Evaluation of fluorimetric pH sensors for bioprocess monitoring at low pH

Automation of RNA-Seq Sample Preparation and Miniaturized Parallel Bioreactors Enable High-Throughput Differential Gene Expression Studies

A powerful strategy to accelerate bioprocess development is to complement parallel bioreactor systems with an automated approach, often achieved using liquid handling stations. The benefit of such high-throughput experiments is determined by the employed monitoring procedures. To gain a molecular understanding of the microbial production strains in miniaturized parallel single-use bioreactors, we extended the at-line monitoring procedures to transcriptome analysis in a parallel approach using RNA-Seq. To perform automated RNA-Seq experiments, we developed a sample preparation workflow consisting of at-line cell disruption by enzymatic cell lysis, total RNA extraction, nucleic acid concentration normalization, and Nanopore cDNA Library preparation. The pH-controlled aerobic batch growth of Saccharomyces cerevisiae was studied with six different carbon sources (glucose, pyruvate, fructose, galactose, sucrose, and mannose) on a 11 mL scale using 24 parallel stirred tank bioreactors integrated into a liquid handling station while performing at-line sample preparation for RNA-Seq on the same deck. With four biological replicates per condition, 24 cDNA libraries were prepared over 11.5 h. Off-line Nanopore sequencing yielded 20.97 M classified reads with a Q-score > 9. Differential gene expression analysis revealed significant differences in transcriptomic profiles when comparing growth with glucose (exponential growth) to growth with pyruvate (stress conditions), allowing identification of 674 downregulated and 709 upregulated genes. Insignificant changes in gene expression patterns were measured when comparing growth with glucose and fructose, yielding only 64 differentially expressed genes. The expected differences in cellular responses identified in this study show a promising approach for transcriptomic profiling of bioreactor cultures, providing valuable insights on a molecular level at-line in a high-throughput fashion.

Towards homogenous multiwell plate based pH sensors using a responsive triangulenium dye and an ATTO-647 reference dye

pH remains the most important chemical parameter and must be monitored for positive outcomes in areas as different as cheese making and in vitro fertilisation (IVF). Where blood gas analysers enable patient monitoring, starter cultures in cheese manufacturing are still monitored using conventional pH electrodes. Here, we present a homogeneous multiwell plate sensor for monitoring pH, with the same sensitivity as a pH electrode. The homogenous sensor operates in small liquid samples and uses two components: a pH responsive triangulenium dye on a polystyrene nanoparticle, and a freely diffusing commercial reference dye. Sensor measurements were made in triplicate to investigate and document the performance and robustness of the individual components, before we moved on to investigate the multiwell plate sensor design. The pH sensor was first tested in cuvettes, before moving to microwells and smaller volumes. The target is to monitor pH in IVF cultures, and the sensor proved to be operational in the pH range found in in vitro fertilisation buffers, but the references dye was shown not to be suitable for sensors. We conclude that the homogeneous sensor design is sound, but reaching the required precision of ΔpH = 0.01 can only be done with a different reference dye.

Adaptive laboratory evolution in a novel parallel shaken pH-auxostat

Adaptive laboratory evolution (ALE) is a widely used microbial strain development and optimization method. ALE experiments, to select for faster-growing strains, are commonly performed as serial batch cultivations in shake flasks, serum bottles, or microtiter plates or as continuous cultivations in bioreactors on a laboratory scale. To combine the advantages of higher throughput in parallel shaken cultures with continuous fermentations for conducting ALE experiments, a new Continuous parallel shaken pH-auxostat (CPA) was developed. The CPA consists of six autonomous parallel shaken cylindrical reactors, equipped with real-time pH control of the culture medium. The noninvasive pH measurement and control are realized by biocompatible pH sensor spots and a programmable pump module, to adjust the dilution rate of fresh medium for each reactor separately. Two different strains of the methylotrophic yeast Ogataea polymorpha were used as microbial model systems for parallel chemostat and pH-auxostat cultivations. During cultivation, the medium is acidified by the microbial activity of the yeast. For pH-auxostat cultivations, the growth-dependent acidification triggers the addition of fresh feed medium into the reactors, leading to a pH increase and thereby to the control of the pH to a predetermined set value. By controlling the pH to a predetermined set value, the dilution rate of the continuous cultivation is adjusted to values close to the washout point, in the range of the maximum specific growth rate of the yeast. The pH control was optimized by conducting a step-response experiment and obtaining tuned PI controller parameters by the Chien-Hrones-Reswick (CHR) PID tuning method. Two pH-auxostat cultivations were performed with two different O. polymorpha strains at high dilution rates for up to 18 days. As a result, up to 4.8-fold faster-growing strains were selected. The increased specific maximum growth rates of the selected strains were confirmed in subsequent batch cultivations.

