Calorespirometric feeding control enhances bioproduction from toxic feedstocks-Demonstration for biopolymer production out of methanol

Biocalorimetry-aided monitoring of fungal pretreatment of lignocellulosic agricultural residues

The present study aimed to investigate whether and how non-invasive biocalorimetric measurements could serve for process monitoring of fungal pretreatment during solid-state fermentation (SSF) of lignocellulosic agricultural residues such as wheat straw. Seven filamentous fungi representing different lignocellulose decay types were employed. Water-soluble sugars being immediately available after fungal pretreatment and those becoming water-extractable after enzymatic digestion of pretreated wheat straw with hydrolysing (hemi)cellulases were considered to constitute the total bioaccessible sugar fraction. The latter was used to indicate the success of pretreatments and linked to corresponding species-specific metabolic heat yield coefficients (YQ/X) derived from metabolic heat flux measurements during fungal wheat straw colonisation. An YQ/X range of about 120 to 140 kJ/g was seemingly optimal for pretreatment upon consideration of all investigated fungi and application of a non-linear Gaussian fitting model. Upon exclusion from analysis of the brown-rot basidiomycete Gloeophyllum trabeum, which differs from all other here investigated fungi in employing extracellular Fenton chemistry for lignocellulose decomposition, a linear relationship where amounts of total bioaccessible sugars were suggested to increase with increasing YQ/X values was obtained. It remains to be elucidated whether an YQ/X range being optimal for fungal pretreatment could firmly be established, or if the sugar accessibility for post-treatment generally increases with increasing YQ/X values as long as "conventional" enzymatic, i.e. (hemi)cellulase-based, lignocellulose decomposition mechanisms are operative. In any case, metabolic heat measurement-derived parameters such as YQ/X values may become very valuable tools supporting the assessment of the suitability of different fungal species for pretreatment of lignocellulosic substrates. KEY POINTS: • Biocalorimetry was used to monitor wheat straw pretreatment with seven filamentous fungi. • Metabolic heat yield coefficients (YQ/X) seem to indicate pretreatment success. • YQ/X values may support the selection of suitable fungal strains for pretreatment.

Unveiling the potential of specific growth rate control in fed-batch fermentation: bridging the gap between product quantity and quality

During the epoch of sustainable development, leveraging cellular systems for production of diverse chemicals via fermentation has garnered attention. Industrial fermentation, extending beyond strain efficiency and optimal conditions, necessitates a profound understanding of microorganism growth characteristics. Specific growth rate (SGR) is designated as a key variable due to its influence on cellular physiology, product synthesis rates and end-product quality. Despite its significance, the lack of real-time measurements and robust control systems hampers SGR control strategy implementation. The narrative in this contribution delves into the challenges associated with the SGR control and presents perspectives on various control strategies, integration of soft-sensors for real-time measurement and control of SGR. The discussion highlights practical and simple SGR control schemes, suggesting their seamless integration into industrial fermenters. Recommendations provided aim to propose new algorithms accommodating mechanistic and data-driven modelling for enhanced progress in industrial fermentation in the context of sustainable bioprocessing.

Recent progress in the engineering of C1-utilizing microbes

The global climate crisis has led to the transition toward the sustainable production of chemicals and fuels with a low carbon footprint. Microbial utilization of one-carbon (C1) substrates, such as carbon dioxide, carbon monoxide, methane, formate, and methanol, may be a promising replacement for the current fossil fuel-based industry. However, natural C1-utilizing microbes are currently unsuitable for industrial applications because of their slow growth and low carbon conversion efficiency, which results in low productivity and yield. Here, we review the recent achievements in engineering C1-utilizing microbes with improved carbon assimilation efficiency and describe the development of synthetic microorganisms by introducing natural C1 assimilation pathways in non-C1-utilizing microbes. Finally, we outline the future directions for realizing the industrial potential of C1-utilizing microbes.

