156 Advances in Biochemical Engineering/Biotechnology

Transcription

1 156 Advances in Biochemical Engineering/Biotechnology Series editor T. Scheper, Hannover, Germany Editorial Board S. Belkin, Jerusalem, Israel T. Bley, Dresden, Germany J. Bohlmann, Vancouver, Canada P.M. Doran, Hawthorn, Australia M.B. Gu, Seoul, Korea W.-S. Hu, Minneapolis, MN, USA B. Mattiasson, J. Nielsen, Gothenburg, Sweden H. Seitz, Potsdam, Germany R. Ulber, Kaiserslautern, Germany A.-P. Zeng, Hamburg, Germany J.-J. Zhong, Shanghai, China W. Zhou, Shanghai, China

2 Aims and Scope This book series reviews current trends in modern biotechnology and biochemical engineering. Its aim is to cover all aspects of these interdisciplinary disciplines, where knowledge, methods and expertise are required from chemistry, biochemistry, microbiology, molecular biology, chemical engineering and computer science. Volumes are organized topically and provide a comprehensive discussion of developments in the field over the past 3 5 years. The series also discusses new discoveries and applications. Special volumes are dedicated to selected topics which focus on new biotechnological products and new processes for their synthesis and purification. In general, 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 cited as a journal. More information about this series at

3 Rajni Hatti-Kaul Gashaw Mamo Bo Mattiasson Editors Anaerobes in Biotechnology With contributions by F. Burton R.A. B orner A. Dabir J. Daniell P.K. Dhakephalkar H. El Enshasy E.A. Elsayed M.E. Ersahin N.-U. Frigaard C.T.M.J. Frijters R. Hatti-Kaul V. Honkalas M.E. Kokko M. K opke S. Lal D.B. Levin M. Lin A.E. Mäkinen K. Malik R.A. Malek G. Mamo B. Mattiasson R. Munir S. Nagaraju N.Z. Othman J.A. Puhakka A. Schn urer S.D. Simpson R. Sparling M. Taillefer F.P. van der Zee J.B. van Lier E.W.J. van Niel M. Wadaan J. Wang M. Xu S.-T. Yang

4 Editors Rajni Hatti-Kaul Biotechnology, Department of Chemistry Center for Chemistry & Chemical Engineering Lund University Gashaw Mamo Biotechnology, Department of Chemistry Center for Chemistry & Chemical Engineering Lund University Bo Mattiasson Biotechnology, Department of Chemistry Center for Chemistry & Chemical Engineering Lund University ISSN ISSN (electronic) Advances in Biochemical Engineering/Biotechnology ISBN ISBN (ebook) DOI / Library of Congress Control Number: Springer International Publishing Switzerland 2016 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, 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. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer International Publishing AG Switzerland

5 Preface Anaerobes, the microorganisms that live and grow in environments deficient in oxygen, play a significant role in many processes which occur in nature, such as the production of biological dinitrogen, methane and hydrogen sulphide, the degradation of wastes, fermentation of organic matter and carbon dioxide fixation. They also play a vital role in human health in terms of causing infections but also constitute important microflora inside humans and animals that determines the state of their health. Long before the nature of anaerobes was understood, man has been using these microorganisms for the production of alcoholic beverages and for fermenting foods by lactic acid bacteria for preservation. Because of their complex metabolism, special cultivation requirements and slow growth, anaerobes have been less explored than their aerobic counterparts. Over the years, however, the applications of these microorganisms have been growing dramatically. Several of the initial well, known large-scale applications include biogas production, wastewater treatment, and vinegar and wine production. In spite of these important processes, anaerobes have often been neglected in favour of aerobes, which are easier to handle. However, the anaerobic microflora promise an interesting metabolic potential which seems to show promise for future development in industrial biotechnology. Lately, driven by the emergence of new techniques and research and development activities to enable a transition from fossil-based to biobased economy to lower greenhouse gas emissions and toxic wastes, there has been a surge in the amount of information concerning anaerobes and in exploiting their potential in depolymerisation of biomass and production of different chemicals and energy carriers. This volume on Anaerobes in Biotechnology was thus planned to bring attention to this important group of diverse microorganisms and to highlight their potential beyond what is commonly known. As many anaerobes are living in very complex microbial consortia, isolation of individual organisms has been rather cumbersome. While next-generation sequencing technologies have started to provide new insights into the total community of v

