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

Genome-guided approaches and evaluation of the strategies to influence bioprocessing assisted morphological engineering of Streptomyces cell factories

Streptomyces genera serve as adaptable cell factories for secondary metabolites with various and distinctive chemical structures that are relevant to the pharmaceutical industry. Streptomyces' complex life cycle necessitated a variety of tactics to enhance metabolite production. Identification of metabolic pathways, secondary metabolite clusters, and their controls have all been accomplished using genomic methods. Besides this, bioprocess parameters were also optimized for the regulation of morphology. Kinase families were identified as key checkpoints in the metabolic manipulation (DivIVA, Scy, FilP, matAB, and AfsK) and morphology engineering of Streptomyces. This review illustrates the role of different physiological variables during fermentation in the bioeconomy coupled with genome-based molecular characterization of biomolecules responsible for secondary metabolite production at different developmental stages of the Streptomyces life cycle.

Intensification of bioprocesses with filamentous microorganisms

Many industrial biotechnological processes use filamentous microorganisms to produce platform chemicals, proteins, enzymes and natural products. Product formation is directly linked to their cellular morphology ranging from dispersed mycelia over loose clumps to compact pellets. Therefore, the adjustment and control of the filamentous cellular morphology pose major challenges for bioprocess engineering. Depending on the filamentous strain and desired product, optimal morphological shapes for achieving high product concentrations vary. However, there are currently no overarching strain- or product-related correlations to improve process understanding of filamentous production systems. The present book chapter summarizes the extensive work conducted in recent years in the field of improving product formation and thus intensifying biotechnological processes with filamentous microorganisms. The goal is to provide prospective scientists with an extensive overview of this scientifically diverse, highly interesting field of study. In the course of this, multiple examples and ideas shall facilitate the combination of their acquired expertise with promising areas of future research. Therefore, this overview describes the interdependence between filamentous cellular morphology and product formation. Moreover, the currently most frequently used experimental techniques for morphological structure elucidation will be discussed in detail. Developed strategies of morphology engineering to increase product formation by tailoring and controlling cellular morphology and thus to intensify processes with filamentous microorganisms will be comprehensively presented and discussed.

Flavoprotein StnP2 Catalyzes the β-Carboline Formation during the Streptonigrin Biosynthesis

β-Carboline (βC) alkaloids constitute a large family of indole alkaloids that exhibit diverse pharmacological properties, such as antitumor, antiviral, antiparasitic, and antimicrobial activities. Here, we report that a flavoprotein StnP2 catalyzes the dehydrogenation at C1-N2 of a tetrahydro-β-carboline (THβC) generating a 3,4-dihydro-β-carboline (DHβC), and the DHβC subsequently undergoes a spontaneous dehydrogenation to βC formation involved in the biosynthesis of the antitumor agent streptonigrin. Biochemical characterization showed that StnP2 catalyzed the highly regio- and stereo-selective dehydrogenation, and StnP2 exhibits promiscuity toward different THβCs. This study provides an alternative kind of enzyme catalyzing the biosynthesis of βC alkaloids and enhances the importance of flavoproteins.

Individual effect of shear rate and oxygen transfer on clavulanic acid production by Streptomyces clavuligerus

The production of biocompounds through the cultivation of filamentous microorganisms is mainly affected by Oxygen Transfer Rate (OTR) and shear rate ([Formula: see text]) conditions. Despite efforts have been made to evaluate the effect of operating variables (impeller speed, N; and airflow rate, ϕ_air) on clavulanic acid production, no analysis regarding the effect of OTR and [Formula: see text] was made. Then, the aim of this study was to evaluate the dissociated effect of physical phenomena such as oxygen transfer and shear rate in the production of clavulanic acid from Streptomyces clavuligerus using a stirred tank bioreactor. Streptomyces clavuligerus cultivations were performed at five different OTR and [Formula: see text] conditions by manipulating the operating conditions (N, ϕ_air, and gas inlet composition). Cultivations performed at equal impeller speed (600 rpm, similar [Formula: see text]) using oxygen enrichment, showed that CA productivity (Prod_CA) was positively affected by OTR increase. Subsequently, the different shear conditions (achieved by varying the impeller speed) lead to an increase in CA production levels. Despite both OTR and shear rate positively enhanced CA productivity, [Formula: see text] exhibited the highest impact: an increase of 145% in OTR_initial enhanced the clavulanic acid productivity of about 29%, while an increment in the shear rate of 134% raised the Prod_CA in 53%.

