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creativepro.com Omics in Soil Science Soil metagenome Microbial proteomic Strain resolution databases proteomic responses Strains Y O Q E X X M G K P I D T N U DPPPV DTDGN ADANY J L A F LPANR GGGLT PGHGR RCPLF VSQEA DGQRD C Z B M E H GLPVR IAPHG GAPSD W KIIRL STDVR ISFRA S G R YTTCV QSTEW HIDSE LVSGR RHVIT GPVRD PSPSG RENAF RIEKY OTUs-COGs KEGG Edited by Paolo Nannipieri Giacomo Pietramellara and Caister Academic Press Giancarlo Renella Omics in Soil Science Edited by Paolo Nannipieri Giacomo Pietramellara and Giancarlo Renella Department of Agrifood Production and Environmental Sciences University of Florence Italy Caister Academic Press Copyright © 2014 Caister Academic Press Norfolk, UK www.caister.com British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library ISBN: 978-1-908230-32-4 (hardback) ISBN: 978-1-908230-94-2 (ebook) Description or mention of instrumentation, software, or other products in this book does not imply endorsement by the author or publisher. The author and publisher do not assume responsibility for the validity of any products or procedures mentioned or described in this book or for the consequences of their use. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without the prior permission of the publisher. No claim to original U.S. Government works. Cover design adapted from Figure 6.1. Printed and bound in Great Britain Contents Contributors v Preface ix 1 Soil as a Biological System 1 Paolo Nannipieri, Giacomo Pietramellara and Giancarlo Renella 2 Functional Genomics Analysis of Key Bacterial Traits Involved in Rhizosphere Competence During Microbial–Host Interactions 9 Matthieu Barret, John P. Morrissey and Fergal O’Gara 3 Soil Metagenomics – Potential Applications and Methodological Problems 31 Jan Dirk van Elsas, Mariana Silvia Cretoiu, Anna Maria Kielak and Francisco Dini-Andreote 4 Screening Phylogenetic and Functional Marker Genes in Soil Microbial Ecology 45 Sotirios Vasileiadis, Edoardo Puglisi, PierSandro Cocconcelli and Marco Trevisan 5 Soil Metatranscriptomics 63 Yongkyu Kim, Carl-Eric Wegner and Werner Liesack 6 Soil Proteomics 95 Giancarlo Renella, Laura Giagnoni, Mariarita Arenella and Paolo Nannipieri 7 Soil Volatile Organic Compounds as Tracers for Microbial Activities in Soils 127 Heribert Insam 8 Proteogenomics: A New Integrative Approach for a Better Description of Protein Diversity Found in Soil Microflora 139 Céline Bland and Jean Armengaud iv | Contents 9 Analysis of Soil Metagenomes using the MEtaGenome ANalyser (MEGAN) 163 Daniel H. Huson and Nico Weber 10 Classical Techniques Versus Omics Approaches 179 David D. Myrold and Paolo Nannipieri Index 189 Contributors Mariarita Arenella Mariana Silvia Cretoiu Department of Agrifood Production and University of Groningen Environmental Sciences Groningen University of Firenze The Netherlands Italy [email protected] [email protected] Francisco Dini-Andreote Jean Armengaud Linneausborg CEA, DSV, IBEB, Lab Biochim System Perturb Groningen Bagnols-sur-Cèze The Netherlands France [email protected] [email protected] Jan Dirk van Elsas Matthieu Barret University of Groningen BIOMERIT Research Centre Groningen Department of Microbiology The Netherlands University College Cork [email protected] Cork Ireland Laura Giagnoni [email protected] Department of Agrifood Production and Environmental Sciences Céline Bland University of Firenze CEA, DSV, IBEB, Lab Biochim System Perturb Italy Bagnols-sur-Cèze [email protected] France [email protected] Daniel H. Huson Center for Bioinformatics PierSandro Cocconcelli University of Tübingen Istituto di Microbiologia Tübingen Università Cattolica del Sacro Cuore Germany Piacenza [email protected] Italy [email protected] vi | Contributors Heribert Insam Paolo