Methods in Molecular Biology 1399 Francis Martin Stéphane Uroz Editors Microbial Environmental Genomics (MEG) M M B ETHODS IN OLECULAR IOLOGY Series Editor John M. Walker School of Life and Medical Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB , UK For further volumes: http://www.springer.com/series/7651 Microbial Environmental Genomics (MEG) Edited by Francis Martin UMR1136 INRA/University of Lorraine “Tree-Microbe Interactions” (IAM), Labex ARBRE, Champenoux, France Stéphane Uroz UMR1136 INRA/University of Lorraine “Tree-Microbe Interactions” (IAM), Labex ARBRE, Champenoux, France UMR1138 INRA “Biogeochemistry of Forest Ecosystems” (BEF), Labex ARBRE, Champenoux, France Editors Francis Martin Stéphane U roz UMR1136 INRA/University of Lorraine UMR1136 INRA/University of Lorraine “Tree-Microbe Interactions” (IAM) “Tree-Microbe Interactions” (IAM) Labex ARBRE Labex ARBRE Champenoux, France Champenoux, France UMR1138 INRA “Biogeochemistry of Forest Ecosystems” (BEF) Labex ARBRE Champenoux, F rance ISSN 1064-3745 ISSN 1940-6029 (electronic) Methods in Molecular Biology ISBN 978-1-4939-3367-9 ISBN 978-1-4939-3369-3 (eBook) DOI 10.1007/978-1-4939-3369-3 Library of Congress Control Number: 2015957951 Springer New York Heidelberg Dordrecht London © Springer Science+Business Media New York 2 016 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfi lms 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 specifi c 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 Humana Press is a brand of Springer Springer Science+Business Media LLC New York is part of Springer Science+Business Media (www.springer.com) Prefa ce Although microorganisms (archaea, bacteria), micro-eukaryotes (fungi), and macro- and mesofauna represent major components of the environment, we are far from appreciating their identity, diversity, functions, the interactions established between them, and lastly their relative impact on the ecosystem functioning [1, 2]. In both terrestrial and aquatic ecosys- tems, they represent a considerable fraction of the living biomass [3] and several studies have now highlighted their key role in processes such as nitrogen and methane cycles, organic matter degradation, soil quality, and plant health and nutrition [4]. Most of the current knowledge was generated using monospecifi c or reductionist approaches, balancing between cultivation-dependent (sampling of organisms, morpho/phenotyping, physiological and biochemical characterization) and -independent approaches mostly based on low-through- put sequencing technologies (e.g., fi ngerprinting or cloning/sequencing). Such approaches were, and remain, very important as they enroot the current physiological and biochemical knowledge of the microorganisms, macro- and mesofauna, and give the relevance to the content of gene or protein sequences of the international databases. However, the recent revolution in sequencing technologies with the advent of the high-t hroughput methods (454 pyrosequencing, Illumina, Ion Torrent, PacBio, etc.), associated with a real decrease in the sequencing cost, is now opening the way to really appreciate the tremendous distribution and diversity of our micro- and macroorganisms neighbors [5]. Aside from the sequence- based approach, more and more analysis based on high-t hroughput chemical screening of environmental libraries (genomic DNA and cDNA cloned in expression vectors) are devel- oped, revealing the common effort of the biologists to decipher the diversity and function of these organisms, especially the nonculturable and rare ones. At last, statistical analysis, mod- eling, and bioinformatics are rapidly becoming more accessible to single investigator labora- tories [6]. All these aspects have really revolutionized microbial ecology giving emergence to a new research fi eld entitled “Microbial Environmental Genomics.” Microbial environmen- tal genomics seeks to understand how organisms and gene functions are infl uenced by envi- ronmental (biotic and abiotic) cues while accounting for variation that takes place within and among environmental populations and communities. By combining multiscale and multidis- ciplinary methods, we are now able to depict the complex assembly of organisms of the environment and to decipher their functional role (Fig. 1 ). Such developments should per- mit to improve our ability to develop predictive models to better integrate the relative role of these organisms in the biogeochemical cycles and the ecosystem functioning [7]. In this context, this book presents a series of 17 chapters to guide research into the identifi cation of still unknown organisms, of novel functional genes, and how environmental conditions drive gene responses and the