Oxygen supply controls the onset of pristinamycins production by Streptomyces pristinaespiralis in shaking flasks

Methodology for awakening the potential secondary metabolic capacity in actinomycetes

Secondary metabolites produced by actinomycete strains undoubtedly have great potential for use in applied research areas such as drug discovery. However, it is becoming difficult to obtain novel compounds because of repeated isolation around the world. Therefore, a new strategy for discovering novel secondary metabolites is needed. Many researchers believe that actinomycetes have as yet unanalyzed secondary metabolic activities, and the associated undiscovered secondary metabolite biosynthesis genes are called "silent" genes. This review outlines several approaches to further activate the metabolic potential of actinomycetes.

Pristinamycin production using Streptomyces pristinaespiralis and date sirup as substrate-process modeling, optimization, and scale-up

Pristinamycin biosynthesis using Streptomyces pristinaespiralis and date sirup (DS) as substrates was optimized before scale-up. DS was filter sterilized as heat sterilization primes Maillard reactions having negative effects on antibiotic production. Multilinear regression modeling (MLR) predicted optimum medium composition, specifying components with positive and negative effects on production. The MLR showed that to maximize bacterial growth, DS, arginine, CaCl₂, and KH₂PO₄ must be fixed at the highest concentration, but to maximize antibiotic production, these factors have to be fixed at a low level. A noticeable difference in productivity was observed in a shake flask experiments with 50.4 and 43.1 mg/L pristinamycin final concentration for the DS and the glucose substrates, respectively. In the 2 L bioreactor, the DS medium resulted in a 66.6 mg/L antibiotic, while the scale-up in the 100 L resulted in 39.0 mg/L. The low yield in the 100 L bioreactor could be attributed to the relatively high stirring rate applied which was the minimum possible in the bioreactor used. This high stirring rate prevented pellet formation by the cells, which is described as necessary for antibiotic formation by the bacterium. Hence, a successful scale-up to pilot-scale should consider the effect of stirring rate.

Use of elicitors to enhance or activate the antibiotic production in streptomyces

Streptomyces is the largest and most significant genus of Actinobacteria, comprising 961 species. These Gram-positive bacteria produce many versatile and important bioactive compounds; of these, antibiotics, specifically the enhancement or activation of their production, have received extensive research attention. Recently, various biotic and abiotic elicitors have been reported to modify the antibiotic metabolism of Streptomyces, which promotes the production of new antibiotics and bioactive metabolites for improvement in the yields of endogenous products. However, some elicitors that obviously contribute to secondary metabolite production have not yet received sufficient attention. In this study, we have reviewed the functions and mechanisms of chemicals, novel microbial metabolic elicitors, microbial interactions, enzymes, enzyme inhibitors, environmental factors, and novel combination methods regarding antibiotic production in Streptomyces. This review has aimed to identify potentially valuable elicitors for stimulating the production of latent antibiotics or enhancing the synthesis of subsistent antibiotics in Streptomyces. Future applications and challenges in the discovery of new antibiotics and enhancement of existing antibiotic production using elicitors are discussed.

Corynebacterium glutamicum, a natural overproducer of succinic acid?

Corynebacterium glutamicum is well known as an important industrial amino acid producer. For a few years, its ability to produce organic acids, under micro-aerobic or anaerobic conditions was demonstrated. This study is focused on the identification of the culture parameters influencing the organic acids production and, in particular, the succinate production, by this bacterium. Corynebacterium glutamicum 2262, used throughout this study, was a wild-type strain, which was not genetically designed for the production of succinate. The oxygenation level and the residual glucose concentration appeared as two critical parameters for the organic acids production. The maximal succinate concentration (4.9 g L-1) corresponded to the lower kLa value of 5 h-1. Above 5 h-1, a transient accumulation of the succinate was observed. Interestingly, the stop in the succinate production was concomitant with a lower threshold glucose concentration of 9 g L-1. Taking into account this threshold, a fed-batch culture was performed to optimize the succinate production with C. glutamicum 2262. The results showed that this wild-type strain was able to produce 93.6 g L-1 of succinate, which is one of the highest concentration reported in the literature.