Effect of Agitation and Aeration on Keratinase Production in Bioreactors Using Bioprocess Engineering Aspects

Streptomyces sp. 2M21 was evaluated for keratinase production in bioreactors using chicken feathers. Firstly, optimization of bioengineering parameters (agitation and aeration rates) using Response Surface Methodology was carried out in 2 L bioreactors. Optimized conditions identified by the modified quadratic model were verified as 150 rpm and 1 vvm experimentally corresponding to 351 U/ml of keratinase activity. Moreover, scaling up sequentially to 20 L bioreactors was implemented using constant impeller tip speed and constant mass transfer coefficient as key scale-up parameters. The keratinase activity in 5, 10 and 20 L bioreactors showed similar results with the one of shake flasks (412 U/ml) and 2 L bioreactors (351 U/ml)with respect to the keratinase activity values of 336, 385 and 344 U/ml, respectively. The results suggest keratinase production by evaluating chicken feathers in commercial level. Furthermore, this study has potential to contribute industrial scale production of keratinase by Streptomyces sp. 2M21 using the proposed bioreactor conditions.

Production of lipopeptide biosurfactant in batch and fed-batch Streptomyces sp. PBD-410L cultures growing on palm oil

The present study focused on lipopeptide biosurfactant production by Streptomyces sp. PBD-410L in batch and fed-batch fermentation in a 3-L stirred-tank reactor (STR) using palm oil as a sole carbon source. In batch cultivation, the impact of bioprocessing parameters, namely aeration rate and agitation speed, was studied to improve biomass growth and lipopeptide biosurfactant production. The maximum oil spreading technique (OST) result (45 mm) which corresponds to 3.74 g/L of biosurfactant produced, was attained when the culture was agitated at 200 rpm and aeration rate of 0.5 vvm. The best aeration rate and agitation speed obtained from the batch cultivation was adopted in the fed-batch cultivation using DO-stat feeding strategy to further improve the lipopeptide biosurfactant production. The lipopeptide biosurfactant production was enhanced from 3.74 to 5.32 g/L via fed-batch fermentation mode at an initial feed rate of 0.6 mL/h compared to that in batch cultivation. This is the first report on the employment of fed-batch cultivation on the production of biosurfactant by genus Streptomyces.

Optimization of fermentation conditions and medium compositions for the production of chrysomycin a by a marine-derived strain Streptomyces sp. 891

Chrysomycin A is one of the valuable drug leads used to treat infectious diseases such as tuberculosis and methicillin-resistant Staphylococcus aureus. In order to increase its yield, this work firstly focuses on optimization of fermentation conditions and medium compositions of a wild-type chrysomycin A-producing strain Streptomyces sp. 891 from marine sediment. By single-factor experiment, effects of fermentation conditions (fermentation time, seed age, initial pH, inoculum amount, liquid loading, shaking speed) and medium composition (carbon sources, nitrogen sources, inorganic salts) on the yield of chrysomycin A were carefully evaluated and analyzed followed by optimization at shake-flask level. The results indicated its optimal fermentation conditions for producing chrysomycin A were as follows: fermentation time 168 h, seed age 48 h, initial pH 6.5, inoculum amount 5.0%, liquid loading 30 mL in 250-mL Erlenmeyer flask and shaking speed 220 rpm. By orthogonal test, the optimal fermentation medium constitutes 40 g/L glucose, 20 g/L corn starch, 25 g/L hot-pressed soybean flour, 3 g/L CaCO₃. Verification tests suggested the yield of chrysomycin A under optimized conditions reaches up to 3648 ± 119 mg/L, which is increased by almost 5 times. These findings definitely pave the way for scale-up preparation of chrysomycin A and application in the pharmaceutical industry.