fi tness of the complex guilds of organisms inhabit- ing our environment. Methods to analyze the diversity of different organism types are pre- sented in Chapters 1 – 8 , covering the archaea, bacteria, fungi, protists, and soil fauna. Chapter 9 presents a method to decipher the interactions between fungi and trees using RNA stable isotope probing (RNA-SIP). Notably, methods to identify and characterize functions and functional diversity of both pro- and eukaryotes are presented in Chapters 1 0 – 16 . Those include protocols for gene hybridization (gene capture, geochips), DNA stable iso- tope probing, construction and screening of metagenomic and metatranscriptomic libraries, v vi Preface Fig. 1 C onceptual questioning in microbial environmental genomics. (a ) The different challenging questioning in microbial environmental genomics. (b ) The conceptual framework that needs to be integrated in models and for bioinformatics analyses (MG-RAST). Chapter 1 7 presents a method to analyze both taxonomic and functional diversity using ancient DNA. We envision that this book will serve as a primary research reference for researchers and research managers in environmental microbiology working in the expanding fi eld of molecular ecology and environmental genomics. The level of presentation is technically advanced with a strong emphasis on describing cutting-edge protocols in light of the possible future directions for research. Champenoux, France Francis Martin Stéphane Uroz Acknowledgments S. Uroz and F. Martin are supported by the French National Agency of Research (ANR) through the Laboratory of Excellence Arbre (ANR-11-LABX-0002-01). References 1 . Averill C, Turner BL, Finzi AC (2014) 5 . Z hou J, He Z, Yang Y, Deng Y, Tringe SG, Mycorrhiza-mediated competition between Alvarez-Cohen L (2015) High-throughput plants and decomposers drives soil carbon stor- metagenomic technologies for complex micro- age. Nature 505:543–545 bial community analysis: open and closed for- 2 . Bardgett RD, van der Putten WH (2014) mats. mBio 6:e02288-14 Belowground biodiversity and ecosystem func- 6 . Segata N, Boernigen D, Tickle TL, Morgan XC, tioning. Nature 515:505–511 Garrett WS, Huttenhower C (2013) 3 . Reid A, Greene SE (2012) How microbes can help Computational meta’omics for microbial com- feed the world. Report on an American Academy munity studies. Mol Syst Biol 9(1) of Microbiology Colloquium, Washington, DC 7. Treseder KK, Balser TC, Bradford MA, Brodie 4. Chaparro JM, Shefl in AM, Manter DK, Vivanco EL, Dubinsky EA, Eviner VT et al (2012) JM (2012) Manipulating the soil microbiome Integrating microbial ecology into ecosystem to increase soil health and plant fertility. Biol models: challenges and priorities. Biogeochemistry Fertil Soils 48:489–499 109:7–18 Contents Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x 1 “Deciphering Archaeal Communities” Omics Tools in the Study of Archaeal Communities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Lejla Pašić , Ana-Belen Martin-Cuadrado , and P urificación López-García 2 I nvestigating the Endobacteria Which Thrive in Arbuscular Mycorrhizal Fungi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 Alessandro Desirò , A lessandra S alvioli , and Paola B onfante 3 G enoSol Platform: A Logistic and Technical Platform for Conserving and Exploring Soil Microbial Diversity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 Samuel D equiedt , Pierre-Alain M aron , and Lionel R anjard 4 Sample Preparation for Fungal Community Analysis by High-Throughput Sequencing of Barcode Amplicons. . . . . . . . . . . . . . . . 61 Karina Engelbrecht C lemmensen , Katarina Ihrmark , Mikael B randström D urling , and B jörn D. L indahl 5 F ungal Communities in Soils: Soil Organic Matter Degradation . . . . . . . . . . 8 9 Tomáš Větrovský , Martina Š tursová , and Petr B aldrian 6 D NA-Based Characterization and Identification of Arbuscular Mycorrhizal Fungi Species. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 01 Carolina Senés-Guerrero and Arthur S chüßler 7 M olecular Identification of Soil Eukaryotes and Focused Approaches Targeting Protist and Faunal Groups Using High-Throughput Metabarcoding . . . . . . . . . . . . . . . . . . . . . . . . . . . 125 G. Arjen de Groot , I vo Laros , and Stefan G eisen 8 I dentification and In Situ Distribution of a Fungal Gene Marker: The Mating Type Genes of the Black Truffle. . . . . . . . . . . . . . . . . . . . . . . . . 141 Herminia De la Varga and Claude M urat 9 Stable-Isotope Probing RNA to Study Plant/Fungus Interactions. . . . . . . . . 