Standardisation of methods in soil microbiology: progress and challenges PDF
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Microbiology/Mycology VOL Praise for the First Edition: 28 MYCOLOGY VOLUME 28 “…an important volume. …a comprehen- Second sive review of the state of our knowledge Edition about how fungi function as individuals, populations, and members of the global economy of nature. Maheshwari has done F Fungi an exemplary job. …the integration of u information from such a broad area and n the general clarity of presentation found g Experimental Methods In Biology i in this volume deserve wide readership among mycologists, plant pathologists, E geneticists, and molecular biologists.” x Second Edition p —David S. Yohalem, East Malling Research, Kent, UK e r “The book is simply written and easy to digest, which is aided by the consistent i m editorial style throughout the book.” e —N. Louise Glass, Mycopathologia, 2006 n t “This book, in describing the modernization of mycology that has come from a l advances in biochemistry, genetics, and molecular biology, will serve as an M excellent introduction and reference for students and investigators …. As such, e the book sets an agenda for fungal research in the 21st century.” t h —Rowland H. Davis, University of California, Irvine o d “It should prove useful both for undergraduate students and postgraduate s researchers.” I n —David J. Adams, Microbiology Today B Fungi are now at the forefront of research on mechanisms in gene silencing, biological i o rhythm, mating processes, biogenesis of intracellular organelles, adaptations to l o hostile habitats, structure of natural populations, and speciation. The ease with g which yeasts and fungi can be cultivated in simple nutritive media has made these y eukaryotic organisms the choice material for basic and applied research. Following in the footsteps of its highly-praised predecessor, Fungi: Experimental Methods in Ramesh Maheshwari M Biology, Second Edition continues to be a comprehensive review of the state of our a knowledge about how fungi function. Extensively revised and updated, this second h e edition includes a glossary and new chapters on spores’ dormancy, germination, and s h uses; fungi as scavengers; and fungi as chemical factories. w a r K11776 i K11776_Cover.indd 1 8/23/11 9:27 AM Fungi Experimental Methods In Biology Second Edition MYCOLOGY SERIES Editor J. W. Bennett Professor Department of Plant Biology and Pathology Rutgers University New Brunswick, New Jersey Founding Editor Paul A. Lemke 1. Viruses and Plasmids in Fungi, edited by Paul A. Lemke 2. The Fungal Community: Its Organization and Role in the Ecosystem, edited by Donald T. Wicklow and George C. Carroll 3. Fungi Pathogenic for Humans and Animals (in three parts), edited by Dexter H. Howard 4. Fungal Differentiation: A Contemporary Synthesis, edited by John E. Smith 5. Secondary Metabolism and Differentiation in Fungi, edited by Joan W. Bennett and Alex Ciegler 6. Fungal Protoplasts, edited by John F. Peberdy and Lajos Ferenczy 7. Viruses of Fungi and Simple Eukaryotes, edited by Yigal Koltin and Michael J. Leibowitz 8. Molecular Industrial Mycology: Systems and Applications for Filamentous Fungi, edited by Sally A. Leong and Randy M. Berka 9. The Fungal Community: Its Organization and Role in the Ecosystem, Second Edition, edited by George C. Carroll and Donald T. Wicklow 10. Stress Tolerance of Fungi, edited by D. H. Jennings 11. Metal Ions in Fungi, edited by Günther Winkelmann and Dennis R. Winge 12. Anaerobic Fungi: Biology, Ecology, and Function, edited by Douglas O. Mountfort and Colin G. Orpin 13. Fungal Genetics: Principles and Practice, edited by Cees J. Bos 14. Fungal Pathogenesis: Principles and Clinical Applications, edited by Richard A. Calderone and Ronald L. Cihlar 15. Molecular Biology of Fungal Development, edited by Heinz D. Osiewacz 16. Pathogenic Fungi in Humans and Animals: Second Edition, edited by Dexter H. Howard 17. Fungi in Ecosystem Processes, John Dighton 18. Genomics of Plants and Fungi, edited by Rolf A. Prade and Hans J. Bohnert 19. Clavicipitalean Fungi: Evolutionary Biology, Chemistry, Biocontrol, and Cultural Impacts, edited by James F. White, Jr., Charles W. Bacon, Nigel L. Hywel-Jones, and Joseph W. Spatafora 20. Handbook of Fungal Biotechnology, Second Edition, edited by Dilip K. Arora 21. Fungal Biotechnology in Agricultural, Food, and Environmental Applications, edited by Dilip K. Arora 22. Handbook of Industrial Mycology, edited by Zhiqiang An 23. The Fungal Community: Its Organization and Role in the Ecosystem, Third Edition, edited by John Dighton, James F. White, and Peter Oudemans 24. F ungi: Experimental Methods in Biology, Ramesh Maheshwari 25. Food Mycology: A Multifaceted Approach to Fungi and Food, edited by Jan Dijksterhuis and Robert A. Samson 26. The Aspergilli: Genomics, Medical Aspects, Biotechnology, and Research Methods, edited by Gustavo H. Goldman and Stephen A. Osmani 27. Defensive Mutualism in Microbial Symbiosis, edited by James F. White, Jr. and Mónica S. Torres 28. Fungi: Experimental Methods In Biology, Second Edition, Ramesh Maheshwari Fungi Experimental Methods In Biology Second Edition Ramesh Maheshwari Indian Institute of Science Bangalore, India Front cover: The tube-like hyphae of the pink-orange mold Neurospora crassa are divided into multinuclear compartments by cross walls. The fungus was transformed with a gene from a jellyfish that encodes a green-fluorescent protein. Nuclei in living hyphae tagged by fusion of GFP to histone H1 gene were visualized by confocal microscopy. The nuclei become spindle-shaped (inset) as they move from one compartment to another compartment of branched hyphae through centrally perforated cross walls. This image was provided by Nick D. Read of the University of Edinburgh and is used with permission from Elsevier. Back cover: The plant-parasitic fungus Puccinia graminis tritici has been a scourge of mankind since ancient times. It infects stems and leaves of the wheat plant and forms rust-colored pustules. Each pustule contains countless numbers of wind-dissem- inated urediospores shown at top right. The fungus survives in stubble in the form of thick-walled bi-celled teliospores. The photographs were provided by Jacolyn A. Morrison of Cereal Rust Research Laboratory at the University of Minnesota. CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2012 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Version Date: 2011922 International Standard Book Number-13: 978-1-4398-3904-1 (eBook - PDF) This book contains information obtained from authentic and highly regarded sources. Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright holders of all material repro- duced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint. 