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Microorganisms
Special Issues
Microbial Cultivation and Analysis in Microsystems
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Microbial Cultivation and Analysis in Microsystems

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

Deadline for manuscript submissions: closed (30 November 2020) | Viewed by 17783

Special Issue Editors

Prof. Dr. Arum Han

E-Mail Website
Guest Editor
Dept. Electrical and Computer Engineering & Dept. Biomedical Engineering, Texas A&M University, College Station, TX, USA
Interests: microfluidics; lab-on-a-chip; biomems; microphysiological systems; organ on a chip
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

Special Issue Information

Dear Colleagues,

Cultivating microorganisms to produce renewable and high-value products, both at a laboratory scale and a production scale, requires a large amount of testing and analysis to be conducted. Microfluidic devices and lab-on-a-chip systems that can cultivate and analyze microorganisms in small nano- to pico-liter scale bioreactors have been developed extensively in the past decade, enabling microbial analysis down to single-cell resolution. In addition, micro-scale sensors that can be easily integrated into bioreactors, or made portable for sensing and analysis in the field, have been also developed. However, the true potential of such microdevices for microbial cultivation and analysis are only now being uncovered. It is expected that these sets of new technologies and devices will drive the field of microbial biotechnology in the decades to come. We are seeking excellent and innovative papers in the field of microdevices that will push the limit of current technologies to the next level, which can be broadly utilized in a range of microbial cultivation and analysis applications.

Possible example topics of interest for this Special Issue includes but is not limited to the following:

  • Micro-scale microfluidic bioreactors and bioreactor arrays;
  • Microfluidic systems for single cell analysis;
  • Microfluidic systems for high-throughput cultivation of microorganisms;
  • Microfluidic systems of high-throughput microorganism analysis;
  • Microfluidic systems for microorganism separation based on their properties;
  • Microfabricated sensors for portable microbial applications;
  • Microfabricated sensors that can be integrated into bioreactors of any sizes;
  • Integrated lab-on-a-chip systems that can conduct multiple microorganism handlings and analysis steps on a single chip.

Prof. Dr. Arum Han
Prof. Dr. Peter Neubauer
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.

Keywords

  • Microsystem
  • Microdevice
  • Microfluidics
  • Lab-on-a-chip
  • Bioprocess development
  • Microbial bioproduction
  • Microbial analysis
  • Single cell analysis
  • Microbioreactor

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Published Papers (3 papers)