Clavulanic Acid Production by Streptomyces clavuligerus: Insights from Systems Biology, Strain Engineering, and Downstream Processing

Clavulanic acid (CA) is an irreversible β-lactamase enzyme inhibitor with a weak antibacterial activity produced by Streptomyces clavuligerus (S. clavuligerus). CA is typically co-formulated with broad-spectrum β‑lactam antibiotics such as amoxicillin, conferring them high potential to treat diseases caused by bacteria that possess β‑lactam resistance. The clinical importance of CA and the complexity of the production process motivate improvements from an interdisciplinary standpoint by integrating metabolic engineering strategies and knowledge on metabolic and regulatory events through systems biology and multi-omics approaches. In the large-scale bioprocessing, optimization of culture conditions, bioreactor design, agitation regime, as well as advances in CA separation and purification are required to improve the cost structure associated to CA production. This review presents the recent insights in CA production by S. clavuligerus, emphasizing on systems biology approaches, strain engineering, and downstream processing.

Microparticles globally reprogram Streptomyces albus toward accelerated morphogenesis, streamlined carbon core metabolism, and enhanced production of the antituberculosis polyketide pamamycin

Streptomyces spp. are a rich source for natural products with recognized industrial value, explaining the high interest to improve and streamline the performance of in these microbes. Here, we studied the production of pamamycins, macrodiolide homologs with a high activity against multiresistant pathogenic microbes, using recombinant Streptomyces albus J1074/R2. Talc particles (hydrous magnesium silicate, 3MgO·4SiO₂ ·H₂ O) of micrometer size, added to submerged cultures of the recombinant strain, tripled pamamycin production up to 50 mg/L. Furthermore, they strongly affected morphology, reduced the size of cell pellets formed by the filamentous microbe during the process up to sixfold, and shifted the pamamycin spectrum to larger derivatives. Integrated analysis of transcriptome and precursor (CoA thioester) supply of particle-enhanced and control cultures provided detailed insights into the underlying molecular changes. The microparticles affected the expression of 3,341 genes (56% of all genes), revealing a global and fundamental impact on metabolism. Morphology-associated genes, encoding major regulators such as SsgA, RelA, EshA, Factor C, as well as chaplins and rodlins, were found massively upregulated, indicating that the particles caused a substantially accelerated morphogenesis. In line, the pamamycin cluster was strongly upregulated (up to 1,024-fold). Furthermore, the microparticles perturbed genes encoding for CoA-ester metabolism, which were mainly activated. The altered expression resulted in changes in the availability of intracellular CoA-esters, the building blocks of pamamycin. Notably, the ratio between methylmalonyl CoA and malonyl-CoA was increased fourfold. Both metabolites compete for incorporation into pamamycin so that the altered availability explained the pronounced preference for larger derivatives in the microparticle-enhanced process. The novel insights into the behavior of S. albus in response to talc appears of general relevance to further explore and upgrade the concept of microparticle enhanced cultivation, widely used for filamentous microbes.

Characterization of the Metabolic Response of Streptomyces clavuligerus to Shear Stress in Stirred Tanks and Single-Use 2D Rocking Motion Bioreactors for Clavulanic Acid Production

Streptomyces clavuligerus is a gram-positive filamentous bacterium notable for producing clavulanic acid (CA), an inhibitor of β-lactamase enzymes, which confers resistance to bacteria against several antibiotics. Here we present a comparative analysis of the morphological and metabolic response of S. clavuligerus linked to the CA production under low and high shear stress conditions in a 2D rocking-motion single-use bioreactor (CELL-tainer ^®) and stirred tank bioreactor (STR), respectively. The CELL-tainer^® guarantees high turbulence and enhanced volumetric mass transfer at low shear stress, which (in contrast to bubble columns) allows the investigation of the impact of shear stress without oxygen limitation. The results indicate that high shear forces do not compromise the viability of S. clavuligerus cells; even higher specific growth rate, biomass, and specific CA production rate were observed in the STR. Under low shear forces in the CELL-tainer^® the mycelial diameter increased considerably (average diameter 2.27 in CELL-tainer^® vs. 1.44 µm in STR). This suggests that CA production may be affected by a lower surface-to-volume ratio which would lead to lower diffusion and transport of nutrients, oxygen, and product. The present study shows that there is a strong correlation between macromorphology and CA production, which should be an important aspect to consider in industrial production of CA.