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Perkins (1919–2007) Contents Preface to the First Edition ..............................................................................................................xv Preface to Second Edition ..............................................................................................................xvii About the Author ............................................................................................................................xix Part I The Unique Features of Fungi Chapter 1 The Hyphal Mode of Life ..................................................................................................................3 1.1 Features of Hyphae .................................................................................................................3 1.1.1 Apical Extension ........................................................................................................3 1.1.2 Spread and Longevity ................................................................................................4 1.1.3 Large Surface Area ....................................................................................................6 1.2 Hyphal Structure .....................................................................................................................8 1.2.1 Cell Wall ....................................................................................................................8 1.2.2 Glucan ........................................................................................................................9 1.2.3 Hydrophobin ............................................................................................................11 1.3 Internal Structure ..................................................................................................................12 1.3.1 Microtubules and Actin Filaments ..........................................................................12 1.3.2 Spitzenkörper and Polarisome .................................................................................16 1.3.3 Calcium ....................................................................................................................17 1.3.4 Vacuole .....................................................................................................................18 1.3.5 Septa and Woronin Body .........................................................................................18 1.4 Networking ............................................................................................................................18 1.4.1 Branching .................................................................................................................18 1.4.2 Hyphal Fusion ..........................................................................................................19 1.5 Main Functions .....................................................................................................................20 1.5.1 Nutrient Uptake ........................................................................................................20 1.5.2 Protein Secretion ......................................................................................................20 1.6 Morphogenesis ......................................................................................................................21 1.6.1 Hyphal Differentiation .............................................................................................22 1.6.2 Rhizomorph .............................................................................................................23 1.6.3 Mushroom Fruiting Body ........................................................................................23 1.7 Autophagy .............................................................................................................................24 1.8 Concluding Remarks .............................................................................................................24 References ........................................................................................................................................24 Chapter 2 The Multinuclear Condition .............................................................................................................29 2.1 Nuclear Number and Hyphal Growth Rate ...........................................................................29 2.2 Chromosome Numbers .........................................................................................................29 2.2.1 Classical Methods ....................................................................................................29 2.2.2 New Methods ...........................................................................................................30 2.3 Multiple Genomes in Individual Nuclei ................................................................................32 2.4 Nuclear Division Cycle .........................................................................................................33 2.4.1 Temperature-Sensitive Mutants ...............................................................................34 2.4.2 Stages in Nuclear Division Cycle .............................................................................34 vii viii Contents 2.5 Asynchronous Nuclear Divisions ..........................................................................................35 2.6 Nuclear Migration .................................................................................................................36 2.7 Nuclear Positioning and Gene Regulation ............................................................................36 2.8 Heterokaryosis ......................................................................................................................38 2.8.1 Sheltering of Lethal Mutation ..................................................................................39 2.8.2 Change in Nuclear Ratio ..........................................................................................40 2.8.3 Nuclear Competence ................................................................................................42 2.9 Parasexual Recombination ....................................................................................................43 2.10 Are All Nuclei Active Simultaneously? ................................................................................43 2.11 Concluding Remarks .............................................................................................................44 References ........................................................................................................................................44 Chapter 3 Spores: Their Dormancy, Germination, and Uses ...........................................................................47 3.1 Models for Cellular Processes ...............................................................................................47 3.2 Pleomorphism .......................................................................................................................48 3.3 Dissemination .......................................................................................................................50 3.4 Longevity ..............................................................................................................................50 3.5 Structure ................................................................................................................................50 3.5.1 Topography ..............................................................................................................50 3.5.2 Wall Structure ..........................................................................................................52 3.6 Water Relations .....................................................................................................................53 3.7 Endogenous Substrates ..........................................................................................................53 3.7.1 Lipids .......................................................................................................................53 3.7.2 Polyols ......................................................................................................................54 3.7.3 Trehalose ..................................................................................................................55 3.8 Link between Sporulation and Secondary Metabolism ........................................................55 3.9 Self-Reconditioning of Substratum .......................................................................................55 