The metabolic switch can be activated in a recombinant strain of Streptomyces lividans by a low oxygen transfer rate in shake flasks

Background

In Streptomyces, understanding the switch from primary to secondary metabolism is important for maximizing the production of secondary metabolites such as antibiotics, as well as for optimizing recombinant glycoprotein production. Differences in Streptomyces lividans bacterial aggregation as well as recombinant glycoprotein production and O-mannosylation have been reported due to modifications in the shake flask design. We hypothetized that such differences are related to the metabolic switch that occurs under oxygen-limiting conditions in the cultures.

Results

Shake flask design was found to affect undecylprodigiosin (RED, a marker of secondary metabolism) production; the RED yield was 12 and 385 times greater in conventional normal Erlenmeyer flasks (NF) than in baffled flasks (BF) and coiled flasks (CF), respectively. In addition, oxygen transfer rates (OTR) and carbon dioxide transfer rates were almost 15 times greater in cultures in CF and BF as compared with those in NF. Based on these data, we obtained respiration quotients (RQ) consistent with aerobic metabolism for CF and BF, but an RQ suggestive of anaerobic metabolism for NF.

Conclusion

Although the metabolic switch is usually related to limitations in phosphate and nitrogen in Streptomyces sp., our results reveal that it can also be activated by low OTR, dramatically affecting recombinant glycoprotein production and O-mannosylation and increasing RED synthesis in the process.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-1035-3) contains supplementary material, which is available to authorized users.

Enhancing nemadectin production by Streptomyces cyaneogriseus ssp. noncyanogenus through quantitative evaluation and optimization of dissolved oxygen and shear force

In this study, effects of oxygen supply and shear stress on nemadectin production by Streptomyces cyaneogriseus ssp. noncyanogenus (S. cyaneogriseus) fermentation were investigated in shake flasks and 5-L bioreactors. Results showed sufficient dissolved oxygen level was essential for cells growth and nemadectin biosynthesis, while strong shear stress had negative impacts on both cell growth and nemadectin synthesis. Furthermore, when a combined paddle type was applied in culturing S. cyaneogriseus, the nemadectin production was increased by 23.6%. The influence of different agitation rates and paddle types on volumetric oxygen transfers coefficient (K_La) and shear stress were quantitatively studied through computational fluid dynamics simulation (CFD). The results of CFD revealed that high K_La as well as low shear stress co-existed under the combined impeller configuration at 650rpm. This study is expected to be helpful to the scale-up of nemadectin fermentation and other stress-sensitive but high-oxygen-consumption filamentous microorganism.

SParticle, an algorithm for the analysis of filamentous microorganisms in submerged cultures

Streptomycetes are filamentous bacteria that produce a plethora of bioactive natural products and industrial enzymes. Their mycelial lifestyle typically results in high heterogeneity in bioreactors, with morphologies ranging from fragments and open mycelial mats to dense pellets. There is a strong correlation between morphology and production in submerged cultures, with small and open mycelia favouring enzyme production, while most antibiotics are produced mainly in pellets. Here we describe SParticle, a Streptomyces Particle analysis method that combines whole slide imaging with automated image analysis to characterize the morphology of submerged grown Streptomyces cultures. SParticle allows the analysis of over a thousand particles per hour, offering a high throughput method for the imaging and statistical analysis of mycelial morphologies. The software is available as a plugin for the open source software ImageJ and allows users to create custom filters for other microbes. Therefore, SParticle is a widely applicable tool for the analysis of filamentous microorganisms in submerged cultures.

Plasma modified PLA electrospun membranes for actinorhodin production intensification in Streptomyces coelicolor immobilized-cell cultivations

Most of industrially relevant bioproducts are produced by submerged cultivations of actinomycetes. The immobilization of these Gram-positive filamentous bacteria on suitable porous supports may prevent mycelial cell-cell aggregation and pellet formation which usually negatively affect actinomycete submerged cultivations, thus, resulting in an improved biosynthetic capability. In this work, electrospun polylactic acid (PLA) membranes, subjected or not to O₂-plasma treatment (PLA-plasma), were used as support for immobilized-cell submerged cultivations of Streptomyces coelicolor M145. This strain produces different bioactive compounds, including the blue-pigmented actinorhodin (ACT) and red-pigmented undecylprodigiosin (RED), and constitutes a model for the study of antibiotic-producing actinomycetes. Wet contact angles and X-ray photoelectron spectroscopy analysis confirmed the increased wettability of PLA-plasma due to the formation of polar functional groups such as carboxyl and hydroxyl moieties. Scanning electron microscope observations, carried out at different incubation times, revealed that S. coelicolor immobilized-cells created a dense "biofilm-like" mycelial network on both kinds of PLA membranes. Cultures of S. coelicolor immobilized-cells on PLA or PLA-plasma membranes produced higher biomass (between 1.5 and 2 fold) as well as higher levels of RED and ACT than planktonic cultures. In particular, cultures of immobilized-cells on PLA and PLA-plasma produced comparable levels of RED that were approximatively 4 and 5 fold higher than those produced by planktonic cultures, respectively. In contrast, levels of ACT produced by immobilized-cell cultures on PLA and PLA-plasma were different, being 5 and 10 fold higher than those of planktonic cultures, respectively. Therefore, this is study demonstrated the positive influence of PLA membrane on growth and secondary metabolite production in S. coelicolor and also revealed that O₂-plasma treated PLA membranes specifically promoted higher ACT production than not treated membranes.