6 vi Preface microorganisms, new technologies to isolate and cultivate anaerobes have also been developed which are covered in this book. It is clearly seen from this volume that dramatic developments have taken place during a few decades in understanding the diversity of anaerobes in different anoxic environments, including deep sea sediments associated with enormous methane hydrate deposits, and identification of new enzymes and metabolic pathways used by the anaerobes for the breakdown of complex organic matter and metabolism of sugars and gases that are now utilized to develop processes. There is also an improved understanding of the role of anaerobes as engines that run the biogeochemical cycles, which greatly benefit environmental technology such as bioremediation. This volume not only updates the roles of anaerobes in the production of energy carriers but also elucidates the advantages of anaerobe-based microbial fuel cells that extract energy from organic matter and generate electricity. The relatively recent progress made in the applications of anaerobes and their enzyme systems for production of solvents and organic acids is highlighted. Furthermore, the important role of anaerobes as probiotics and as a source of novel antimicrobial drugs for providing health benefits and overcoming the problem of bacterial drug resistance is described. The human microbiome is playing a far more important role in the wellbeing of individuals than anticipated earlier. All the applications of anaerobes require good cultivation systems and hence progress made in anaerobic bioreactors has been included. Novel process concepts have been applied to develop high cell density fermentations and for harvesting the inhibitory products in situ while maintaining the cells in a viable, active state. One can expect much more focus on anaerobes in the years to come with respect to the discovery of novel organisms, a better understanding of their genome, metabolic pathways, enzymes, etc. and the development of tools for their genetic manipulation concomitantly with the emergence of new applications using pure or mixed cultures, and their molecules. We, as editors of this volume, have learnt a lot from the various contributions from scientists who are experts in the field. We would like to thank all the authors for their efforts and for making this book an interesting, valuable source of information on anaerobic biotechnology. We would also like to thank the Series editor of Advances in Biochemical Engineering/Biotechnology for believing in the importance of anaerobes for biotechnology and encouraging us to edit this volume. Rajni Hatti-Kaul Gashaw Mamo Bo Mattiasson

7 Contents Anaerobes in Industrial- and Environmental Biotechnology... 1 Rajni Hatti-Kaul and Bo Mattiasson Isolation and Cultivation of Anaerobes Rosa Arag~ao B orner Glycolysis as the Central Core of Fermentation M. Taillefer and R. Sparling Comparative Genomics of Core Metabolism Genes of Cellulolytic and Non-cellulolytic Clostridium Species Sadhana Lal and David B. Levin Enzyme Systems of Anaerobes for Biomass Conversion Riffat Munir and David B. Levin Biotechnology of Anoxygenic Phototrophic Bacteria Niels-Ulrik Frigaard Biological Processes for Hydrogen Production Ed W. J. van Niel Biogas Production: Microbiology and Technology Anna Schn urer Life in the Anoxic Sub-Seafloor Environment: Linking Microbial Metabolism and Mega Reserves of Methane Hydrate Varsha Honkalas, Ashwini Dabir, and Prashant K. Dhakephalkar Anaerobes in Bioelectrochemical Systems Marika E. Kokko, Annukka E. Mäkinen, and Jaakko A. Puhakka vii

8 viii Contents Low-Carbon Fuel and Chemical Production by Anaerobic Gas Fermentation James Daniell, Shilpa Nagaraju, Freya Burton, Michael K opke, and Séan Dennis Simpson Anaerobic Fermentation for Production of Carboxylic Acids as Bulk Chemicals from Renewable Biomass Jufang Wang, Meng Lin, Mengmeng Xu, and Shang-Tian Yang Development of Anaerobic High-Rate Reactors, Focusing on Sludge Bed Technology J.B. van Lier, F.P. van der Zee, C.T.M.J. Frijters, and M.E. Ersahin Anaerobic Probiotics: The Key Microbes for Human Health Hesham El Enshasy, Khairuddin Malik, Roslinda Abd Malek, Nor Zalina Othman, Elsayed Ahmed Elsayed, and Mohammad Wadaan Anaerobes as Sources of Bioactive Compounds and Health Promoting Tools Gashaw Mamo Index