Advances in Biochemical Engineering/Biotechnology. Series Editor: T. Scheper.
Recently Published and Forthcoming Volumes. High Resolution Microbial.
124 Advances in Biochemical Engineering/Biotechnology Series Editor: T. Scheper
Editorial Board: S. Belkin • I. Endo • S.-O. Enfors • W.-S. Hu • B. Mattiasson • J. Nielsen • G. Stephanopoulos • G. T. Tsao R. Ulber • A.-P. Zeng • J.-J. Zhong • W. Zhou
Advances in Biochemical Engineering/Biotechnology Series Editor: T. Scheper Recently Published and Forthcoming Volumes High Resolution Microbial Single Cell Analytics Volume Editors: Müller S., Bley, T. Vol. 124, 2011 Bioreactor Systems for Tissue Engineering II Strategies for the Expansion and Directed Differentiation of Stem Cells Volume Editors: Kasper C., van Griensven M., Pörtner, R. Vol. 123, 2010 Biotechnology in China II Chemicals, Energy and Environment Volume Editors: Tsao, G.T., Ouyang, P., Chen, J. Vol. 122, 2010 Biosystems Engineering II Linking Cellular Networks and Bioprocesses Volume Editors: Wittmann, C., Krull, R. Vol. 121, 2010 Biosystems Engineering I Creating Superior Biocatalysts Volume Editors: Wittmann, C., Krull, R. Vol. 120, 2010
Disposable Bioreactors Volume Editor: Eibl, R., Eibl, D. Vol. 115, 2009 Engineering of Stem Cells Volume Editor: Martin, U. Vol. 114, 2009 Biotechnology in China I From Bioreaction to Bioseparation and Bioremediation Volume Editors: Zhong, J.J., Bai, F.-W., Zhang, W. Vol. 113, 2009 Bioreactor Systems for Tissue Engineering Volume Editors: Kasper, C., van Griensven, M., Poertner, R. Vol. 112, 2008 Food Biotechnology Volume Editors: Stahl, U., Donalies, U. E. B., Nevoigt, E. Vol. 111, 2008 Protein-Protein Interaction Volume Editors: Seitz, H., Werther, M. Vol. 110, 2008 Biosensing for the 21st Century Volume Editors: Renneberg, R., Lisdat, F. Vol. 109, 2007
Nano/Micro Biotechnology Volume Editors: Endo, I., Nagamune, T. Vol. 119, 2010
Biofuels Volume Editor: Olsson, L. Vol. 108, 2007
Whole Cell Sensing Systems II Volume Editors: Belkin, S., Gu, M.B. Vol. 118, 2010
Green Gene Technology Research in an Area of Social Conflict Volume Editors: Fiechter, A., Sautter, C. Vol. 107, 2007
Whole Cell Sensing Systems I Volume Editors: Belkin, S., Gu, M.B. Vol. 117, 2010 Optical Sensor Systems in Biotechnology Volume Editor: Rao, G. Vol. 116, 2009
Cell Separation Fundamentals, Analytical and Preparative Methods Volume Editors: Kumar, A., Galaev, I.Y., Mattiasson, B. Vol. 106, 2007
High Resolution Microbial Single Cell Analytics Volume Editors: Susann Müller Thomas Bley
With contributions by M. Berney L. M. Blank T. Bley P. Bombach C. L. Davey H. M. Davey T. Egli I. Fetzer R. Geyer J. A. J. Haagensen F. Hammes H. Harms T. Hübschmann S. Jakobs S. Kleinsteuber H. Kortmann S. Müller D. Neumann B. Regenberg A. Schmid J. D. Stenson C. Sternberg S. Stoldt C. R. Thomas K. Yasuda Z. Zhang
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Editors PH Dr. Susann Müller Helmholtz-Zentrum für Umweltforschung GmbH (UFZ) Dept. Umweltmikrobiologie Permoserstr. 15 04318 Leipzig Germany Email:
[email protected]
Prof. Dr. Thomas Bley TU Dresden Fak. Maschinenwesen Inst. Lebensmittel- und Bioverfahrenstechnik Bergstr. 120 01069 Dresden Sachsen Germany Email:
[email protected]
ISSN 0724-6145
e-ISSN 1616-8542
ISBN 978-3-642-16886-4
e-ISBN 978-3-642-16887-1
DOI 10.1007/978-3-642-16887-1 Springer Heidelberg Dordrecht London New York Springer-Verlag Berlin Heidelberg 2011 This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable to prosecution under the German Copyright Law. The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Cover design: WMXDesign GmbH, Heidelberg, Germany Printed on acid-free paper. Springer is part of Springer Science+Business Media (www.springer.com)
Series Editor Prof. Dr. T. Scheper Institute of Technical Chemistry University of Hannover Callinstraße 3 30167 Hannover, Germany
[email protected]
Volume Editors PH Dr. Susann Müller
Prof. Dr. Thomas Bley
Helmholtz-Zentrum für Umweltforschung GmbH (UFZ) Dept. Umweltmikrobiologie Permoserstr. 15 04318 Leipzig Germany
[email protected]
TU Dresden Fak. Maschinenwesen Inst. Lebensmittel- und Bioverfahrenstechnik Bergstr. 120 01069 Dresden Sachsen Germany
[email protected]
Editorial Board Prof. Dr. S. Belkin
Prof. Dr. W.-S. Hu
Interfaculty Biotechnology Program Institute of Life Sciences The Hebrew University of Jerusalem Jerusalem 91904, Israel
[email protected]
Chemical Engineering and Materials Science University of Minnesota 421 Washington Avenue SE Minneapolis, MN 55455-0132, USA
[email protected]
Prof. Dr. I. Endo Saitama Industrial Technology Center 3-12-18, Kamiaoki Kawaguchi-shi Saitama, 333-0844, Japan
[email protected]
Prof. Dr. B. Mattiasson Department of Biotechnology Chemical Center, Lund University P.O. Box 124, 221 00 Lund, Sweden
[email protected]
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Editorial Board
Prof. Dr. S.-O. Enfors
Prof. Dr. J. Nielsen
Department of Biochemistry and Biotechnology Royal Institute of Technology Teknikringen 34, 100 44 Stockholm, Sweden
[email protected]
