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Microorganisms
Special Issues
Strategies for the Efficient Development of Microbial Bioprocesses
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Strategies for the Efficient Development of Microbial Bioprocesses

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: closed (31 January 2023) | Viewed by 9181

Special Issue Editors

Prof. Dr. Peter Neubauer

E-Mail Website
Guest Editor
Department of Bioprocess Engineering, Technische Universität Berlin, Ackerstraβe 76, ACK24, D-13355 Berlin, Germany
Interests: bioprocess development; Escherichia coli physiology; recombinant proteins; cocultivation; fed-batch; continuous culture
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Christoph Herwig

E-Mail Website
Guest Editor
Lisalis GmbH, Jenbachgasse 73-2, 1130 Vienna, Austria
Interests: biopharmaceutical process development
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The consistent development of new bioprocesses needs to be performed at the perspective of the final process scale. Therefore, an efficient bioprocess development should consider large‑scale effects and integrate them from early stages onwards together with process analytical technologies (PAT) and quality by design (QbD). This includes technical challenges (sensors, modelling), the cellular dynamic regulatory networks and population dynamics. Current progresses in automation and parallelization demand for a higher degree of digitalization and advanced data treatment. The aim of this Special Issue is to discuss the efficiency of the whole product and process life cycle, from the raw materials and early screening stages to industrial scale production and final application. This Special Issue is a joint project of the journals Microorganisms and Bioengineering and focuses on contributions at the 6th BioProScale Symposium and 7th BioProScale Symposium, which were organized as a digital event from 29–31 March 2021 and 28–31 March 2022, but further contributions are also invited on the following subjects:

Industrial-scale bioprocessing (scale-down and scale-up approaches, industrial-scale operation, population heterogeneity, process monitoring and advanced control, modelling of industrial-scale processes, mixing and reactor characterization, process robustness and repeatability, integrated upstream and downstream operations), process analytical technologies (PAT, multiparameter analysis, non-invasive sensors, single-cell based monitoring, soft sensors, fault identification and diagnosis, multiposition measurements, data handling and exploration, monitoring and control of co- and mixed cultures), high-throughput bioprocessing and automation (lab automation and robotics, automated screenings in bioprocess development, DoE, model‑based experimental designs, algorithm based operations and operational space characterisation, evolutionary strategies for strains and processes, communication trends for dynamic device operation and data flow, high-throughput strain engineering) and bioprocesses for a circular economy (waste streams to value-added products, pretreatment, feedstock flexibility, scale-up/scale-down of biorefinery concepts, closed carbon cycles, smart bioproduction grids, decentralised production).

The papers related to microbiology are welcome for Microorganisms, related to engineering and other fields are welcome for Bioengineering. The Joint Special Issue in Bioengineering: Strategies for the Efficient Development of Microbial Bioprocesses

Prof. Dr. Peter Neubauer
Prof. Dr. Christoph Herwig
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (3 papers)