Methanol-essential growth of Escherichia coli

Methanol represents an attractive substrate for biotechnological applications. Utilization of reduced one-carbon compounds for growth is currently limited to methylotrophic organisms, and engineering synthetic methylotrophy remains a major challenge. Here we apply an in silico-guided multiple knockout approach to engineer a methanol-essential Escherichia coli strain, which contains the ribulose monophosphate cycle for methanol assimilation. Methanol conversion to biomass was stoichiometrically coupled to the metabolization of gluconate and the designed strain was subjected to laboratory evolution experiments. Evolved strains incorporate up to 24% methanol into core metabolites under a co-consumption regime and utilize methanol at rates comparable to natural methylotrophs. Genome sequencing reveals mutations in genes coding for glutathione-dependent formaldehyde oxidation (frmA), NAD(H) homeostasis/biosynthesis (nadR), phosphopentomutase (deoB), and gluconate metabolism (gntR). This study demonstrates a successful metabolic re-routing linked to a heterologous pathway to achieve methanol-dependent growth and represents a crucial step in generating a fully synthetic methylotrophic organism.

Engineering synthetic methylotrophy remains challenging. Here, the authors engineer a methanol-essential E. coli by an in silico-guided multiple knockout approach and show a laboratory evolved strain can incorporate up to 24% methanol into core metabolites during growth.

Application of heat compensation calorimetry to an E. coli fed-batch process

The application of biocalorimetry to fermentation processes offers advantageous insights, while being less complex compared to other, sophisticated PAT solutions. Although the general concept is established, calorimetric methods vary in detail. In this work, a special approach, called heat compensation calorimetry, was applied to an E. coli fed-batch process. Much work has been done for batch processes, proving the validity and accuracy of this calorimetric mode. However, the adaption of this strategy to fed-batch processes has some implications. In the first section of this work, batch fermentations were performed, comparing heat capacity calorimetry to the compensation mode. Both processes showed very good agreement by means of growth behavior. The heat related differences, e.g. temperature profiles, were obvious. In addition, the impact of the chosen mode on the calculation of in-process heat transfer coefficients was shown. Finally, a fed-batch fermentation was performed. The compensation mode was kept sufficiently, up to the point where the metabolic heat production accelerated strongly. Controller tuning was a neuralgic point, which would have needed further optimization under these conditions. Nevertheless, in the present work it was possible to realize a working compensation process while demonstrating critical aspects that must be considered when establishing such approach.

Metabolic pathway and role of individual species in the bacterial consortium for biodegradation of azo dye: A biocalorimetric investigation

In this study, an attempt was made to investigate the functional role and metabolic behaviour of the monoculture (Staphylococcus lentus (SL), Bacillus flexus (BF) and Pseudomonas aeruginosa (PA)) in the bacterial biocenosis for biotransformation of an azo dye. The power-time profile obtained from consortia depicted three distinct peaks, which correlated well with the individual bacterial growth (PA > SL > BF), indicating the synergistic relation and division of labour in the biocenosis. The heat release pattern was used to identify the sequential behaviour of microbial consortia in real time. Yield calculation based on total heat liberated to the complete substrate utilization Y _(Q/S) for PA, SL, and BF were 15.99, 16.68, 7.32 kJ/L respectively. Similarly, the oxy calorific values Y _(Q/O) for the above species are respectively 386, 375, 440 kJ/mol and indicates the aerobic nature of microorganism employed. Further, the metabolome produced during the biotransformation were identified using Gas Chromatography-Mass Spectrometry (GC-MS), based on which a plausible pathway was predicted. The abundant metabolites were palmitic acid (m/z = 256) and diethyl phthalate (m/z = 222.2). The abundance of diethyl phthalate was much lesser in the consortia compared to the monoculture. Thus, the biocalorimetric heat yield calculation along with the stoichiometry and plausible pathway based biochemical elucidation provides a mechanistic basis for understanding the azo-dye biotransformation by the monocultures in consortia.

Study of Electrochemical Reduction of CO2 for Future Use in Secondary Microbial Electrochemical Technologies

The fluctuation and decentralization of renewable energy have triggered the search for respective energy storage and utilization. At the same time, a sustainable bioeconomy calls for the exploitation of CO₂ as feedstock. Secondary microbial electrochemical technologies (METs) allow both challenges to be tackled because the electrochemical reduction of CO₂ can be coupled with microbial synthesis. Because this combination creates special challenges, the electrochemical reduction of CO₂ was investigated under conditions allowing microbial conversions, that is, for their future use in secondary METs. A reproducible electrodeposition procedure of In on a graphite backbone allowed a systematic study of formate production from CO₂ with a high number of replicates. Coulomb efficiencies and formate production rates of up to 64.6±6.8 % and 0.013±0.002 mmol_formate  h^-1  cm^-2 , respectively, were achieved. Electrode redeposition, reusability, and long-term performance were investigated. Furthermore, the effect of components used in microbial media, that is, yeast extract, trace elements, and phosphate salts, on the electrode performance was addressed. The results demonstrate that the integration of electrochemical reduction of CO₂ in secondary METs can become technologically relevant.

