Multivariate models for prediction of rheological characteristics of filamentous fermentation broth from the size distribution

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.

Shear and solid-liquid separation behaviour of anaerobic digested sludge across a broad range of solids concentrations

Due to the non-homogeneous and multiphase nature of anaerobic lagoon constituents, CFD modelling for process optimisation requires continuous functions for shear and solid-liquid separation properties across a large range of solids concentrations. Unfortunately, measurement of existing material properties of anaerobic sludges is limited to only shear or solid-liquid separation, or to a limited solids concentration. In this work, the shear properties of an anaerobic sludge were measured from 0.4 to 12.5 vol%, which corresponds to the solids concentrations seen in lagoons. The sludge showed Newtonian behaviour at 0.4 vol% and Herschel-Bulkley yield stress fluid behaviour for higher concentrations ranging from 0.5 to 12 vol%. We compared multiple approaches to determine relationships between the model fitting parameters of consistency, k, flow index, n, and shear yield stress, τ_y with solids volume fraction ϕ.The solid-liquid separation properties were measured from sedimentation and filtration experiments to obtain compressibility and permeability properties across all the above-mentioned concentrations, enabling development of hindered velocity sedimentation curves. Comparison to full-scale anaerobic digestate identified that the pilot lagoon sludge had faster sedimentation at a given solids concentration in comparison to the digestate. This is the first study on simultaneous rheological characterisation and solid-liquid separation behaviour of an anaerobic sludge across a wide range of concentrations, thus enabling CFD modelling of the hydrodynamics and performance of anaerobic lagoons.

Toward More Universal Prediction of Polymer Solution Viscosity for Solvent-Based Recycling

The viscosity of polymer solutions is important for both polymer synthesis and recycling. Polymerization reactions can become hampered by diffusional limitations once a viscosity threshold is reached, and viscous solutions complicate the cleaning steps during the dissolution–precipitation technique. Available experimental data is limited, which is more severe for green solvents, justifying dedicated viscosity data recording and interpretation. In this work, a systematic study is therefore performed on the viscosity of polystyrene solutions, considering different concentrations, temperatures, and conventional and green solvents. The results show that for the shear rate range of 1–1000 s^–1, the solutions with concentrations between 5 and 39 wt % display mainly Newtonian behavior, which is further confirmed by the applicability of the segment-based Eyring-NRTL and Eyring-mNRF models. Moreover, multivariate data analysis successfully predicts the viscosity of polystyrene solutions under different conditions. This approach will facilitate future data recording for other polymer–solvent combinations while minimizing experimental effort.

Understanding and controlling filamentous growth of fungal cell factories: novel tools and opportunities for targeted morphology engineering

Filamentous fungal cell factories are efficient producers of platform chemicals, proteins, enzymes and natural products. Stirred-tank bioreactors up to a scale of several hundred m³ are commonly used for their cultivation. Fungal hyphae self-assemble into various cellular macromorphologies ranging from dispersed mycelia, loose clumps, to compact pellets. Development of these macromorphologies is so far unpredictable but strongly impacts productivities of fungal bioprocesses. Depending on the strain and the desired product, the morphological forms vary, but no strain- or product-related correlations currently exist to improve process understanding of fungal production systems. However, novel genomic, genetic, metabolic, imaging and modelling tools have recently been established that will provide fundamental new insights into filamentous fungal growth and how it is balanced with product formation. In this primer, these tools will be highlighted and their revolutionary impact on rational morphology engineering and bioprocess control will be discussed.

A fast and simple method to estimate relative, hyphal tensile-strength of filamentous fungi used to assess the effect of autophagy

Fungal hyphal strength is an important phenotype which can have a profound impact on bioprocess behavior. Until now, there is not an efficient method which allows its characterization. Currently available methods are very time consuming, thus, compromising their applicability in strain selection and process development. To overcome this issue, a method for fast and easy, statistically verified quantification of relative hyphal tensile strength was developed. It involves off-line fragmentation in a high shear mixer followed by quantification of fragment size using laser diffraction. Particle size distribution (PSD) is determined, with analysis time on the order of minutes. Plots of PSD 90th percentile versus time allow estimation of the specific fragmentation rate. This novel method is demonstrated by estimating relative hyphal strength during growth in control conditions and rapamycin-induced autophagy for Aspergillus nidulans (parental strain) and a mutant strain (ΔAnatg8) lacking an important autophagy gene. Both strains were grown in shake flasks and relative hyphal tensile strength was compared. The mutant strain grown in control conditions appears to be weaker than the parental strain, suggesting that Anatg8 may play a role in other processes involving cell wall biosynthesis. Furthermore, rapamycin-induced autophagy resulted in apparently weaker cells even for the mutant strain. These findings confirm the utility of the developed method in strain selection and process development.

