Microbial Environmental Genomics (MEG)

326 Pages·2016·9.014 MB·English

by  Francis Martin, Stephane Uroz (eds.)

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
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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