Effects of Tween 80 on the liquid fermentation of Lentinus edodes

This paper explored the effects of Tween 80 on the biomass, intracellular polysaccharide (IPS) content, fermentation parameters, the pellets size of mycelium, and the antioxidant activity of IPS in Lentinus edodes liquid fermentation. With adding to Tween 80, the outputs of biomass and IPS increased during the L. edodes fermentation, respectively, while the reducing sugar content was decreased, as well as, the time courses of pH value were different. It was also shown that the addition of Tween 80 could protect the intact of pellets from breaking down. The effects of Tween 80 on the main structure of IPS were no obvious, and the IPS were revealed similar infrared spectrum, as was indicated by the infrared spectrum analysis. Improvements in the scavenging capacity of DPPH radicals of IPS were observed in Tween 80 treated group compared with the control group. Tween 80 exerts impacts on the liquid fermentation of L. edodes.

Dynamics of Pellet Fragmentation and Aggregation in Liquid-Grown Cultures of Streptomyces lividans

Streptomycetes are extensively used for the production of valuable products, including various antibiotics and industrial enzymes. The preferred way to grow these bacteria in industrial settings is in large-scale fermenters. Growth of streptomycetes under these conditions is characterized by the formation of complex mycelial particles, called pellets. While the process of pellet formation is well characterized, little is known about their disintegration. Here, we use a qualitative and quantitative approach to show that pellet fragmentation in Streptomyces lividans is initiated when cultures enter the stationary phase, which coincides with a remarkable change in pellet architecture. Unlike young pellets, aging pellets have a less dense appearance and are characterized by the appearance of filaments protruding from their outer edges. These morphological changes are accompanied by a dramatic increase in the number of mycelial fragments in the culture broth. In the presence of fresh nutrients, these fragments are able to aggregate with other small fragments, but not with disintegrating pellets, to form new mycelial particles. Altogether, our work indicates that fragmentation might represent an escape mechanism from the environmental stress caused by nutrient scarcity, with striking similarities to the disassembly of bacterial biofilms.

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.

Streptomyces clavuligerus shows a strong association between TCA cycle intermediate accumulation and clavulanic acid biosynthesis

Clavulanic acid (CA) is produced by Streptomyces clavuligerus (S. clavuligerus) as a secondary metabolite. Knowledge about the carbon flux distribution along the various routes that supply CA precursors would certainly provide insights about metabolic performance. In order to evaluate metabolic patterns and the possible accumulation of tricarboxylic acid (TCA) cycle intermediates during CA biosynthesis, batch and subsequent continuous cultures with steadily declining feed rates were performed with glycerol as the main substrate. The data were used to in silico explore the metabolic capabilities and the accumulation of metabolic intermediates in S. clavuligerus. While clavulanic acid accumulated at glycerol excess, it steadily decreased at declining dilution rates; CA synthesis stopped when glycerol became the limiting substrate. A strong association of succinate, oxaloacetate, malate, and acetate accumulation with CA production in S. clavuligerus was observed, and flux balance analysis (FBA) was used to describe the carbon flux distribution in the network. This combined experimental and numerical approach also identified bottlenecks during the synthesis of CA in a batch and subsequent continuous cultivation and demonstrated the importance of this type of methodologies for a more advanced understanding of metabolism; this potentially derives valuable insights for future successful metabolic engineering studies in S. clavuligerus.

Production and partial characterization of biosurfactant produced by Streptomyces sp. R1

The present study focused on developing a wild-type actinomycete isolate as a model for a non-pathogenic filamentous producer of biosurfactants. A total of 33 actinomycetes isolates were screened and their extracellular biosurfactants production was evaluated using olive oil as the main substrate. Out of 33 isolates, 32 showed positive results in the oil spreading technique (OST). All isolates showed good emulsification activity (E₂₄) ranging from 84.1 to 95.8%. Based on OST and E₂₄ values, isolate R1 was selected for further investigation in biosurfactant production in an agitated submerged fermentation. Phenotypic and genotypic analyses tentatively identified isolate R1 as a member of the Streptomyces genus. A submerged cultivation of Streptomyces sp. R1 was carried out in a 3-L stirred-tank bioreactor. The influence of impeller tip speed on volumetric oxygen transfer coefficient (k _L a), growth, cell morphology and biosurfactant production was observed. It was found that the maximum biosurfactant production, indicated by the lowest surface tension measurement (40.5 ± 0.05 dynes/cm) was obtained at highest k _L a value (50.94 h^-1) regardless of agitation speed. The partially purified biosurfactant was obtained at a concentration of 7.19 g L^-1, characterized as a lipopeptide biosurfactant and was found to be stable over a wide range of temperature (20-121 °C), pH (2-12) and salinity [5-20% (w/v) of NaCl].