Morphological analysis of the filamentous fungus Penicillium chrysogenum using flow cytometry-the fast alternative to microscopic image analysis

An important parameter in filamentous bioreactor cultivations is the morphology of the fungi, due to its interlink to productivity and its dependency on process conditions. Filamentous fungi show a large variety of morphological forms in submerged cultures. These range from dispersed hyphae, to interwoven mycelial aggregates, to denser hyphal aggregates, the so-called pellets. Depending on the objective function of the bioprocess, different characteristics of the morphology are favorable and need to be quantified accurately. The most common method to quantitatively characterize morphology is image analysis based on microscopy. This method is work intensive and time consuming. Therefore, we developed a faster, at-line applicable, alternative method based on flow cytometry. Within this contribution, this novel method is compared to microscopy for a penicillin production process. Both methods yielded in comparable distinction of morphological sub-populations and described their morphology in more detail. In addition to the appropriate quantification of size parameters and the description of the hyphal region around pellets, the flow cytometry method even revealed a novel compactness parameter for fungal pellets which is not accessible via light microscopy. Hence, the here presented flow cytometry method for morphological analysis is a fast and reliable alternative to common tools with some new insights in the pellet morphology, enabling at-line use in production environments.

Simplifying multidimensional fermentation dataset analysis and visualization: One step closer to capturing high-quality mutant strains

In this study, we analyzed mutants of Clostridium acetobutylicum, an organism used in a broad range of industrial processes related to biofuel production, to facilitate future studies of bioreactor and bioprocess design and scale-up, which are very important research projects for industrial microbiology applications. To accomplish this, we generated 329 mutant strains and applied principal component analysis (PCA) to fermentation data gathered from these strains to identify a core set of independent features for comparison. By doing so, we were able to explain the differences in the mutant strains' fermentation expression states and simplify the analysis and visualization of the multidimensional datasets related to the strains. Our study has produced a high-efficiency PCA application based on a data analytics tool that is designed to visualize screening results and to support several hundred sets of data on fermentation interactions to assist researchers in more precisely screening and capturing high-quality mutant strains. More importantly, although this study focused on the use of PCA in microbial fermentation engineering, its results are broadly applicable.

Using a flexible shaft agitator to enhance the rheology of a complex fungal fermentation culture

The rheology behavior of biological fluids particularly when the viscosity is high and rheology is complex, is an important issue to understand, particularly for studies in mass-transfer and for solving technical problems with mixing in stirred bioreactors. In this paper, the use of a Swingstir(®) impeller during the fermentation of Aspergillus oryzae resulted in decreases from the parameters of a power-law model, in viscosity and in the thixotropic behavior of a cultivation broth. The results showed that both the K L a and the alpha amylase activity were improved when using the Swingstir(®) in comparison with Fullzone(®) impeller (FZ) at the same level of energy consumption. Increasing the pellet porosity during mixing via the Swingstir(®) resulted in increases in oxygen mass transfer and the average shear stress.

The Taming of the Shrew--Controlling the Morphology of Filamentous Eukaryotic and Prokaryotic Microorganisms

One of the most sensitive process characteristics in the cultivation of filamentous biological systems is their complex morphology. In submerged cultures, the observed macroscopic morphology of filamentous microorganisms varies from freely dispersed mycelium to dense spherical pellets consisting of a more or less dense, branched and partially intertwined network of hyphae. Recently, the freely dispersed mycelium form has been in high demand for submerged cultivation because this morphology enhances the growth and production of several valuable products. A distinct filamentous morphology and productivity are influenced by the environment and can be controlled by inoculum concentration, spore viability, pH value, cultivation temperature, dissolved oxygen concentration, medium composition, mechanical stress or process mode as well as through the addition of inorganic salts or microparticles, which provides the opportunity to tailor a filamentous morphology. The suitable morphology for a given bioprocess varies depending on the desired product. Therefore, the advantages and disadvantages of each morphological type should be carefully evaluated for every biological system. Because of the high industrial relevance of filamentous microorganisms, research in previous years has aimed at the development of tools and techniques to characterise their growth and obtain quantitative estimates of their morphological properties. The focus of this review is on current advances in the characterisation and control of filamentous morphology with a separation of eukaryotic and prokaryotic systems. Furthermore, recent strategies to tailor the morphology through classical biochemical process parameters, morphology and genetic engineering to optimise the productivity of these filamentous systems are discussed.

