A robust flow cytometry-based biomass monitoring tool enables rapid at-line characterization of S. cerevisiae physiology during continuous bioprocessing of spent sulfite liquor

Use of a sample injection loop for an accurate measurement of particle number concentration by flow cytometry

Flow cytometry plays a pivotal role in biotechnology by providing quantitative measurements for a wide range of applications. Nonetheless, achieving precise particle quantification, particularly without relying on counting beads, remains a challenge. In this study, we introduce a novel exhaustive counting method featuring a sample loop-based injection system that delivers a defined sample volume to a detection system to enhance quantification in flow cytometry. We systematically assess the performance characteristics of this system with micron-sized polystyrene beads, addressing issues related to sample introduction, adsorption, and volume measurement. Results underscore the excellent analytical performance of the proposed method, characterized by high linearity and repeatability. We compare our approach to counting bead-based measurements, and while an approximate bias value was observed, the measured values were found to be similar between the methods, demonstrating its comparability and reliability. This method holds great promise for improving the accuracy and precision of particle quantification in flow cytometry, with implications for various fields including healthcare and environmental monitoring.

Comparative Zymocidial Effect of Three Different Killer Toxins against Brettanomyces bruxellensis Spoilage Yeasts

Three killer toxins that were previously investigated, one excreted by Kluyveromyces wickerhamii and two by different strains of Wickerhamomyces anomalus, were produced at the pilot scale, lyophilized and characterized, and the formulates were assessed for their zymocidial effect against Brettanomyces bruxellensis spoilage yeast. A comparative analysis allowed the evaluation of the minimum inhibitory concentration (MIC) against a sensitive strain. Fungicidal and fungistatic concentrations were used to evaluate the cytocidal effect using a cytofluorimetric approach that confirmed the lethal effect of all lyophilized formulates against B. bruxellensis spoilage yeasts. Moreover, the potential killer toxins' cytotoxicity against human intestinal cells (Caco-2) were evaluated to exclude any possible negative effect on the consumers. Finally, the effective lethal effect of all three lyophilized killer toxins toward B. bruxellensis sensitive strain were tested. The results indicated that all of them acted without dangerous effects on the human epithelial cells, opening the way for their possible commercial application. In particular, D15 showed the lowest MIC and the highest activity, was evaluated also in wine, revealing a strong reduction of Brettamonyces yeast growth and, at the same time, a control of ethyl phenols production.

Flow cytometry-based viability staining: an at-line tool for bioprocess monitoring of Sulfolobus acidocaldarius

Determination of the viability, ratio of dead and live cell populations, of Sulfolobus acidocaldarius is still being done by tedious and material-intensive plating assays that can only provide time-lagged results. Although S. acidocaldarius, an extremophilic Archaeon thriving at 75 °C and pH 3.0, and related species harbor great potential for the exploitation as production hosts and biocatalysts in biotechnological applications, no industrial processes have been established yet. One hindrance is that during development and scaling of industrial bioprocesses timely monitoring of the impact of process parameters on the cultivated organism is crucial—a task that cannot be fulfilled by traditional plating assays. As alternative, flow cytometry (FCM) promises a fast and reliable method for viability assessment via the use of fluorescent dyes. In this study, commercially available fluorescent dyes applicable in S. acidocaldarius were identified. The dyes, fluorescein diacetate and concanavalin A conjugated with rhodamine, were discovered to be suitable for viability determination via FCM. For showing the applicability of the developed at-line tool for bioprocess monitoring, a chemostat cultivation on a defined growth medium at 75 °C, pH 3.0 was conducted. Over the timeframe of 800 h, this developed FCM method was compared to the plating assay by monitoring the change in viability upon controlled pH shifts. Both methods detected an impact on the viability at pH values of 2.0 and 1.5 when compared to pH 3.0. A logarithmic relationship between the viability observed via plating assay and via FCM was observed.

Development of a flow cytometry (FCM) method for viability determination of S. acidocaldarius using the fluorescent dyes fluorescein diacetate and concanavalin A conjugated with rhodamine.

Applicability of the developed method was shown via viability monitoring during a continuous cultivation with triggered pH shifts.

A logarithmic trend was observed between the developed FCM method and the state-of-the-art method, plating assay.