Chalmers University of Technology Department of Chemical and Biological Engineering Systems Biology Kemivägen 10 41296 Göteborg Sweden
[email protected]
Prof. Dr. G. Stephanopoulos Department of Chemical Engineering Massachusetts Institute of Technology Cambridge, MA 02139-4307, USA
[email protected] Prof. Dr. G. T. Tsao Professor Emeritus Purdue University West Lafayette, IN 47907, USA
[email protected] [email protected] Prof. Dr. Roland Ulber FB Maschinenbau und Verfahrenstechnik Technische Universität Kaiserslautern Gottlieb-Daimler-Straße 67663 Kaiserslautern, Germany
[email protected] Prof. Dr. A.-P. Zeng Technische Universität Hamburg-Harburg Institut für Bioprozess- und Biosystemtechnik Denickestrasse 1 21073 Hamburg, Germany
[email protected]
Honorary Editors Prof. Dr. K. Schügerl Institute of Technical Chemistry University of Hannover, Callinstraße 3 30167 Hannover, Germany
[email protected]
Prof. Dr. J.-J. Zhong Bio-Building #3-311 College of Life Science & Biotechnology Key Laboratory of Microbial Metabolism, Ministry of Education Shanghai Jiao Tong University 800 Dong-Chuan Road Minhang, Shanghai 200240, China
[email protected] Dr. W. Zhou Sr. Director, BioProcess Engineering Technology Development Genzyme Corporation 45 New York Avenue Framingham, MA 01701-9322, USA
[email protected]
Advances in Biochemical Engineering/Biotechnology
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Advances in Biochemical Engineering/Biotechnology
Aims and Scope Advances in Biochemical Engineering/Biotechnology reviews actual trends in modern biotechnology. Its aim is to cover all aspects of this interdisciplinary technology where knowledge, methods and expertise are required for chemistry, biochemistry, microbiology, genetics, chemical engineering and computer science. Special volumes are dedicated to selected topics which focus on new biotechnological products and new processes for their synthesis and purification. They give the state-of-the-art of a topic in a comprehensive way thus being a valuable source for the next 3–5 years. It also discusses new discoveries and applications. In general, special volumes are edited by well-known guest editors. The series editor and publisher will however always be pleased to receive suggestions and supplementary information. Manuscripts are accepted in English. In references Advances in Biochemical Engineering/Biotechnology is abbreviated as Adv. Biochem. Engin./Biotechnol. and is cited as a journal. Special volumes are edited by well-known guest editors who invite reputed authors for the review articles in their volumes. Impact Factor in 2009: 4.165; Section ‘‘Biotechnology and Applied Microbiology’’: Rank 23 of 150
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Preface
Cells are individuals. Even microbial cells, which in case of some environmental bacteria present a size down to 0.4 or 0.5 lm, deviate from each other in terms of life cycle, protein composition, and metabolism. This heterogeneity results from distinct intrinsic cell features like age, stage in cell cycle and position of the division plane, gene transfer or loss, mutations, or epigenetic inheritance. Similarly, external parameters influence cellular features due to various micro-environmental inhomogeneities comprising, e.g., the availability of carbon or other sources of energy and of electron acceptors like oxygen and the prevalence of stress conditions like, e.g., mechanical pressure. All these parameters influence the efficiency of a cell in a biotechnological process. Since every cell contributes to the product yield of, e.g., a fermentation process in industrial biotechnology, dead, inactive or weakly active cells will limit this productivity. Therefore, single cell-related analytical techniques need to be involved in the evaluation and control of such processes. Although many of such technologies are already successfully used in medical sciences, where human cell populations are investigated with a new generation of amazing instruments, this is not true for microorganisms. One reason for this discrepancy is the priority of medical research in terms of funding. A more scientific point is the fact that microbial cells comprise only a thousandth of the volume of a normal blood cell and are therefore much more difficult to observe and to analyse. In recent years, however, microorganisms have started to come into the focus of many fields as, e.g., chemistry, which were since long thought to have no interest in these ‘un-steerable’ organisms. This is because microorganisms are not only tremendously diverse from a phylogenetic point of view, they also catalyse a wealth of biochemical processes which can be used, e.g., in white biotechnology or in energy producing processes like biogas production. Very often the organisms involved in such applications are still unknown with regard to affiliation and function. Since most of these microorganisms still cannot be cultivated as a pure culture, single cell techniques to follow their performance are of utmost interest and necessity.