A simple method for the measurement of metabolic heat production rates during solid-state fermentations using β-carotene production with Blakeslea trispora as a model system

Solid-state fermentation (SSF) technology has been rapidly developed for the past 10 years as a production platform for secondary metabolites, biofuels, food, and pharmaceuticals. Yet, the main drawback of SSF is the local temperature rise of up to 20 K, which potentially reduces the strain activity and inactivates heat sensible products. Due to the low heat capacity and thermal conductivity of mixtures of air with plant material, in comparison to aqueous suspensions in submerged fermentations, heat from metabolic processes is less efficiently dissipated. The exact knowledge of the metabolic heat generation during SSF processes is crucial to guide strategies against overheating. In this work, a simple method using a cost-efficient multichannel instrument is proposed, which allows the determination of heat generation during SSF processes. This method was successfully tested and validated with Blakeslea trispora producing β-carotene during growth on barley. Additionally, the consequences of the generated metabolic heat during SSF on temperature rise and water evaporation were discussed. Finally, changes in growth and product concentration could also be detected by the heat signal, implying the potential as a timesaving screening method.

Production of 2-Hydroxyisobutyric Acid from Methanol by Methylobacterium extorquens AM1 Expressing (R)-3-Hydroxybutyryl Coenzyme A-Isomerizing Enzymes

The biotechnological production of the methyl methacrylate precursor 2-hydroxyisobutyric acid (2-HIBA) via bacterial poly-3-hydroxybutyrate (PHB) overflow metabolism requires suitable (R)-3-hydroxybutyryl coenzyme A (CoA)-specific coenzyme B₁₂-dependent mutases (RCM). Here, we characterized a predicted mutase from Bacillus massiliosenegalensis JC6 as a mesophilic RCM closely related to the thermophilic enzyme previously identified in Kyrpidia tusciae DSM 2912 (M.-T. Weichler et al., Appl Environ Microbiol 81:4564-4572, 2015, https://doi.org/10.1128/AEM.00716-15). Using both RCM variants, 2-HIBA production from methanol was studied in fed-batch bioreactor experiments with recombinant Methylobacterium extorquens AM1. After complete nitrogen consumption, the concomitant formation of PHB and 2-HIBA was achieved, indicating that both sets of RCM genes were successfully expressed. However, although identical vector systems and incubation conditions were chosen, the metabolic activity of the variant bearing the RCM genes from strain DSM 2912 was severely inhibited, likely due to the negative effects caused by heterologous expression. In contrast, the biomass yield of the variant expressing the JC6 genes was close to the wild-type performance, and 2-HIBA titers of 2.1 g liter^-1 could be demonstrated. In this case, up to 24% of the substrate channeled into overflow metabolism was converted to the mutase product, and maximal combined 2-HIBA plus PHB yields from methanol of 0.11 g g^-1 were achieved. Reverse transcription-quantitative PCR analysis revealed that metabolic genes, such as methanol dehydrogenase and acetoacetyl-CoA reductase genes, are strongly downregulated after exponential growth, which currently prevents a prolonged overflow phase, thus preventing higher product yields with strain AM1.

IMPORTANCE

In this study, we genetically modified a methylotrophic bacterium in order to channel intermediates of its overflow metabolism to the C₄ carboxylic acid 2-hydroxyisobutyric acid, a precursor of acrylic glass. This has implications for biotechnology, as it shows that reduced C₁ substrates, such as methanol and formic acid, can be alternative feedstocks for producing today's commodities. We found that product titers and yields depend more on host physiology than on the activity of the introduced heterologous function modifying the overflow metabolism. In addition, we show that the fitness of recombinant strains substantially varies when they express orthologous genes from different origins. Further studies are needed to extend the overflow production phase in methylotrophic microorganisms for the implementation of biotechnological processes.