In situ quantification of poly(3-hydroxybutyrate) and biomass in Cupriavidus necator by a fluorescence spectroscopic assay

Abstract

Fluorescence spectroscopy offers a cheap, simple, and fast approach to monitor poly(3-hydroxybutyrate) (PHB) formation, a biodegradable polymer belonging to the biodegradable polyester class polyhydroxyalkanoates. In the present study, a fluorescence and side scatter-based spectroscopic setup was developed to monitor in situ biomass, and PHB formation of biotechnological applied Cupriavidus necator strain. To establish PHB quantification of C. necator, the dyes 2,2-difluoro-4,6,8,10,12-pentamethyl-3-aza-1-azonia-2-boranuidatricyclo[7.3.0.03,7]dodeca-1(12),4,6,8,10-pentaene (BODIPY^493/503), ethyl 5-methoxy-1,2-bis(3-methylbut-2-enyl)-3-oxoindole-2-carboxylate (LipidGreen2), and 9-(diethylamino)benzo[a]phenoxazin-5-one (Nile red) were compared with each other. Fluorescence staining efficacy was obtained through 3D-excitation-emission matrix and design of experiments. The coefficients of determination were ≥ 0.98 for all three dyes and linear to the high-pressure liquid chromatography obtained PHB content, and the side scatter to the biomass concentration. The fluorescence correlation models were further improved by the incorporation of the biomass-related side scatter. Afterward, the resulting regression fluorescence models were successfully applied to nitrogen-deficit, phosphor-deficit, and NaCl-stressed C. necator cultures. The highest transferability of the regression models was shown by using LipidGreen2. The novel approach opens a tailor-made way for a fast and simultaneous detection of the crucial biotechnological parameters biomass and PHB content during fermentation.

Key points

• Intracellular quantification of PHB and biomass using fluorescence spectroscopy.

• Optimizing fluorescence staining conditions and 3D-excitation-emission matrix.

• PHB was best obtained by LipidGreen2, followed by BODIPDY^493/503 and Nile red.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11670-8.

Adaptation of Saccharomyces cerevisiae in a concentrated spent sulphite liquor waste stream for increased inhibitor resistance

The fermentation of spent sulphite liquor (SSL) from the pulping of hardwoods is limited by the combination of xylose, the primary fermentable sugar and high concentrations of microbial inhibitors that decrease the yeast fermentation ability. The inhibitor resistance phenotypes of xylose-capable Saccharomyces cerevisiae strains were therefore enhanced by combining rational engineering for multi-inhibitor tolerance, with adaptation in concentrated hardwood SSL as selective pressure. The adapted strains were assessed in fermentations with 60-80% v/v concentrated SSL under industrially relevant fermentation conditions. During adaptation, strains produced ethanol concentrations between 11.0 and 15.4 g/L in the range of that reported in literature. The adapted TFA40 and TP50 strains displayed enhanced inhibitor resistance phenotypes and were able to ferment xylose-rich SSL at pH below 5, exhibiting improved ethanol yields relative to the reference strain. Using yeast extract and peptone as nitrogen source in concentrated SSL fermentations further improved ethanol yields. However, strains exhibited a trade-off between resistance and ethanol productivity, indicating a carbon/energy cost for the expression of this inhibitor tolerance phenotype. KEY POINTS : • Achieved fermentation of xylose-rich hardwood spent sulphite liquor at pH below 5.0 • Adaptation of xylose-capable S. cerevisiae in concentrated spent sulphite liquor • Adapted strains exhibited enhanced inhibitor resistance phenotypes.

AI-based forecasting of ethanol fermentation using yeast morphological data

Several industries require getting information of products as soon as possible during fermentation. However, the trade-off between sensing speed and data quantity presents challenges for forecasting fermentation product yields. In this study, we tried to develop AI models to forecast ethanol yields in yeast fermentation cultures, using cell morphological data. Our platform involves the quick acquisition of yeast morphological images using a non-staining protocol, extraction of high-dimensional morphological data using image processing software, and forecasting of ethanol yields via supervised machine learning. We found that the neural network algorithm produced the best performance, which had a coefficient of determination of > 0.9 even at 30 and 60 min in the future. The model was validated using test data collected using the CalMorph-PC(10) system, which enables rapid image acquisition within 10 min. AI-based forecasting of product yields based on cell morphology will facilitate the management and stable production of desired biocommodities.

Study of Oenological Fermentation: Which Strategy and Which Tools?

Wine fermentation is a specific and complex research subject and its control is essential to ensure full process completion while improving wine quality. It displays several specificities, in particular, (i) musts with a very high sugar content, low pH, and some limiting nutrients, as well as a great variability in must composition according to the year, grape variety, and so on; (ii) atypical fermentation conditions with non-isothermal temperature profiles, a quasi-anaerobiosis and legal constraints with a limited and predefined list of authorized operations. New challenges have emerged, related to the increasing diversity of commercially available yeast strains; the fluctuating composition of musts, particularly owing to climate change; and sustainability, which has become a key issue. This paper synthesizes approaches implemented to address all these issues. It details the example of our laboratory that, for many years, has been developing an integrated approach to study yeast diversity, understand their metabolism, and develop new fermentation control strategies. This approach requires the development of specific fermentation devices to study yeast metabolism in a controlled environment that mimics practical conditions and to develop original fermentation control strategies. All these tools are described here, together with their role in the overall scientific strategy and complementary approaches in the literature.