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.

Engineering microbial hosts for production of bacterial natural products

Covering up to end 2015Microbial fermentation provides an attractive alternative to chemical synthesis for the production of structurally complex natural products. In most cases, however, production titers are low and need to be improved for compound characterization and/or commercial production. Owing to advances in functional genomics and genetic engineering technologies, microbial hosts can be engineered to overproduce a desired natural product, greatly accelerating the traditionally time-consuming strain improvement process. This review covers recent developments and challenges in the engineering of native and heterologous microbial hosts for the production of bacterial natural products, focusing on the genetic tools and strategies for strain improvement. Special emphasis is placed on bioactive secondary metabolites from actinomycetes. The considerations for the choice of host systems will also be discussed in this review.

Impact of two ionic liquids, 1-ethyl-3-methylimidazolium acetate and 1-ethyl-3-methylimidazolium methylphosphonate, on Saccharomyces cerevisiae: metabolic, physiologic, and morphological investigations

BACKGROUND

Ionic liquids (ILs) are considered as suitable candidates for lignocellulosic biomass pretreatment prior enzymatic saccharification and, obviously, for second-generation bioethanol production. However, several reports showed toxic or inhibitory effects of residual ILs on microorganisms, plants, and animal cells which could affect a subsequent enzymatic saccharification and fermentation process.

RESULTS

In this context, the impact of two hydrophilic imidazolium-based ILs already used in lignocellulosic biomass pretreatment was investigated: 1-ethyl-3-methylimidazolium acetate [Emim][OAc] and 1-ethyl-3-methylimidazolium methylphosphonate [Emim][MeO(H)PO2]. Their effects were assessed on the model yeast for ethanolic fermentation, Saccharomyces cerevisiae, grown in a culture medium containing glucose as carbon source and various IL concentrations. Classical fermentation parameters were followed: growth, glucose consumption and ethanol production, and two original factors: the respiratory status with the oxygen transfer rate (OTR) and carbon dioxide transfer rate (CTR) of yeasts which were monitored online by respiratory activity monitoring systems (RAMOS). In addition, yeast morphology was characterized by environmental scanning electron microscope (ESEM). The addition of ILs to the growth medium inhibited the OTR and switched the metabolism from respiration (conversion of glucose into biomass) to fermentation (conversion of glucose to ethanol). This behavior could be observed at low IL concentrations (≤5% IL) while above there is no significant growth or ethanol production. The presence of IL in the growth medium also induced changes of yeast morphology, which exhibited wrinkled, softened, and holed shapes. Both ILs showed the same effects, but [Emim][MeO(H)PO2] was more biocompatible than [Emim][OAc] and could be better tolerated by S. cerevisiae.

CONCLUSIONS

These two imidazolium-derived ILs were appropriate candidates for useful pretreatment of lignocellulosic biomass in the context of second-generation bioethanol production. This fundamental study provides additional information about the toxic effects of ILs. Indeed, the investigations highlighted the better tolerance by S. cerevisiae of [Emim][MeO(H)PO2] than [Emim][OAc].