Mycelium transformation of Streptomyces toxytricini into pellet: Role of culture conditions and kinetics

The present study envisages the role of different carbon sources, nitrogen sources, metals, pH, inoculum volume and agitation rate in pellet formation of S. toxytricini at shake-flask level. It was found that galactose, ammonium sulphate, sodium nitrate, Cu²⁺, Zn²⁺, higher inoculum volume (5% v/v) and agitation rate at 300rpm caused significant reduction in pellet size (up to the range of 30μm-0.5mm) but biomass formations was also reduced subsequently. Interestingly diffused type of morphology was obtained in Fe²⁺ supplemented medium with reduced biomass (1.5gL^-1). Rheological study revealed that non-Newtonian behaviour of culture broth. Besides this, kinetics study was also made to understand the growth kinetics (0.39gL^-1h^-1), oxygen uptake rate (0.1146mgL^-1h^-1), and production of lipstatin (0.0072gh^-1).

Significance of Heavy-Ion Beam Irradiation-Induced Avermectin B1a Production by Engineered Streptomyces avermitilis

Heavy-ion irradiation technology has advantages over traditional methods of mutagenesis. Heavy-ion irradiation improves the mutation rate, broadens the mutation spectrum, and shortens the breeding cycle. However, few data are currently available regarding its effect on Streptomyces avermitilis morphology and productivity. In this study, the influence of heavy-ion irradiation on S. avermitilis when cultivated in approximately 10 L stirred-tank bioreactors was investigated. The specific productivity of the avermectin (AVM) B1a-producing mutant S. avermitilis 147-G₅8 increased notably, from 3885 to 5446 μg/mL, approximately 1.6-fold, compared to the original strain. The mycelial morphology of the mutant fermentation processes was microscopically examined. Additionally, protein and metabolite identification was performed by using SDS-PAGE, 2- and 3-dimensional electrophoresis (2DE and 3DE). The results showed that negative regulation gene deletion of mutants led to metabolic process upregulating expression of protein and improving the productivity of an avermectin B1a. The results showed that the heavy-ion beam irradiation dose that corresponded to optimal production was well over the standard dose, at approximately 80 Gy at 220 AMeV (depending on the strain). This study provides reliable data and a feasible method for increasing AVM productivity in industrial processes.

Dissolved oxygen control strategy for improvement of TL1-1 production in submerged fermentation by Daldinia eschscholzii

BACKGROUND

2,3-Dihydro-5-hydroxy-2-methylchromen-4-one (TL1-1) is a phenolic compound with significant anti-fungal and anti-cancer activities produced by Daldinia eschscholzii (D. eschscholzii). However, studies have rarely been reported on the fermentation process of D. eschscholzii due to the urgent demand for its pharmaceutical researches and applications.

RESULTS

In this work, the optimal fermentation medium for improved TL1-1 yield was first obtained in a shake flask. As the fermentation process was scaling up, the marked effects of dissolved oxygen (DO) on cell growth and TL1-1 biosynthesis were observed and confirmed. Controlling a suitable DO level by the adjustment of agitation speed and aeration rate remarkably enhanced TL1-1 production in a lab-scale bioreactor. Moreover, the fermentation of D. eschscholzii was successfully applied in 500-L bioreactor, and TL1-1 production has achieved 873.63 mg/L, approximately 15.4-fold than its initial production (53.27 mg/L).

CONCLUSIONS

Dissolved oxygen control strategy for enhancing TL1-1 production was first proposed. Furthermore, control of the appropriate DO level has successfully performed for improving TL1-1 yield and scale-up of D. eschscholzii fermentation process.

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.