspended. DO-threshold values for cessation of filter-feeding and movements, as well as mortality indicated S. variegatum to be the most sensitive species in respect to oxygen depletion, while S. noelleri seems to be the most tolerant among the four blackfly species tested here.     

Microplates with integrated oxygen sensing for medium optimization in animal cell culture

A new approach using microtiter plate cultivation with on-line measurement of dissolved oxygen (DO) was applied for medium optimization of mammalian cell culture. Applying dynamic liquid phase balance, oxygen uptake rates were calculated from the DO level and used as an indicator for culture viability. The developed method was successfully applied to optimization of the concentration of glucose, glutamine and inorganic salts for cultivation of a Chinese Hamster Ovary (CHO) cell line. Using 2³ full factorial central composite design, the optimum medium composition could be identified in one single run. The concentration of inorganic salts had a significant influence on cultivation. The developed method exhibits high potential to improve procedures of medium optimization for animal cell cultivation by allowing the investigation of large sets of potentially important variables in short time and with reduced effort.     

Estimating oxygen exchange across the air–water interface of a hypereutrophic lake

Patterns of estimates of oxygen flux (J) across the air–water interface of hypereutrophic Onondaga Lake, NY, U.S.A., are characterized for time scales ranging from diel to seasonal for an 8-month period. The analysis is supported by a high frequency (most often hourly) monitoring program, conducted with a robotic buoy, that included measurements of dissolved oxygen (DO), temperature, and fluorometric chlorophyll a in the lake's surface waters, vertical profiles of DO through the epilimnion, and wind speed and solar radiance. The magnitude and direction of J is demonstrated to vary dramatically at diel, day-to-day, and seasonal time scales. Thus, large errors in estimates of J may result from extrapolating flux calculations made from short-term data to longer time periods. The variations in J were driven by variations in metabolic activity and meteorology, and were mediated by departures from equilibrium DO concentrations and wind-driven turbulence. Extended periods of high J values are shown to coincide with intervals of large departures from equilibrium DO concentrations, but day-to-day differences are driven mostly by variations in wind. A distinct diel pattern of J estimates is manifested for average conditions, with substantially higher J values during daylight hours. This pattern reflects the common diel patterns of the drivers of both higher DO oversaturation and wind speed over those hours. It is demonstrated that the magnitude of J is substantial relative to net changes in the epilimnetic DO pool, and thus must be accommodated accurately in estimates of primary production and community respiration that are to be based on diel monitoring of DO in the water columns of productive lakes.     

Operation of partial nitrification to nitrite of landfill leachate and its performance with respect to different oxygen conditions

The coupled system of partial nitrification and anaerobic ammonium oxidation (Anammox) is efficient in nitrogen removal from wastewater. In this study, the effect of different oxygen concentrations on partial nitrification performance with a sequencing batch reactor (SBR) was investigated. Results indicate that, partial nitrification of landfill leachate could be successfully achieved under the 1.0–2.0 mg L⁻¹ dissolved oxygen (DO) condition after 118 d long-term operation, and that the effluent is suitable for an Anammox reactor. Further decreasing or increasing the DO concentration, however, would lead to a decay of nitrification performance. Additionally, the MLSS concentration in the reactor increased with increasing DO concentration. Respirometric assays suggest that low DO conditions (<2 mg L⁻¹) favor the ammonia-oxidizing bacteria (AOB) and significantly inhibit nitrite oxidizing bacteria (NOB) and aerobic heterotrophic bacteria (AHB); whereas high DO conditions (>3 mg L⁻¹) allow AHB to dominate and significantly inhibit AOB. Therefore, the optimal condition for partial nitrification of landfill leachate is 1.0–2.0 mg L⁻¹ DO concentration.     

Oxygen transfer characteristics of miniaturized bioreactor systems

Since their introduction in 2001 miniaturized bioreactor systems have made great advances in function and performance. In this article the dissolved oxygen (DO) transfer performance of submilliliter microbioreactors, and 1–10 mL minibioreactors was examined. Microbioreactors have reached k_La values of 460 h^?1, and are offering instrumentation and some functionality comparable to production systems, but at high throughput screening volumes. Minibioreactors, aside from one 1,440 h^?1 k_La system, have not offered as high rates of DO transfer, but have demonstrated superior integration with automated fluid handling systems. Microbioreactors have been typically limited to studies with E. coli, while minibioreactors have offered greater versatility in this regard. Further, mathematical relationships confirming the applicability of k_La measurements across all scales have been derived, and alternatives to fluorescence lifetime DO sensors have been evaluated. Finally, the influence on reactor performance of oxygen uptake rate (OUR), and the possibility of its real‐time measurement have been explored. Biotechnol. Bioeng. 2013; 110: 1005–1019. © 2012 Wiley Periodicals, Inc.     

Heterologous production of epothilones B and D in Streptomyces venezuelae

Epothilones, produced from the myxobacterium Sorangium cellulosum, are potential anticancer agents that stabilize microtubules in a similar manner to paclitaxel. The entire epothilone biosynthetic gene cluster was heterologously expressed in an engineered strain of Streptomyces venezuelae bearing a deletion of pikromycin polyketide synthase gene cluster. The resulting strains produced approximately 0.1 μg/l of epothilone B as a sole product after 4 days cultivation. Deletion of an epoF encoding the cytochrome P450 epoxidase gave rise to a mutant that selectively produces 0.4 μg/l of epothilone D. To increase the production level of epothilones B and D, an additional copy of the positive regulatory gene pikD was introduced into the chromosome of both S. venezuleae mutant strains. The resulting strains showed enhanced production of corresponding compounds (approximately 2-fold). However, deletion of putative transport genes, orf3 and orf14 in the epothilone D producing S. venezuelae mutant strain, led to an approximately 3-fold reduction in epothilone D production. These results introduce S. venezuelae as an alternative heterologous host for the production of these valuable anticancer agents and demonstrate the possibility of engineering this strain as a generic heterologous host for the production of polyketides and hybrid polyketide-nonribosomal peptides.