Rheology of Lignocellulose Suspensions and Impact of Hydrolysis: A Review

White biotechnologies have several challenges to overcome in order to become a viable industrial process. Achieving highly concentrated lignocellulose materials and releasing fermentable substrates, with controlled kinetics in order to regulate micro-organism activity, present major technical and scientific bottlenecks. The degradation of the main polymeric fractions of lignocellulose into simpler molecules is a prerequisite for an integrated utilisation of this resource in a biorefinery concept. The characterisation methods and the observations developed for rheology, morphology, etc., that are reviewed here are strongly dependent on the fibrous nature of lignocellulose, are thus similar or constitute a good approach to filamentous culture broths. This review focuses on scientific works related to the study of the rheological behaviour of lignocellulose suspensions and their evolution during biocatalysis. In order to produce the targeted molecules (synthon), the lignocellulose substrates are converted by enzymatic degradation and are then metabolised by micro-organisms. The dynamics of the mechanisms is limited by coupled phenomena between flow, heat and mass transfers in regard to diffusion (within solid and liquid phases), convection (mixing, transfer coefficients, homogeneity) and specific inhibitors (concentration gradients). As lignocellulose suspensions consist of long entangled fibres for the matrix of industrial interest, they exhibit diverse and complex properties linked to this fibrous character (rheological, morphological, thermal, mechanical and biochemical parameters). Among the main variables to be studied, the rheological behaviour of such suspensions appears to be determinant for process efficiency. It is this behaviour that will determine the equipment to be used and the strategies applied (substrate and biocatalysis feed, mixing, etc.). This review provides an overview of (i) the rheological behaviour of fibrous materials in suspension, (ii) the methods and experimental conditions for their measurements, (iii) the main models used and (iv) their evolution during biocatalytic reactions with a focus on enzymatic hydrolysis.

Fungal Morphology in Industrial Enzyme Production--Modelling and Monitoring

Filamentous fungi are widely used in the biotechnology industry for the production of industrial enzymes. Thus, considerable work has been done with the purpose of characterizing these processes. The ultimate goal of these efforts is to be able to control and predict fermentation performance on the basis of "standardized" measurements in terms of morphology, rheology, viscosity, mass transfer and productivity. However, because the variables are connected or dependent on each other, this task is not trivial. The aim of this review article is to gather available information in order to explain the interconnectivity between the different variables in submerged fermentations. An additional factor which makes the characterization of a fermentation broth even more challenging is that the data obtained are also dependent on the way they have been collected-meaning which technologies or probes have been used, and on the way the data is interpreted-i.e. which models were applied. The main filamentous fungi used in industrial fermentation are introduced, ranging from Trichoderma reesei to Aspergillus species. Due to the fact that secondary metabolites, like antibiotics, are not to be considered bulk products, organisms like e.g. Penicillium chrysogenum are just briefly touched upon for the description of some characterization techniques. The potential for development of different morphological phenotypes is discussed as well, also in view of what this could mean to productivity and-equally important-the collection of the data. An overview of the state of the art techniques for morphology characterization is provided, discussing methods that finally can be employed as the computational power has grown sufficiently in the recent years. Image analysis (IA) clearly benefits most but it also means that methods like near infrared measurement (NIR), capacitance and on-line viscosity now provide potential alternatives as powerful tools for characterizing morphology. These measuring techniques, and to some extent their combination, allow obtaining the data necessary for supporting the creation of mathematical models describing the fermentation process. An important part of this article will indeed focus on describing the different models, and on discussing their importance to fermentations of filamentous fungi in general. The main conclusion is that it has not yet been attempted to develop an overarching model that spans across strains and scales, as most studies indeed conclude that their respective results might be strain specific and not necessarily valid across scales.

Challenges in industrial fermentation technology research

Industrial fermentation processes are increasingly popular, and are considered an important technological asset for reducing our dependence on chemicals and products produced from fossil fuels. However, despite their increasing popularity, fermentation processes have not yet reached the same maturity as traditional chemical processes, particularly when it comes to using engineering tools such as mathematical models and optimization techniques. This perspective starts with a brief overview of these engineering tools. However, the main focus is on a description of some of the most important engineering challenges: scaling up and scaling down fermentation processes, the influence of morphology on broth rheology and mass transfer, and establishing novel sensors to measure and control insightful process parameters. The greatest emphasis is on the challenges posed by filamentous fungi, because of their wide applications as cell factories and therefore their relevance in a White Biotechnology context. Computational fluid dynamics (CFD) is introduced as a promising tool that can be used to support the scaling up and scaling down of bioreactors, and for studying mixing and the potential occurrence of gradients in a tank.