1 51 Amandine L ê Van , Marie D uhamel , Achim Q uaiser , and Philippe V andenkoornhuyse 10 T argeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167 Céline Ribière , Réjane B eugnot , Nicolas P arisot , Cyrielle Gasc , Clémence D efois , J érémie D enonfoux , Delphine Boucher , Eric Peyretaillade , and Pierre Peyret 11 Hybridization of Environmental Microbial Community Nucleic Acids by GeoChip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 83 Joy D . V an Nostrand , Huaqin Y in , Liyou W u , T ong Y uan , and Jizhong Z hou vii viii Contents 12 Reconstruction of Transformation Processes Catalyzed by the Soil Microbiome Using Metagenomic Approaches . . . . . . . . . . . . . . . 197 Anne Schöler , Maria d e Vries , Gisle V estergaard , and Michael S chloter 13 M G-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207 Kevin P. Keegan , E lizabeth M . Glass , and Folker Meyer 14 Analysis of Active Methylotrophic Communities: When DNA-SIP Meets High-Throughput Technologies. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235 Martin T aubert , C arolina Grob , A lexandra M. Howat , Oliver J . Burns , Y in C hen , Josh D . N eufeld , and J. Colin M urrell 15 F unctional Metagenomics: Construction and High-T hroughput Screening of Fosmid Libraries for Discovery of Novel Carbohydrate-Active Enzymes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257 Lisa U farté , S ophie B ozonnet , E lisabeth L aville , D avide A . C ecchini , Sandra Pizzut-Serin , S amuel J acquiod , Sandrine Demanèche , Pascal Simonet , Laure F ranqueville , and G abrielle Potocki-Veronese 16 M etatranscriptomics of Soil Eukaryotic Communities . . . . . . . . . . . . . . . . . . 2 73 Rajiv K. Yadav , Claudia B ragalini , L aurence F raissinet-Tachet , Roland Marmeisse , and Patricia L uis 17 Analysis of Ancient DNA in Microbial Ecology. . . . . . . . . . . . . . . . . . . . . . . 289 Olivier Gorgé , E . A ndrew Bennett , Diyendo Massilani , J ulien Daligault , Melanie P ruvost , Eva-Maria G eigl , and T hierry Grange Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 17 Contributors E. A NDREW BENNETT • Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot , P aris , F rance G. A RJEN DE GROOT • ALTERRA-Wageningen UR , W ageningen, The Netherlands PETR BALDRIAN • Laboratory of Environmental Microbiology, I nstitute of Microbiology of the CAS , P raha 4, Czech Republic RÉJANE BEUGNOT • EA 4678, CIDAM, Clermont Université, Université d’Auvergne, Clermont-Ferrand, F rance PAOLA B ONFANTE • Department of Life Sciences and Systems Biology, U niversity of Turin , Turin, Italy DELPHINE B OUCHER • EA 4678, CIDAM, Clermont Université, Université d’Auvergne , Clermont-Ferrand, F rance SOPHIE B OZONNET • INSA, UPS, INP; LISBP, U niversité de Toulouse , T oulouse, F rance ; UMR792 Ingénierie des Systèmes Biologiques et des Procédés , INRA , Toulouse , France ; UMR5504, CNRS , Toulouse, France CLAUDIA BRAGALINI • Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364 , Université Lyon 1, Université de Lyon , Villeurbanne Cedex, F rance ; Department of Life Sciences and Systems Biology , U niversity of Turin , Turin, Italy MIKAEL B RANDSTRÖM DURLING • Department of Forest Mycology and Plant Pathology, Uppsala BioCenter , S wedish University of Agricultural Sciences, Uppsala, Sweden OLIVER J. BURNS • School of Biological Sciences, U niversity of East Anglia , Norwich, U K DAVIDE A. C ECCHINI • INSA, UPS, INP; LISBP, Université de Toulouse , T oulouse, France ; UMR792 Ingénierie des Systèmes Biologiques et des Procédés , INRA , Toulouse , France ; U MR5504, CNRS , Toulouse , France YIN CHEN • School of Life Sciences, University of Warwick , C oventry , U K JULIEN DALIGAULT • Institut Jacques Monod, UMR 7592, CNRS, U niversité Paris Diderot , Paris , F rance CLÉMENCE DEFOIS • EA 4678, CIDAM, Clermont Université, Université d’Auvergne , Clermont-Ferrand, F rance SANDRINE D EMANÈCHE • Laboratoire Ampère, CNRS UMR5005, Ecole Centrale de Lyon, Université de Lyon , E cully, France JÉRÉMIE D ENONFOUX • EA 4678, CIDAM, Clermont Université, Université d’Auvergne, Clermont-Ferrand, France ; G enoscreen, Campus de l’Institut Pasteur de Lille , L ille, France SAMUEL DEQUIEDT • INRA, UMR Agroécologie , D ijon Cedex, F rance ALESSANDRO D ESIRÒ • Department of Life Sciences and Systems Biology, University of Turin , Turin , I taly; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA MARIE DUHAMEL • UMR 6553 Ecobio, CNRS, Université de Rennes 1 , R ennes, F rance ; Department of Biology, Stanford University , Stanford , CA , USA KARINA ENGELBRECHT CLEMMENSEN • Department of Forest Mycology and Plant Pathology, Uppsala BioCenter , S wedish University of Agricultural Sciences , U ppsala , Sweden LAURENCE FRAISSINET-TACHET • Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364 , U niversité Lyon 1, Université de Lyon , V illeurbanne Cedex, F rance ix