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Still such techniques are expensive and often difficult to operate. Usually they are used in research laboratories to understand the very basic principles of microbial life. In a few cases, however, people have already tried to obtain information referring to individual microorganisms by using single cell technologies, either relying on sophisticated but also on cheaper equipment, based on chip- and microfluidic devices. Remarkable insights into cell behaviour have already been obtained by using such small-scale and sometimes partly disposable instrumentations. Population dynamics or subpopulation dynamics in biotechnologically or environmentally relevant processes are responsible for the variability in seemingly homogeneous populations under seemingly homogeneous micro-environmental conditions and result in surprisingly quick intra-population changes within a ‘stable’ process. Here, not only live/dead states play a crucial role in population development but also the above mentioned intrinsic parameters. For a deeper understanding and forecasting of the behaviour of microbial populations quantitative analysis and mapping into mathematical models will provide the indispensable theoretical foundations. In this context, we can make use of a broad panel of different model concepts. Their usefulness has to be proven by their ability to assign the characteristic features of single cells or of segregated subpopulations to the model variables. These models will ultimately allow to develop, control and enhance microbial performances in bioreactors or in locally confined, natural systems where microorganisms are used for distinct tasks. All in all, microbial single cell analytics evolved to a large degree within the last 10 years. Nevertheless, these technologies are still on the edge and have the potential to become far more usable and useful for basic research and for application in already well established microbial processes. We hope that this volume intrigues the reader to learn more about microorganism and their complexity but mainly on the techniques which can be used to understand their basic principles of live and survival. Highly resolved information on these small organisms will enable us to quantify their life and to orchestrate their abilities to a successful control and optimisation of bioprocesses. We would like to thank all the authors for their valuable contributions and discussions on the topic. We also want to thank Springer for implementation of this project as well as Thomas Scheper and Ingrid Samide for suggestions, ideas, and patience during the preparation of the volume. Spring, 2011
Susann Müller Thomas Bley
Contents
Light Microscopic Analysis of Mitochondrial Heterogeneity in Cell Populations and Within Single Cells. . . . . . . . . . . . . . . . . . . . . . . . . . Stefan Jakobs, Stefan Stoldt and Daniel Neumann Advanced Microscopy of Microbial Cells . . . . . . . . . . . . . . . . . . . . . . Janus A. J. Haagensen, Birgitte Regenberg and Claus Sternberg Algebraic and Geometric Understanding of Cells: Epigenetic Inheritance of Phenotypes Between Generations . . . . . . . . . . . . . . . . . Kenji Yasuda
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Measuring the Mechanical Properties of Single Microbial Cells . . . . . Colin R. Thomas, John D. Stenson and Zhibing Zhang
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Single Cell Analytics: An Overview . . . . . . . . . . . . . . . . . . . . . . . . . . Hendrik Kortmann, Lars M. Blank and Andreas Schmid
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Cultivation-independent Assessment of Bacterial Viability . . . . . . . . . Frederik Hammes, Michael Berney and Thomas Egli
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Resolution of Natural Microbial Community Dynamics by Community Fingerprinting, Flow Cytometry, and Trend Interpretation Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Petra Bombach, Thomas Hübschmann, Ingo Fetzer, Sabine Kleinsteuber, Roland Geyer, Hauke Harms and Susann Müller
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Multivariate Data Analysis Methods for the Interpretation of Microbial Flow Cytometric Data . . . . . . . . . . . . . . . . . . . . . . . . . . Hazel M. Davey and Christopher L. Davey
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From Single Cells to Microbial Population Dynamics: Modelling in Biotechnology Based on Measurements of Individual Cells . . . . . . . Thomas Bley
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Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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