3.10 Germination Triggers ............................................................................................................56 3.10.1 Adhesion ..................................................................................................................56 3.10.2 Heat ..........................................................................................................................57 3.10.3 Light .........................................................................................................................57 3.10.4 Chemicals ................................................................................................................57 3.11 Material for Probing Fungal Physiology ...............................................................................58 3.11.1 Prerequisites for Development .................................................................................58 3.11.2 Release of Self-Inhibitors and Efflux of Carbon Compounds .................................58 3.11.3 Cold Dormancy ........................................................................................................59 3.11.4 Genome Activation ..................................................................................................59 3.11.5 Dark Fixation of CO ...............................................................................................60 2 3.11.6 Respiratory Increase ................................................................................................60 3.11.7 Regeneration of Reducing Power .............................................................................62 3.11.8 Synthetic Pathways ..................................................................................................62 3.11.9 Sensing, Signaling, and Transcriptional Changes ...................................................63 3.12 Applications ..........................................................................................................................64 3.12.1 Biocatalysis ..............................................................................................................64 3.12.2 Biocontrol .................................................................................................................64 3.13 Concluding Remarks .............................................................................................................65 References ........................................................................................................................................65 Contents ix Part II Fungi in Biosphere and Human Health Chapter 4 Fungi as Scavengers .........................................................................................................................71 4.1 Decay of Wood and Litter .....................................................................................................71 4.2 Clues from Microscopy .........................................................................................................72 4.3 White- and Brown-Rot Fungi ...............................................................................................73 4.4 Litter Decomposers ...............................................................................................................74 4.5 Degradation of Cell Wall Polymers ......................................................................................75 4.5.1 Lignin .......................................................................................................................75 4.5.2 Cellulose ..................................................................................................................84 4.5.3 Hemicellulose ..........................................................................................................86 4.6 Reactive Oxygen Species ......................................................................................................86 4.7 Unsolved Problems ................................................................................................................87 4.8 Clues from Genome Sequence ..............................................................................................87 4.9 Physiological Processes .........................................................................................................88 4.10 Concluding Remarks .............................................................................................................88 References ........................................................................................................................................89 Chapter 5 Fungi as Symbiotic Partners ............................................................................................................91 5.1 Mycorrhiza ............................................................................................................................91 5.1.1 Types of Mycorrhiza ................................................................................................91 5.1.2 Identification ............................................................................................................93 5.1.3 Development ............................................................................................................93 5.1.4 Carbohydrate Transfer .............................................................................................94 5.1.5 Phosphorus Transfer ................................................................................................95 5.1.6 Nitrogen Transfer .....................................................................................................95 5.1.7 Decomposition of Plant Residues ............................................................................96 5.1.8 Mycorrhiza as Conduits of Photosynthetically Fixed Carbon Compounds ............96 5.1.9 Cheating in Plant-Fungus Marriages .......................................................................99 5.1.10 Genome Sequence ..................................................................................................100 5.2 Endophytic Fungi ................................................................................................................100 5.3 Lichens ................................................................................................................................101 5.3.1 Mycobiont and Photobiont .....................................................................................102 5.3.2 In Situ Study ...........................................................................................................102 5.3.3 Synthesis ................................................................................................................102 5.3.4 Movement of Carbohydrate ...................................................................................103 5.4 Concluding Remarks ...........................................................................................................103 References ......................................................................................................................................103 Chapter 6 Fungi as Plant Pathogens ...............................................................................................................107 6.1 The Rust Fungi ....................................................................................................................107 6.1.1 Thigmotropism and Thigmomorphogenesis ..........................................................108 6.1.2 Haustorium .............................................................................................................110
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