Hydrodynamics, Fungal Physiology, and Morphology

Filamentous cultures, such as fungi and actinomycetes, contribute substantially to the pharmaceutical industry and to enzyme production, with an annual market of about 6 billion dollars. In mechanically stirred reactors, most frequently used in fermentation industry, microbial growth and metabolite productivity depend on complex interactions between hydrodynamics, oxygen transfer, and mycelial morphology. The dissipation of energy through mechanically stirring devices, either flasks or tanks, impacts both microbial growth through shearing forces on the cells and the transfer of mass and energy, improving the contact between phases (i.e., air bubbles and microorganisms) but also causing damage to the cells at high energy dissipation rates. Mechanical-induced signaling in the cells triggers the molecular responses to shear stress; however, the complete mechanism is not known. Volumetric power input and, more importantly, the energy dissipation/circulation function are the main parameters determining mycelial size, a phenomenon that can be explained by the interaction of mycelial aggregates and Kolmogorov eddies. The use of microparticles in fungal cultures is also a strategy to increase process productivity and reproducibility by controlling fungal morphology. In order to rigorously study the effects of hydrodynamics on the physiology of fungal microorganisms, it is necessary to rule out the possible associated effects of dissolved oxygen, something which has been reported scarcely. At the other hand, the processes of phase dispersion (including the suspended solid that is the filamentous biomass) are crucial in order to get an integral knowledge about biological and physicochemical interactions within the bioreactor. Digital image analysis is a powerful tool for getting relevant information in order to establish the mechanisms of mass transfer as well as to evaluate the viability of the mycelia. This review focuses on (a) the main characteristics of the two most common morphologies exhibited by filamentous microorganisms; (b) how hydrodynamic conditions affect morphology and physiology in filamentous cultures; and (c) techniques using digital image analysis to characterize the viability of filamentous microorganisms and mass transfer in multiphase dispersions. Representative case studies of fungi (Trichoderma harzianum and Pleurotus ostreatus) exhibiting different typical morphologies (disperse mycelia and pellets) are discussed.

Induction of ganoderic acid biosynthesis by Mn2+ in static liquid cultivation of Ganoderma lucidum

Metal ions affect cell physiology and metabolism significantly, but the role of Mn(2+) in the secondary metabolism of mushrooms is yet unclear. In static liquid cultivation of Ganoderma lucidum for producing antitumor ganoderic acids (GAs), the Mn(2+) addition was performed. Addition of 10 mM Mn(2+) at the start of the static liquid cultivation resulted in 2.2-fold improvement of total GAs production. The expression levels of GA biosynthetic and Ca(2+) sensors' genes were up-regulated with Mn(2+) induction while down-regulated by adding cyclosporin A (calcineurin inhibitor), suggesting that higher GA production might result from calcineurin signal regulation. Intracellular Ca(2+) imaging and calcineurin inhibitor study revealed that addition of Mn(2+) led to Ca(2+) influx from medium to the cells to trigger calcineurin signals. Mn(2+) addition was therefore an efficient induction strategy for improving GAs production, whose regulation mechanism was via calcineurin signaling transduction.

Significance of agitation-induced shear stress on mycelium morphology and lavendamycin production by engineered Streptomyces flocculus

Lavendamycin methyl ester (LME) is a derivative of a highly functionalized aminoquinone alkaloid lavendamycin and could be used as a scaffold for novel anticancer agent development. This work demonstrated LME production by cultivation of an engineered strain of Streptomyces flocculus CGMCC4.1223 ΔstnB1, while the wild-type strain did not produce. To enhance its production, the effect of shear stress and oxygen supply on ΔstnB1 strain cultivation was investigated in detail. In flask culture, when the shaking speed increased from 150 to 220 rpm, the mycelium was altered from a large pellet to a filamentous hypha, and the LME production was almost doubled, while no significant differences were observed among varied filling volumes, which implied a crucial role of shear stress in the morphology and LME production. To confirm this suggestion, experiments with agitation speed ranging from 400 to 1,000 rpm at a fixed aeration rate of 1.0 vvm were conducted in a stirred tank bioreactor. It was found that the morphology became more hairy with reduced pellet size, and the LME production was enhanced threefolds when the agitation speed increased from 400 to 800 rpm. Further experiments by varying initial k L a value at the same agitation speed indicated that oxygen supply only slightly affected the physiological status of ΔstnB1 strain. Altogether, shear stress was identified as a major factor affecting the cell morphology and LME production. The work would be helpful to the production of LME and other secondary metabolites by filamentous microorganism cultivation.