The relationship of oxygen uptake rate and k(L)a with rheological properties in high cell density cultivation of docosahexaenoic acid by Schizochytrium sp. S31

Three independent cultures by fed batch strategy under different oxygen supply levels were investigated with Schizochytrium sp. S31 on glycerol in 50 L bioreactor. Three cultures all achieved high cell density cultivation (HCDC) with more than 100 g/L biomass density. However, the culture with middle oxygen supply level achieved the highest DHA concentration at 21.26 g/L. Dissolved oxygen (DO) limitation was commonly encountered in the present cultures, which was due to the dramatic decrease of kLa in high oxygen supply culture resulted from significantly increasing apparent viscosity of the broth. The rheological properties of the three cultures all exhibited shear-thinning behavior. The oxygen uptake rate (OUR) predominately influenced by kLa was suggested to replace DO as on-line control parameter for scale-up production of DHA.

Activated sludge rheology: a critical review on data collection and modelling

Rheological behaviour is an important fluid property that severely impacts its flow behaviour and many aspects related to this. In the case of activated sludge, the apparent viscosity has an influence on e.g. pumping, hydrodynamics, mass transfer rates, sludge-water separation (settling and filtration). It therefore is an important property related to process performance, including process economics. To account for this, rheological behaviour is being included in process design, necessitating its measurement. However, measurements and corresponding protocols in literature are quite diverse, leading to varying results and conclusions. In this paper, a vast amount of papers are critically reviewed with respect to this and important flaws are highlighted with respect to rheometer choice, rheometer settings and measurement protocol. The obtained rheograms from experimental efforts have frequently been used to build viscosity models. However, this is not that straightforward and a lot of errors can be detected with respect to good modelling practice, including fair model selection criteria, qualitative parameter estimations and proper model validation. These important steps are however recurrently violated, severely affecting the model reliability and predictive power. This is illustrated with several examples. In conclusion, dedicated research is required to improve the rheological measurements and the models derived from them. At this moment, there is no guidance with respect to proper rheological measurements. Moreover, the rheological models are not very trustworthy and remain very "black box". More insight in the physical background needs to be gained. A model-based approach with dedicated experimental data collection is the key to address this.

Comprehension of viscous morphology--evaluation of fractal and conventional parameters for rheological characterization of Aspergillus niger culture broth

The filamentous fungus Aspergillus niger is a widely used host in industrial processes from food, chemical to pharmaceutical industry. The most prominent feature of this filamentous microorganism in submerged cultivation is its complex morphology which comprises dense spherical pellets as well as viscous elongated filaments. Depending on culture conditions, the exhibited morphology has tremendous effect on the overall process, making a precise understanding of fungal growth and morphology indispensable. Morphology, however, is only industrially relevant as long as it can be linked to important cultivation characteristics of filamentous microorganisms such as culture broth flow behavior. In the present study, different conventional and fractal morphological parameters gained from automatic image analysis were tested for their eligibility to predict culture broth rheology from morphologic appearance. The introduced biomass independent rheological parameters K(BDW) and n(BDW) obtained by power law relationship were successfully estimated from morphology related fractal and conventional parameters. For improved characterization of morphologic appearance of filamentous fungi newly introduced fractal quotient and lacunarity were compared to conventional particle shape parameters in form of the earlier established Morphology number (MN).

Characterization and control of fungal morphology for improved production performance in biotechnology

Filamentous fungi have been widely applied in industrial biotechnology for many decades. In submerged culture processes, they typically exhibit a complex morphological life cycle that is related to production performance--a link that is of high interest for process optimization. The fungal forms can vary from dense spherical pellets to viscous mycelia. The resulting morphology has been shown to be influenced strongly by process parameters, including power input through stirring and aeration, mass transfer characteristics, pH value, osmolality and the presence of solid micro-particles. The surface properties of fungal spores and hyphae also play a role. Due to their high industrial relevance, the past years have seen a substantial development of tools and techniques to characterize the growth of fungi and obtain quantitative estimates on their morphological properties. Based on the novel insights available from such studies, more recent studies have been aimed at the precise control of morphology, i.e., morphology engineering, to produce superior bio-processes with filamentous fungi.