Nannipieri University of Innsbruck Department of Agrifood Production and Institute of Microbiology Environmental Sciences Innsbruck University of Florence Austria Florence Italy [email protected] [email protected] Anna Maria Kielak Linneausborg Fergal O’Gara Groningen BIOMERIT Research Centre The Netherlands Department of Microbiology University College Cork [email protected] Cork Ireland Yongkyu Kim Max Planck Institute for Terrestrial [email protected] Microbiology Marburg Giacomo Pietramellara Germany Department of Agrifood Production and Environmental Sciences [email protected] University of Florence Florence Werner Liesack Italy Max Planck Institute for Terrestrial Microbiology [email protected] Marburg Germany Edoardo Puglisi Istituto di Microbiologia [email protected] Univesità Cattolica del Sacro Cuore Piacenza John P. Morrissey Italy Department of Microbiology University College Cork [email protected] Cork Ireland Giancarlo Renella Department of Agrifood Production and [email protected] Environmental Sciences University of Florence David D. Myrold Florence Department of Crop and Soil Science Italy Oregon State University Corvallis, OR [email protected] USA Marco Trevisan [email protected] Istituto di Chimica Agraria ed Ambientale Università Cattolica del Sacro Cuore Piacenza Italy [email protected] Contributors | vii Sotirios Vasileiadis Carl-Eric Wegner Istituto di Chimica Agraria ed Ambientale Max Planck Institute for Terrestrial Università Cattolica del Sacro Cuore Microbiology Piacenza Marburg Italy Germany [email protected] [email protected] Nico Weber Center for Bioinformatics University of Tübingen Tübingen Germany [email protected] Current books of interest Bioinformatics and Data Analysis in Microbiology 2014 The Cell Biology of Cyanobacteria 2014 Pathogenic Escherichia coli: Molecular and Cellular Microbiology 2014 Campylobacter Ecology and Evolution 2014 Burkholderia: From Genomes to Function 2014 Myxobacteria: Genomics, Cellular and Molecular Biology 2014 Next Generation Sequencing: Current Technologies and Applications 2014 Applications of Molecular Microbiological Methods 2014 Mollicutes: Molecular Biology and Pathogenesis 2014 Genome Analysis: Current Procedures and Applications 2014 Bacterial Toxins: Genetics, Cellular Biology and Practical Applications 2013 Bacterial Membranes: Structural and Molecular Biology 2014 Cold-Adapted Microorganisms 2013 Fusarium: Genomics, Molecular and Cellular Biology 2013 Prions: Current Progress in Advanced Research 2013 RNA Editing: Current Research and Future Trends 2013 Real-Time PCR: Advanced Technologies and Applications 2013 Microbial Efflux Pumps: Current Research 2013 Cytomegaloviruses: From Molecular Pathogenesis to Intervention 2013 Oral Microbial Ecology: Current Research and New Perspectives 2013 Bionanotechnology: Biological Self-assembly and its Applications 2013 Real-Time PCR in Food Science: Current Technology and Applications 2013 Bacterial Gene Regulation and Transcriptional Networks 2013 Bioremediation of Mercury: Current Research and Industrial Applications 2013 Neurospora: Genomics and Molecular Biology 2013 Rhabdoviruses 2012 Horizontal Gene Transfer in Microorganisms 2012 Microbial Ecological Theory: Current Perspectives 2012 Two-Component Systems in Bacteria 2012 Malaria Parasites: Comparative Genomics, Evolution and Molecular Biology 2013 Foodborne and Waterborne Bacterial Pathogens 2012 Yersinia: Systems Biology and Control 2012 Full details at www.caister.com Preface In 2013 the ‘genomic’ era gets to the age of 60 after the seminal papers by F. Crick and J. Watson where they showed the DNA molecular structure and formalized the central dogma in biology, i.e. the genetic information is encoded by DNA by the mean of its transcrip- tion into messenger RNA