Effects of bioreactor hydrodynamics on the physiology of Streptomyces

Streptomyces are filamentous bacteria which are widely used industrially for the production of therapeutic biomolecules, especially antibiotics. Bioreactor operating conditions may impact the physiological response of Streptomyces especially agitation and aeration as they influence hydromechanical stress, oxygen and nutrient transfer. The understanding of the coupling between physiological response and bioreactor hydrodynamics lies on a simultaneous description of the flow and transfers encountered by the bacteria and of the microbial response in terms of growth, consumption, morphology, production or intracellular signals. This article reviews the experimental and numerical works dedicated to the study of the coupling between bioreactor hydrodynamics and antibiotics producing Streptomyces. In a first part, the description of hydrodynamics used in these works is presented and then the main relations used. In a second part, the assumptions made in these works are discussed and put into emphasize. Lastly, the various Streptomyces physiological responses observed are detailed and compared.

Development of a modified Respiration Activity Monitoring System for accurate and highly resolved measurement of respiration activity in shake flask fermentations

Background

The Respiration Activity Monitoring System (RAMOS) is an established device to measure on-line the oxygen transfer rate (OTR), thereby, yielding relevant information about metabolic activities of microorganisms and cells during shake flask fermentations. For very fast-growing microbes, however, the RAMOS technique provides too few data points for the OTR. Thus, this current study presents a new model based evaluation method for generating much more data points to enhance the information content and the precision of OTR measurements.

Results

In cultivations with E.coli BL21 pRSET eYFP-IL6, short diauxic and even triauxic metabolic activities were detected with much more detail compared to the conventional evaluation method. The decline of the OTR during the stop phases during oxygen limitations, which occur when the inlet and outlet valves of the RAMOS flask were closed for calibrating the oxygen sensor, were also detected. These declines reflected a reduced oxygen transfer due to the stop phases. In contrast to the conventional calculation method the new method was almost independent from the number of stop phases chosen in the experiments.

Conclusions

This new model based evaluation method unveils new peaks of metabolic activity which otherwise would not have been resolved by the conventional RAMOS evaluation method. The new method yields substantially more OTR data points, thereby, enhancing the information content and the precision of the OTR measurements. Furthermore, oxygen limitations can be detected by a decrease of the OTR during the stop phases.

Cyclic Di-GMP phosphodiesterases RmdA and RmdB are involved in regulating colony morphology and development in Streptomyces coelicolor

Cyclic dimeric GMP (c-di-GMP) regulates numerous processes in Gram-negative bacteria, yet little is known about its role in Gram-positive bacteria. Here we characterize two c-di-GMP phosphodiesterases from the filamentous high-GC Gram-positive actinobacterium Streptomyces coelicolor, involved in controlling colony morphology and development. A transposon mutation in one of the two phosphodiesterase genes, SCO0928, hereby designated rmdA (regulator of morphology and development A), resulted in decreased levels of spore-specific gray pigment and a delay in spore formation. The RmdA protein contains GGDEF-EAL domains arranged in tandem and possesses c-di-GMP phosphodiesterase activity, as is evident from in vitro enzymatic assays using the purified protein. RmdA contains a PAS9 domain and is a hemoprotein. Inactivation of another GGDEF-EAL-encoding gene, SCO5495, designated rmdB, resulted in a phenotype identical to that of the rmdA mutant. Purified soluble fragment of RmdB devoid of transmembrane domains also possesses c-di-GMP phosphodiesterase activity. The rmdA rmdB double mutant has a bald phenotype and is impaired in aerial mycelium formation. This suggests that RmdA and RmdB functions are additive and at least partially overlapping. The rmdA and rmdB mutations likely result in increased local pools of intracellular c-di-GMP, because intracellular c-di-GMP levels in the single mutants did not differ significantly from those of the wild type, whereas in the double rmdA rmdB mutant, c-di-GMP levels were 3-fold higher than those in the wild type. This study highlights the importance of c-di-GMP-dependent signaling in actinomycete colony morphology and development and identifies two c-di-GMP phosphodiesterases controlling these processes.

Advances in shaking technologies

Shaking bioreactors are the most frequently used reactor system for screening and process optimization on a small scale. Their success can be attributed to their simple and functional design, which make shaking systems suitable for a large number of cost-efficient parallel experiments. Recently reported findings for oxygen transfer, power input, out-of-phase operation, hydromechanical stress and mixing in shaken bioreactors are summarized in this article. Novel monitoring techniques for the control of culture conditions in shake flasks and microtiter plates are described. The methods for characterizing culture conditions and the novel online measurement techniques that are summarized in this article can be utilized to tap the full potential of shaking reactor systems.