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Research

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15 pages, 16796 KiB  
Article
The Architecture of Monospecific Microalgae Biofilms
by Andrea Fanesi, Armelle Paule, Olivier Bernard, Romain Briandet and Filipa Lopes
Microorganisms 2019, 7(9), 352; https://doi.org/10.3390/microorganisms7090352 - 13 Sep 2019
Cited by 28 | Viewed by 4433
Abstract
Microalgae biofilms have been proposed as an alternative to suspended cultures in commercial and biotechnological fields. However, little is known about their architecture that may strongly impact biofilm behavior, bioprocess stability, and productivity. In order to unravel the architecture of microalgae biofilms, four [...] Read more.
Microalgae biofilms have been proposed as an alternative to suspended cultures in commercial and biotechnological fields. However, little is known about their architecture that may strongly impact biofilm behavior, bioprocess stability, and productivity. In order to unravel the architecture of microalgae biofilms, four species of commercial interest were cultivated in microplates and characterized using a combination of confocal laser scanning microscopy and FTIR spectroscopy. In all the species, the biofilm biovolume and thickness increased over time and reached a plateau after seven days; however, the final biomass reached was very different. The roughness decreased during maturation, reflecting cell division and voids filling. The extracellular polymeric substances content of the matrix remained constant in some species, and increased over time in some others. Vertical profiles showed that young biofilms presented a maximum cell density at 20 μm above the substratum co-localized with matrix components. In mature biofilms, the maximum density of cells moved at a greater distance from the substratum (30–40 μm), whereas the maximum coverage of matrix components remained in a deeper layer. Carbohydrates and lipids were the main macromolecules changing during biofilm maturation. Our results revealed that the architecture of microalgae biofilms is species-specific. However, time similarly affects the structural and biochemical parameters. Full article
(This article belongs to the Special Issue Microbial Cultivation and Analysis in Microsystems)
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16 pages, 2592 KiB  
Article
Reproduction of Large-Scale Bioreactor Conditions on Microfluidic Chips
by Phuong Ho, Christoph Westerwalbesloh, Eugen Kaganovitch, Alexander Grünberger, Peter Neubauer, Dietrich Kohlheyer and Eric von Lieres
Microorganisms 2019, 7(4), 105; https://doi.org/10.3390/microorganisms7040105 - 19 Apr 2019
Cited by 27 | Viewed by 6343
Abstract
Microbial cells in industrial large-scale bioreactors are exposed to fluctuating conditions, e.g., nutrient concentration, dissolved oxygen, temperature, and pH. These inhomogeneities can influence the cell physiology and metabolism, e.g., decelerate cell growth and product formation. Microfluidic systems offer new opportunities to study such [...] Read more.
Microbial cells in industrial large-scale bioreactors are exposed to fluctuating conditions, e.g., nutrient concentration, dissolved oxygen, temperature, and pH. These inhomogeneities can influence the cell physiology and metabolism, e.g., decelerate cell growth and product formation. Microfluidic systems offer new opportunities to study such effects in great detail by examining responses to varying environmental conditions at single-cell level. However, the possibility to reproduce large-scale bioreactor conditions in microscale cultivation systems has not yet been systematically investigated. Hence, we apply computational fluid dynamics (CFD) simulations to analyze and compare three commonly used microfluidic single-cell trapping and cultivation devices that are based on (i) mother machines (MM), (ii) monolayer growth chambers (MGC), and (iii) negative dielectrophoresis (nDEP). Several representative time-variant nutrient concentration profiles are applied at the chip entry. Responses to these input signals within the studied microfluidic devices are comparatively evaluated at the positions of the cultivated cells. The results are comprehensively presented in a Bode diagram that illustrates the degree of signal damping depending on the frequency of change in the inlet concentration. As a key finding, the MM can accurately reproduce signal changes that occur within 1 s or slower, which are typical for the environmental conditions observed by single cells in large-scale bioreactors, while faster changes are levelled out. In contrast, the nDEP and MGC are found to level out signal changes occurring within 10 s or faster, which can be critical for the proposed application. Full article
(This article belongs to the Special Issue Microbial Cultivation and Analysis in Microsystems)
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Review

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19 pages, 1968 KiB  
Review
Separation, Characterization, and Handling of Microalgae by Dielectrophoresis
by Vinzenz Abt, Fabian Gringel, Arum Han, Peter Neubauer and Mario Birkholz
Microorganisms 2020, 8(4), 540; https://doi.org/10.3390/microorganisms8040540 - 9 Apr 2020
Cited by 28 | Viewed by 5978
Abstract
Microalgae biotechnology has a high potential for sustainable bioproduction of diverse high-value biomolecules. Some of the main bottlenecks in cell-based bioproduction, and more specifically in microalgae-based bioproduction, are due to insufficient methods for rapid and efficient cell characterization, which contributes to having only [...] Read more.
Microalgae biotechnology has a high potential for sustainable bioproduction of diverse high-value biomolecules. Some of the main bottlenecks in cell-based bioproduction, and more specifically in microalgae-based bioproduction, are due to insufficient methods for rapid and efficient cell characterization, which contributes to having only a few industrially established microalgal species in commercial use. Dielectrophoresis-based microfluidic devices have been long established as promising tools for label-free handling, characterization, and separation of broad ranges of cells. The technique is based on differences in dielectric properties and sizes, which results in different degrees of cell movement under an applied inhomogeneous electrical field. The method has also earned interest for separating microalgae based on their intrinsic properties, since their dielectric properties may significantly change during bioproduction, in particular for lipid-producing species. Here, we provide a comprehensive review of dielectrophoresis-based microfluidic devices that are used for handling, characterization, and separation of microalgae. Additionally, we provide a perspective on related areas of research in cell-based bioproduction that can benefit from dielectrophoresis-based microdevices. This work provides key information that will be useful for microalgae researchers to decide whether dielectrophoresis and which method is most suitable for their particular application. Full article
(This article belongs to the Special Issue Microbial Cultivation and Analysis in Microsystems)
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