and by its further translation to proteins. Formalization of the universal biological programming language has indisputably revolutionized our cultural and scientific approaches in all biological sciences. Soil is a peculiar biological system with several distinctive properties including a huge microbial diversity (Chapter 1). Only a small percentage of microoganisms inhabiting soil is culturable and thus the majority of soil microbial species are unknown. Their characteriza- tion can give further insights in soil as a biological system. In addition the expression of genes of these unknown microbial species can synthesize unknown molecules, such as novel enzymes and antibiotics, whose use can have important implications for human activities and health. Chapters 3, 5 and 6 discuss advantages and disadvantages, including methodological problems, of studies on collective genomes, transcripts and proteins of soil. Bibliography on soil metagenomics is more extensive than those on soil metatranscriptomics and soil proteomics also due to the development of second generation sequencing technologies. However, the development of the latter is needed because the integration of metagenomics, metatranscriptomics and proteomics can give a more complete picture of living organisms. Protogenomics, involving both proteomics and metagenomics, is important because the detection of a specific protein can confirm the presence of protein encoding genes hypoth- esized by a metagenomic screening (Chapter 8). Bioinformatics is rapidly developing being important in all omics studies since both sequencing or mass spectrometry reads
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  • Supplementary Fig

    Supplementary Fig

    TAXONOMY phyrellus* L.D. Go´mez & Singer, Xanthoconium Singer, Xerocomus Que´l.) Taxonomical implications.—We have adopted a con- Paxillaceae Lotsy (Alpova C. W. Dodge, Austrogaster* servative approach to accommodate findings from Singer, Gyrodon Opat., Meiorganum*Heim,Melano- recent phylogenies and propose a revised classifica- gaster Corda, Paragyrodon, (Singer) Singer, Paxillus tion that reflects changes based on substantial Fr.) evidence. The following outline adds no additional Boletineae incertae sedis: Hydnomerulius Jarosch & suborders, families or genera to the Boletales, Besl however, excludes Serpulaceae and Hygrophoropsi- daceae from the otherwise polyphyletic suborder Sclerodermatineae Binder & Bresinsky Coniophorineae. Major changes on family level Sclerodermataceae E. Fisch. (Chlorogaster* Laessøe & concern the Boletineae including Paxillaceae (incl. Jalink, Horakiella* Castellano & Trappe, Scleroder- Melanogastraceae) as an additional family. The ma Pers, Veligaster Guzman) Strobilomycetaceae E.-J. Gilbert is here synonymized Boletinellaceae P. M. Kirk, P. F. Cannon & J. C. with Boletaceae in absence of characters or molecular David (Boletinellus Murill, Phlebopus (R. Heim) evidence that would suggest maintaining two separate Singer) families. Chamonixiaceae Ju¨lich, Octavianiaceae Loq. Calostomataceae E. Fisch. (Calostoma Desv.) ex Pegler & T. W. K Young, and Astraeaceae Zeller ex Diplocystaceae Kreisel (Astraeus Morgan, Diplocystis Ju¨lich are already recognized as invalid names by the Berk. & M.A. Curtis, Tremellogaster E. Fisch.) Index Fungorum (www.indexfungorum.com). In ad- Gyroporaceae (Singer) Binder & Bresinsky dition, Boletinellaceae Binder & Bresinsky is a hom- (Gyroporus Que´l.) onym of Boletinellaceae P. M. Kirk, P. F. Cannon & J. Pisolithaceae Ulbr. (Pisolithus Alb. & Schwein.) C. David. The current classification of Boletales is tentative and includes 16 families and 75 genera. For Suillineae Besl & Bresinsky 16 genera (marked with asterisks) are no sequences Suillaceae (Singer) Besl & Bresinsky (Suillus S.F.