Whole-cell bioreporter application for rapid evaluation of hazardous metal bioavailability and toxicity in bioprocess

Assessing heavy metal bioavailability and toxicity during bioprocess is critical for advancing green biotechnology. The capability of whole-cell bioreporters to measure heavy metal bioavailability has been increasingly recognized. The advantages of this technology being applied to bioprocess monitoring are less studied. Here we investigate the potential of a cadmium- and lead-sensitive bioreporter to be used for heavy metals as a class, which holds great interest for bioprocess applications. We evaluated the bioavailability of eight individual heavy metals with bioreporter zntA, as well as the bioavailability and toxicity of mixed metals. The bioavailability and toxicity of heavy metals in bioprocess samples were also evaluated. We have demonstrated for the first time that the zntA bioreporter can effectively detect the bioavailability of zinc, nickel, and cobalt with limit of detection lower than 0.01, 0.08 and 0.5 mg·L-1, respectively. The detection limits meet the requirements of the WHO, the U.S. Environmental Protection Agency, and the China drinking water quality standards, which makes this approach reasonable for monitoring heavy metal bioavailability in bioprocess. LIVE/DEAD toxicity experiments have been conducted for the detection of mixed metal solution toxicity to zntA bioreporter which shows an EC50 (as EC50, concentration for 50% of maximal effect) value of mixed metal solution is 3.84 mg·L-1. Samples from wastewater treatment plants, sludge treatment plants and kitchen waste fermentation processes were analyzed to extend upon the laboratory results. The results of this study confirm the potential for practical applications of bioreporter technology in bioprocess monitoring. In turn, development for such practical applications is key to achieve the necessary level of commercialization to further make the routine use of bioreporters in bioprocess monitoring feasible.

The Good pH probe: non-invasive pH in-line monitoring using Good buffers and Raman spectroscopy

In bioprocesses, the pH value is a critical process parameter that requires monitoring and control. For pH monitoring, potentiometric methods such as pH electrodes are state of the art. However, they are invasive and show measurement value drift. Spectroscopic pH monitoring is a non-invasive alternative to potentiometric methods avoiding this measurement value drift. In this study, we developed the Good pH probe, which is an approach for spectroscopic pH monitoring in bioprocesses with an effective working range between pH 6 and pH 8 that does not require the estimation of activity coefficients. The Good pH probe combines for the first time the Good buffer 3-(N-morpholino)propanesulfonic acid (MOPS) as pH indicator with Raman spectroscopy as spectroscopic technique, and Indirect Hard Modeling (IHM) for the spectral evaluation. During a detailed characterization, we proved that the Good pH probe is reversible, exhibits no temperature dependence between 15 and 40 °C, has low sensitivity to the ionic strength up to 1100 mM, and is applicable in more complex systems, in which other components significantly superimpose the spectral features of MOPS. Finally, the Good pH probe was successfully used for non-invasive pH in-line monitoring during an industrially relevant enzyme-catalyzed reaction with a root mean square error of prediction (RMSEP) of 0.04 pH levels. Thus, the Good pH probe extends the list of critical process parameters monitorable using Raman spectroscopy and IHM by the pH value.

Smart covalent organic frameworks: dual channel sensors for acids and bases

Fully π-conjugated sp² carbon covalent organic frameworks upon integration with carboxylic electrolyte sites on the pore wall become highly luminescent sensors. The sensors feature dual channel responsiveness and are able to detect both acids and bases over a wide pH range and the neurotransmitter dopamine via ultrafast electron transfer under ambient conditions.

Phase Separation in Anaerobic Digestion: A Potential for Easier Process Combination?