Comparison of laser diffraction and image analysis for measurement of Streptomyces coelicolor cell clumps and pellets

Morphology is important in industrial processes involving filamentous organisms because it affects the mixing and mass transfer and can be linked to productivity. Image analysis provides detailed information about the morphology but, in practice, it is often laborious including both collection of high quality images and image processing. Laser diffraction is rapid and fully automatic and provides a volume-weighted distribution of the particle sizes. However, it is based on a number of assumptions that do not always apply to samples. We have evaluated laser diffraction to measure cell clumps and pellets of Streptomyces coelicolor compare to image analysis. Samples, taken five times during fed-batch cultivation, were analyzed by image analysis and laser diffraction. The volume-weighted size distribution was calculated for each sample. Laser diffraction and image analysis yielded similar size distributions, i.e. unimodal or bimodal distributions. Both techniques produced similar estimations of the population means, whereas the estimates of the standard deviations were generally higher using laser diffraction compared to image analysis. Therefore, laser diffraction measurements are high quality and the technique may be useful when rapid measurements of filamentous cell clumps and pellets are required.

Robust, small-scale cultivation platform for Streptomyces coelicolor

BACKGROUND

For fermentation process and strain improvement, where one wants to screen a large number of conditions and strains, robust and scalable high-throughput cultivation systems are crucial. Often, the time lag between bench-scale cultivations to production largely depends on approximate estimation of scalable physiological traits. Microtiter plate (MTP) based screening platforms have lately become an attractive alternative to shake flasks mainly because of the ease of automation. However, there are very few reports on applications for filamentous organisms; as well as efforts towards systematic validation of physiological behavior compared to larger scale are sparse. Moreover, available small-scale screening approaches are typically constrained by evaluating only an end point snapshot of phenotypes.

RESULTS

To address these issues, we devised a robust, small-scale cultivation platform in the form of MTPs (24-square deepwell) for the filamentous bacterium Streptomyces coelicolor and compared its performance to that of shake flasks and bench-scale reactors. We observed that re-designing of medium and inoculum preparation recipes resulted in improved reproducibility. Process turnaround time was significantly reduced due to the reduction in number of unit operations from inoculum to cultivation. The incorporation of glass beads (ø 3 mm) in MTPs not only improved the process performance in terms of improved oxygen transfer improving secondary metabolite production, but also helped to transform morphology from pellet to disperse, resulting in enhanced reproducibility. Addition of MOPS into the medium resulted in pH maintenance above 6.50, a crucial parameter towards reproducibility. Moreover, the entire trajectory of the process was analyzed for compatibility with bench-scale reactors. The MTP cultivations were found to behave similar to bench-scale in terms of growth rate, productivity and substrate uptake rate and so was the onset of antibiotic synthesis. Shake flask cultivations however, showed discrepancy with respect to morphology and had considerably reduced volumetric production rates of antibiotics.

CONCLUSION

We observed good agreement of the physiological data obtained in the developed MTP platform with bench-scale. Hence, the described MTP-based screening platform has a high potential for investigation of secondary metabolite biosynthesis in Streptomycetes and other filamentous bacteria and the use may significantly reduce the workload and costs.

Pilot-scale process development and scale up for antifungal production

A pilot-scale fermentation was developed for an antifungal compound produced by a filamentous fungus. Replacement of galactose with lactose (20-fold cost savings) and a threefold phosphate reduction (15 to 5 g/L) improved productivity 2.5-fold. Addition of supplements--glycine, cobalt chloride, and trace elements--resulted in a further twofold productivity increase, greater process robustness, and less foaming which reduced antifoam addition tenfold (30 to <3 mL/L). Mid-cycle lactose limitations were addressed by raising initial lactose levels (40 to 120 g/L) resulting in another twofold productivity increase. Overall, peak titers increased tenfold from 45 +/- 9 to 448 +/- 39 mg/L, and productivities improved from 3 to 25 mg/L day. Despite its high productivity, process scale up was challenged by high broth viscosity (5,000-6,000 cP at 16.8 s(-1)). Gassed power requirements at the 600 L scale (4.7 kW/1,000 L) exceeded available power at the 15,000 L scale (3.0 kW/1,000 L), and broth transfer to the downstream isolation facility was hindered. Mid-cycle broth dilution with up to five 10 vol% additions of 12 wt% lactose solution or whole medium-reduced viscosity three- to fivefold (1,000-1,500 cP at 16.8 s(-1)), gassed power within scale-up limits (2.5 kW/1,000 L), and peak titer by up to 45%. The process was scaled up to the 15,000 L working volume based on constant aeration rate (vvm) and peak impeller tip speed, raising superficial velocities at similar shear. This strategy maximized mass transfer rates at target gassed power per unit volume levels, and along with controlled broth viscosity, precluded multiple dilution additions. A final titer of 333 mg/L with one dilution addition was achieved, somewhat lower than expected, likely owing to inhibition from some unmeasured volatile compound (not believed to be carbon dioxide) during an extended period of high back-pressure in the early production phase.