A cytofluorimetric analysis of a Saccharomyces cerevisiae population cultured in a fed-batch bioreactor

The yeast Saccharomyces cerevisiae is a reference model system and one of the widely used microorganisms in many biotechnological processes. In industrial yeast applications, combined strategies aim to maximize biomass/product yield, with the fed-batch culture being one of the most frequently used. Flow cytometry (FCM) is widely applied in biotechnological processes and represents a key methodology to monitor cell population dynamics. We propose here an application of FCM in the analysis of yeast cell cycle along the time course of a typical S. cerevisiae fed-batch culture. We used two different dyes, SYTOX Green and SYBR Green, with the aim to better define each stage of cell cycle during S. cerevisiae fed-batch culture. The results provide novel insights in the use of FCM cell cycle analysis for the real-time monitoring of S. cerevisiae bioprocesses.

Application of In-Situ and Soft-Sensors for Estimation of Recombinant P. pastoris GS115 Biomass Concentration: A Case Analysis of HBcAg (Mut+) and HBsAg (MutS) Production Processes under Varying Conditions

Microbial biomass concentration is a key bioprocess parameter, estimated using various labor, operator and process cross-sensitive techniques, analyzed in a broad context and therefore the subject of correct interpretation. In this paper, the authors present the results of P. pastoris cell density estimation based on off-line (optical density, wet/dry cell weight concentration), in-situ (turbidity, permittivity), and soft-sensor (off-gas O₂/CO₂, alkali consumption) techniques. Cultivations were performed in a 5 L oxygen-enriched stirred tank bioreactor. The experimental plan determined varying aeration rates/levels, glycerol or methanol substrates, residual methanol levels, and temperature. In total, results from 13 up to 150 g (dry cell weight)/L cultivation runs were analyzed. Linear and exponential correlation models were identified for the turbidity sensor signal and dry cell weight concentration (DCW). Evaluated linear correlation between permittivity and DCW in the glycerol consumption phase (<60 g/L) and medium (for Mut⁺ strain) to significant (for Mut^S strain) linearity decline for methanol consumption phase. DCW and permittivity-based biomass estimates used for soft-sensor parameters identification. Dataset consisting from 4 Mut⁺ strain cultivation experiments used for estimation quality (expressed in NRMSE) comparison for turbidity-based (8%), permittivity-based (11%), O₂ uptake-based (10%), CO₂ production-based (13%), and alkali consumption-based (8%) biomass estimates. Additionally, the authors present a novel solution (algorithm) for uncommon in-situ turbidity and permittivity sensor signal shift (caused by the intensive stirrer rate change and antifoam agent addition) on-line identification and minimization. The sensor signal filtering method leads to about 5-fold and 2-fold minimized biomass estimate drifts for turbidity- and permittivity-based biomass estimates, respectively.

Single-Cell Technologies to Understand the Mechanisms of Cellular Adaptation in Chemostats

There is a growing interest in continuous manufacturing within the bioprocessing community. In this context, the chemostat process is an important unit operation. The current application of chemostat processes in industry is limited although many high yielding processes are reported in literature. In order to reach the full potential of the chemostat in continuous manufacture, the output should be constant. However, adaptation is often observed resulting in changed productivities over time. The observed adaptation can be coupled to the selective pressure of the nutrient-limited environment in the chemostat. We argue that population heterogeneity should be taken into account when studying adaptation in the chemostat. We propose to investigate adaptation at the single-cell level and discuss the potential of different single-cell technologies, which could be used to increase the understanding of the phenomena. Currently, none of the discussed single-cell technologies fulfill all our criteria but in combination they may reveal important information, which can be used to understand and potentially control the adaptation.

Towards continuous industrial bioprocessing with solventogenic and acetogenic clostridia: challenges, progress and perspectives

The sustainable production of solvents from above ground carbon is highly desired. Several clostridia naturally produce solvents and use a variety of renewable and waste-derived substrates such as lignocellulosic biomass and gas mixtures containing H2/CO2 or CO. To enable economically viable production of solvents and biofuels such as ethanol and butanol, the high productivity of continuous bioprocesses is needed. While the first industrial-scale gas fermentation facility operates continuously, the acetone-butanol-ethanol (ABE) fermentation is traditionally operated in batch mode. This review highlights the benefits of continuous bioprocessing for solvent production and underlines the progress made towards its establishment. Based on metabolic capabilities of solvent producing clostridia, we discuss recent advances in systems-level understanding and genome engineering. On the process side, we focus on innovative fermentation methods and integrated product recovery to overcome the limitations of the classical one-stage chemostat and give an overview of the current industrial bioproduction of solvents.