The flexibilization of bioenergy production has the potential to counteract partly other fluctuating renewable energy sources (such as wind and solar power). As a weather-independent energy source, anaerobic digestion (AD) can offer on-demand energy supply through biogas production. Separation of the stages in anaerobic digestion represents a promising strategy for the flexibilization of the fermentative part of biogas production. Segregation in two reactor systems facilitates monitoring and control of the provision of educts to the second methanogenic stage, thus controlling biogas production. Two-stage operation has proven to reach similar or even higher methane yields and biogas purities than single-stage operation in many different fields of application. It furthermore allows methanation of green hydrogen and an easier combination of material and energy use of many biogenic raw and residual biomass sources. A lot of research has been conducted in recent years regarding the process phase separation in multi-stage AD operation, which includes more than two stages. Reliable monitoring tools, coupled with effluent recirculation, bioaugmentation and simulation have the potential to overcome the current drawbacks of a sophisticated and unstable operation. This review aims to summarize recent developments, new perspectives for coupling processes for energy and material use and a system integration of AD for power-to-gas applications. Thereby, cell physiological and engineering aspects as well as the basic economic feasibility are discussed. As conclusion, monitoring and control concepts as well as suitable separation technologies and finally the data basis for techno-economic and ecologic assessments have to be improved.

Optical Sensing and Imaging of pH Values: Spectroscopies, Materials, and Applications

This is the first comprehensive review on methods and materials for use in optical sensing of pH values and on applications of such sensors. The Review starts with an introduction that contains subsections on the definition of the pH value, a brief look back on optical methods for sensing of pH, on the effects of ionic strength on pH values and pKa values, on the selectivity, sensitivity, precision, dynamic ranges, and temperature dependence of such sensors. Commonly used optical sensing schemes are covered in a next main chapter, with subsections on methods based on absorptiometry, reflectometry, luminescence, refractive index, surface plasmon resonance, photonic crystals, turbidity, mechanical displacement, interferometry, and solvatochromism. This is followed by sections on absorptiometric and luminescent molecular probes for use pH in sensors. Further large sections cover polymeric hosts and supports, and methods for immobilization of indicator dyes. Further and more specific sections summarize the state of the art in materials with dual functionality (indicator and host), nanomaterials, sensors based on upconversion and 2-photon absorption, multiparameter sensors, imaging, and sensors for extreme pH values. A chapter on the many sensing formats has subsections on planar, fiber optic, evanescent wave, refractive index, surface plasmon resonance and holography based sensor designs, and on distributed sensing. Another section summarizes selected applications in areas, such as medicine, biology, oceanography, bioprocess monitoring, corrosion studies, on the use of pH sensors as transducers in biosensors and chemical sensors, and their integration into flow-injection analyzers, microfluidic devices, and lab-on-a-chip systems. An extra section is devoted to current challenges, with subsections on challenges of general nature and those of specific nature. A concluding section gives an outlook on potential future trends and perspectives.

Byproduct-free geraniol glycosylation by whole-cell biotransformation with recombinant Escherichia coli

Objective

Geraniol, a fragrance of great importance in the consumer goods industry, can be glucosylated by the UDP-glucose-dependent glucosyltransferase VvGT14a from Vitis vinifera, yielding more stable geranyl glucoside. Escherichia coli expressing VvGT14a is a convenient whole-cell biocatalyst for this biotransformation due to its intrinsic capability for UDP-glucose regeneration. The low water solubility and high cytotoxicity of geraniol can be overcome in a biphasic system where the non-aqueous phase functions as an in situ substrate reservoir. However, the effect of different process variables on the biphasic whole-cell biotransformation is unknown. Thus, the goal of this study was to identify potential bottlenecks during biotransformation with in situ geraniol supply via isopropyl myristate as second non-aqueous phase.

Results

First, insufficient UDP-glucose supply could be ruled out by measurement of intracellular UDP-glucose concentrations. Instead, oxygen supply was determined as a bottleneck. Moreover, the formation of the byproduct geranyl acetate by chloramphenicol acetyltransferase (CAT) was identified as a constraint for high product yields. The use of a CAT-deficient whole-cell biocatalyst prevented the formation of geranyl acetate, and geranyl glucoside could be obtained with 100% selectivity during a biotransformation on L-scale.