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Research

22 pages, 9331 KiB  
Article
Impact of Elevated Levels of Dissolved CO2 on Performance and Proteome Response of an Industrial 2′-Fucosyllactose Producing Escherichia coli Strain
by Greta Gecse, André Vente, Mogens Kilstrup, Peter Becker and Ted Johanson
Microorganisms 2022, 10(6), 1145; https://doi.org/10.3390/microorganisms10061145 - 01 Jun 2022
Cited by 1 | Viewed by 1909
Abstract
Large-scale microbial industrial fermentations have significantly higher absolute pressure and dissolved CO2 concentrations than otherwise comparable laboratory-scale processes. Yet the effect of increased dissolved CO2 (dCO2) levels is rarely addressed in the literature. In the current work, we have [...] Read more.
Large-scale microbial industrial fermentations have significantly higher absolute pressure and dissolved CO2 concentrations than otherwise comparable laboratory-scale processes. Yet the effect of increased dissolved CO2 (dCO2) levels is rarely addressed in the literature. In the current work, we have investigated the impact of industrial levels of dCO2 (measured as the partial pressure of CO2, pCO2) in an Escherichia coli-based fed-batch process producing the human milk oligosaccharide 2′-fucosyllactose (2′-FL). The study evaluated the effect of high pCO2 levels in both carbon-limited (C-limited) and carbon/nitrogen-limited (C/N-limited) fed-batch processes. High-cell density cultures were sparged with 10%, 15%, 20%, or 30% CO2 in the inlet air to cover and exceed the levels observed in the industrial scale process. While the 10% enrichment was estimated to achieve similar or higher pCO2 levels as the large-scale fermentation it did not impact the performance of the process. The product and biomass yields started being affected above 15% CO2 enrichment, while 30% impaired the cultures completely. Quantitative proteomics analysis of the C-limited process showed that 15% CO2 enrichment affected the culture on the protein level, but to a much smaller degree than expected. A more significant impact was seen in the dual C/N limited process, which likely stemmed from the effect pCO2 had on nitrogen availability. The results demonstrated that microbial cultures can be seriously affected by elevated CO2 levels, albeit at higher levels than expected. Full article
(This article belongs to the Special Issue Strategies for the Efficient Development of Microbial Bioprocesses)
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17 pages, 2547 KiB  
Article
Microbiota Dynamics of Mechanically Separated Organic Fraction of Municipal Solid Waste during Composting
by Vladimir Mironov, Anna Vanteeva, Diyana Sokolova, Alexander Merkel and Yury Nikolaev
Microorganisms 2021, 9(9), 1877; https://doi.org/10.3390/microorganisms9091877 - 03 Sep 2021
Cited by 15 | Viewed by 2812
Abstract
Mechanical-biological treatment of municipal solid waste (MSW) facilitates reducing the landfill workload. The current research aimed to study general activity parameters, content, functions, and diversity of fungal and prokaryotic microbiota in mechanically separated organic fraction of MSW (ms-OFMSW) composting, without using bulking agents [...] Read more.
Mechanical-biological treatment of municipal solid waste (MSW) facilitates reducing the landfill workload. The current research aimed to study general activity parameters, content, functions, and diversity of fungal and prokaryotic microbiota in mechanically separated organic fraction of MSW (ms-OFMSW) composting, without using bulking agents and process-promoting additives. During 35 days of composting, vigorous emission of CO2 (max. 129.4 mg CO2 kg−1 h−1), NH3 (max. 0.245 mg NH3 kg−1 h−1), and heat release (max. 4.28 kJ kg−1 h−1) occurred, indicating intense microbial activity. Immediately following the preparation of the composting mixture, eight genera of lactic acid bacteria and fungal genera Rhizopus, Aspergillus, Penicillium, Agaricus, and Candida were predominant. When the temperature increased to more than 60 °C, the microbial biodiversity decreased. Due to succession, the main decomposers of ms-OFMSW changed. The Bacillaceae family, the genera Planifilum, Thermobifida, and Streptomyces, and the fungal genera Thermomyces and Microascus were involved in the processes of organic matter mineralization at the high-temperature and later stages. The biodiversity of the microbiota increased at the stages of cooling and maturation under conditions of relatively high nitrogen content. Thus, the microbial community and its succession during ms-OFMSW composting were characterized for the first time in this work. Full article
(This article belongs to the Special Issue Strategies for the Efficient Development of Microbial Bioprocesses)
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16 pages, 3266 KiB  
Article
Optimization of Culture Conditions for Oxygen-Tolerant Regulatory [NiFe]-Hydrogenase Production from Ralstonia eutropha H16 in Escherichia coli
by Qin Fan, Giorgio Caserta, Christian Lorent, Oliver Lenz, Peter Neubauer and Matthias Gimpel
Microorganisms 2021, 9(6), 1195; https://doi.org/10.3390/microorganisms9061195 - 31 May 2021
Cited by 6 | Viewed by 3206
Abstract
Hydrogenases are abundant metalloenzymes that catalyze the reversible conversion of molecular H2 into protons and electrons. Important achievements have been made over the past two decades in the understanding of these highly complex enzymes. However, most hydrogenases have low production yields requiring [...] Read more.
Hydrogenases are abundant metalloenzymes that catalyze the reversible conversion of molecular H2 into protons and electrons. Important achievements have been made over the past two decades in the understanding of these highly complex enzymes. However, most hydrogenases have low production yields requiring many efforts and high costs for cultivation limiting their investigation. Heterologous production of these hydrogenases in a robust and genetically tractable expression host is an attractive strategy to make these enzymes more accessible. In the present study, we chose the oxygen-tolerant H2-sensing regulatory [NiFe]-hydrogenase (RH) from Ralstonia eutropha H16 owing to its relatively simple architecture compared to other [NiFe]-hydrogenases as a model to develop a heterologous hydrogenase production system in Escherichia coli. Using screening experiments in 24 deep-well plates with 3 mL working volume, we investigated relevant cultivation parameters, including inducer concentration, expression temperature, and expression time. The RH yield could be increased from 14 mg/L up to >250 mg/L by switching from a batch to an EnPresso B-based fed-batch like cultivation in shake flasks. This yield exceeds the amount of RH purified from the homologous host R. eutropha by several 100-fold. Additionally, we report the successful overproduction of the RH single subunits HoxB and HoxC, suitable for biochemical and spectroscopic investigations. Even though both RH and HoxC proteins were isolated in an inactive, cofactor free apo-form, the proposed strategy may powerfully accelerate bioprocess development and structural studies for both basic research and applied studies. These results are discussed in the context of the regulation mechanisms governing the assembly of large and small hydrogenase subunits. Full article
(This article belongs to the Special Issue Strategies for the Efficient Development of Microbial Bioprocesses)
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