Conclusion

This study is the first to closely analyze the whole-cell biotransformation of geraniol with Escherichia coli expressing an UDP-glucose-dependent glucosyltransferase and can be used as an optimal starting point for the design of other glycosylation processes.

Electronic supplementary material

The online version of this article (10.1007/s10529-020-02993-z) contains supplementary material, which is available to authorized users.

Process adapted calibration improves fluorometric pH sensor precision in sophisticated fermentation processes

Miniaturization and automation have become increasingly popular in bioprocess development in recent years, enabling rapid high-throughput screening and optimization of process conditions. In addition, advances in the bioprocessing industry have led to increasingly complex process designs, such as pH and temperature shifts, in microbial fed-batch fermentations for optimal soluble protein expression in a range of hosts. However, in order to develop an accurate scale-down model for bioprocess screening and optimization, small-scale bioreactors must be able to accurately reproduce these complex process designs. Monitoring methods, such as fluorometric-based pH sensors, provide elegant solutions for the miniaturization of bioreactors, however, previous research suggests that the intrinsic fluorescence of biomass alters the sigmoidal calibration curve of fluorometric pH sensors, leading to inaccurate pH control. In this article, we present results investigating the impact of biomass on the accuracy of a commercially available fluorometric pH sensor. Subsequently, we present our calibration methodology for more precise online measurement and provide recommendations for improved pH control in sophisticated fermentation processes.

9-Acridinemethanamine and Acridine-9-Carboxaldehyde as Potential Fluorescence Lifetime pH Indicators

A significant challenge concerning the development of fluorescence lifetime (FL) based pH sensors is the paucity of fluorophores with sufficiently large FL variation with pH. Acridine is amongst the indicators with highest fluoresce lifetime responses to pH, with a change in lifetime of about 13 ns within a pH range of 5-8. Here we examine the two acridine derivatives, 9-acridinemethanamine (9-AMA) and acridine-9-carbaldehyde (9-ACA) in terms of their FL pH sensitivity and pH sensing range. Both indicators are characterized when dissolved in buffer solutions, as well as when immobilized in support materials. 9-AMA has a change in FL of 11 ns between pH 2-5, both when dissolved in solution and when immobilized in surfactant-filled mesoporous silica. The FL of 9-ACA is not sensitive to pH when dissolved in buffer solutions; however, when covalently bound to amine-modified silica, its FL changes 15 ns between pH 3-6. 9-AMA and 9-ACA represent promising FL in the pH range of pH 2-6, and could potentially form the basis of new FL pH sensors. Graphical Abstract.

Development of Novel Bioreactor Control Systems Based on Smart Sensors and Actuators

Bioreactors of various forms have been widely used in environmental protection, healthcare, industrial biotechnology, and space exploration. Robust demand in the field stimulated the development of novel designs of bioreactor geometries and process control strategies and the evolution of the physical structure of the control system. After the introduction of digital computers to bioreactor process control, a hierarchical structure control system (HSCS) for bioreactors has become the dominant physical structure, having high efficiency and robustness. However, inherent drawbacks of the HSCS for bioreactors have produced a need for a more consolidated solution of the control system. With the fast progress in sensors, machinery, and information technology, the development of a flat organizational control system (FOCS) for bioreactors based on parallel distributed smart sensors and actuators may provide a more concise solution for process control in bioreactors. Here, we review the evolution of the physical structure of bioreactor control systems and discuss the properties of the novel FOCS for bioreactors and related smart sensors and actuators and their application circumstances, with the hope of further improving the efficiency, robustness, and economics of bioprocess control.

Investigating the Time Response of an Optical pH Sensor Based on a Polysiloxane-Polyethylene Glycol Composite Material Impregnated with a pH-Responsive Triangulenium Dye

Determining the time it takes a sensor to report a change in the concentration of its target analyte may appear to be an easy task, but it is not. The dynamic characteristic of a sensor is determined by all components in the sensor system and the hydrodynamics of the sample. Here, the dynamic properties of an optical pH sensor were determined using the IUPAC-recommended activity step method in experimental setups that can determine sensor-limited response times longer than 5 s. In order to do so, experimental setups for the injection and for the dipping method of determining the sensor time response were developed, tested, and shown to be able to determine time-response curves with 1 s time resolution. This time resolution is shown to be sufficient for determining dynamic characterization of this optical pH sensor. The sensor chemistry-limited time-response curves were analyzed using curve fitting. It was found that the optode response time is limited by diffusion of protons within the sensor material when the proton concentration is reduced and limited by diffusion from the bulk to the boundary layer at the optode surface when proton concentration is increased. The latter is dependent on the magnitude of the change in analyte concentration and cannot be reported as a single response time. The investigation of the time response of the optical pH sensor reveals detailed information of the sensor chemistry, but does not yield a single response time of the sensor capable of describing the dynamic sensor characteristics of the optical pH sensor system.

A unified approach for investigating chemosensor properties - dynamic characteristics

Chemosensors are a group of sensors-responsive sensor chemistry, sensor hardware, and software-that report on the composition of solutions and gaseous samples. Dynamic properties are fundamental for all sensor characterization. While electrochemical chemosensors have seen a century of research and are well-described, research on chemosensors using other modes of transductions are still at an early stage. The dynamic properties of chemosensors-independent of their mode of transduction-are not reported consistently in the literature. This makes it impossible to compare sensor performance of chemosensors from different manufacturers and laboratories. To remedy this, standardized experimental methods that exclude the influence of drift and any dependence on activity step change must be used. Subsequently, the resulting data must be treated using a unifying analysis formalism, and robust values must be used to describe chemosensor characteristics. Characterizing the sensor properties in turn enables rationalizing the link between sensor performance and sensor chemistry. Following a review of sensor theory, a thorough discussion of experimental methods and data analysis models for determining dynamic sensor properties, we arrive at evidence-based recommendations for good practice when describing new chemosensors. Adhering to these recommendations, sensor performance can be compared between laboratories, and information on the sensor chemistry may be revealed in the data analysis. This topic is particularly relevant in the rapidly maturing field of optical chemosensors.

Optical Chemical Sensor Using Intensity Ratiometric Fluorescence Signals for Fast and Reliable pH Determination

Optical pH sensors enable noninvasive monitoring of pH, yet in pure sensing terms, the potentiometric method of measuring pH is still vastly superior. Here, we report a full spectrometer-based optical pH sensor system consisting of sensor chemistry, hardware, and software that for the first time is capable of challenging the performance of an electrode-based pH meter in specific applications such as biopharmaceutical process monitoring and in single-use bioproduction. A highly photostable triangulenium fluorophore emitting at 590 nm was immobilized in an organically modified silicon matrix that allows for fast time-response by rapid diffusion of water in and out of the resulting composite polymer deposited on a polycarbonate substrate. Fluctuations from the fiber optical sensor hardware have been reduced by including a highly photostable terrylene-based reference dye emitting at 660 nm, thus enabling intensity-based ratiometric readouts. The dyes were excited by 505 nm light from a light emitting diode. The sensor was operational within a pH range of 4.6-7.6, and was characterized and demonstrated to have properties that are comparable to those of commercial pH electrodes considering time-response ( t₉₀ < 90 s), precision (0.03 pH-units), and drift.

Biocompatible Microporous Organically Modified Silicate Material with Rapid Internal Diffusion of Protons

A new four-component organically modified silicate (ORMOSIL) material was developed with optical pH sensors in mind. Through a sol-gel process, the porosity of an ORMOSIL framework was optimized to allow rapid diffusion of protons, ideal for fast response to pH in an optical sensor. The optically transparent material was produced by catalyzing the dual polymerization of 3-(glycidoxy)propyltrimethoxysilane (GPTMS) and propyltriethoxysilane (PrTES) with boron trifluoride diethyl etherate. The performance of the resulting material in fluorescence based optical pH sensors was evaluated by incorporation of active dye components in the inorganic polymer framework. It is demonstrated that the material has a short response time ( t₉₀ < 30 s) and high stability in medium and during storage, and resulting sensor spots are biocompatible. It is concluded that this ORMOSIL material has excellent properties for optical pH sensors.