Back to the Future of Soil Metagenomics
Joseph Nesme
(1)
,
Wafa Achouak
(2, 3)
,
Spiros N. Agathos
(4)
,
Mark Bailey
(5)
,
Petr Baldrian
(6)
,
Dominique Brunel
(7)
,
Asa Frostegard
(8)
,
Thierry Heulin
(2, 3)
,
Janet K. Jansson
(9)
,
Kristiina Kruus
(10)
,
George Kowalchuk
(11)
,
Antonio Lagares
(12)
,
Hilary Lappin-Scott
(13)
,
Philippe P. Lemanceau
(14)
,
Denis Le Paslier
(15)
,
Ines Mandic-Mulec
(16)
,
J. Colin Murrell
(17)
,
David Myrold
(18)
,
Renaud Nalin
(19)
,
Paolo Nannipieri
(20)
,
Josh Neufeld
(21)
,
Fergal O'Gara
(22)
,
John Parnell
(23)
,
Alfred Pühler
(24)
,
Victor Pylro
(25)
,
Juan Ramos
(26)
,
Luiz Roesch
(25)
,
Michael Schloter
(27)
,
Christa Schleper
(28)
,
Alexander Sczyrba
(29)
,
Angela Sessitsch
(30)
,
Sara Sjoling
(31)
,
Søren Sørensen
(32)
,
Christoph Tebbe
(33)
,
Edward Topp
(34)
,
George Tsiamis
(35)
,
Jan Dirk van Elsas
(36)
,
Geertje van Keulen
(13)
,
Franco Widmer
(37)
,
Michael Wagner
(38)
,
Tong Zhang
(39)
,
Xiaojun Zhang
(1)
,
Liping Zhao
(40)
,
Yong-Guan Zhu
(41)
,
Timothy M. Vogel
(1)
,
Pascal Simonet
(1)
1
BioIng -
Ampère, Département Bioingénierie
2 BIAM - Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB)
3 LEMIRE - Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes
4 UCL - UCL - Unité de Génie Biologique
5 Maclean Building, Benson Lane
6 Institute of Microbiology of the CAS
7 EPGV - Etude du Polymorphisme des Génomes Végétaux
8 Dept. of Chemistry Biotechnology and Food Science
9 PNNL - Pacific Northwest National Laboratory
10 Technical Research Centre of Finland
11 NIOO-KNAW - Netherlands Institute of Ecology
12 UNLP - Universidad Nacional de la Plata [Argentine]
13 Swansea University
14 MSE - Microbiologie du Sol et de l'Environnement
15 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
16 University of Ljubljana
17 School of Environmental Sciences [Norwich]
18 OSU - Oregon State University
19 LIBRAGEN S.A.
20 Dipartimento Scienza del Suolo e Nutrizione della Pianta
21 University of Waterloo [Waterloo]
22 School of Biomedical Science
23 School of Geosciences
24 Institut für Medizinische Mikrobiologie - Institute of Medical Microbiology
25 Fiocruz Minas - René Rachou Research Center / Instituto René Rachou [Belo Horizonte, Brésil]
26 GMRV - Grupo de Modelado y Realidad Virtual [Madrid]
27 Department for Terrestrial Ecogenetics
28 Archaea Biology and Ecogenomics Group
29 CeBiTec - Center for Biotechnology
30 AIT - Austrian Institute of Technology [Vienna]
31 School of Natural Sciences and Environmental Studies
32 Section of Microbiology [Copenhagen]
33 Thünen Institute of Biodiversity
34 AAFC - Agriculture and Agri-Food
35 Department of Environmental and Natural Resources Management
36 GELIFES, Department of Microbial Ecology
37 Institute for Sustainability Sciences
38 University of Kassel
39 RPI - Rensselaer Polytechnic Institute
40 Laboratory of Molecular Microbial Ecology and Ecogenomics, Department of Biological Sciences, School of Life Sciences and Biotechnology
41 Key Lab of Urban Environment and Health, Institute of Urban Environment
2 BIAM - Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB)
3 LEMIRE - Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes
4 UCL - UCL - Unité de Génie Biologique
5 Maclean Building, Benson Lane
6 Institute of Microbiology of the CAS
7 EPGV - Etude du Polymorphisme des Génomes Végétaux
8 Dept. of Chemistry Biotechnology and Food Science
9 PNNL - Pacific Northwest National Laboratory
10 Technical Research Centre of Finland
11 NIOO-KNAW - Netherlands Institute of Ecology
12 UNLP - Universidad Nacional de la Plata [Argentine]
13 Swansea University
14 MSE - Microbiologie du Sol et de l'Environnement
15 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
16 University of Ljubljana
17 School of Environmental Sciences [Norwich]
18 OSU - Oregon State University
19 LIBRAGEN S.A.
20 Dipartimento Scienza del Suolo e Nutrizione della Pianta
21 University of Waterloo [Waterloo]
22 School of Biomedical Science
23 School of Geosciences
24 Institut für Medizinische Mikrobiologie - Institute of Medical Microbiology
25 Fiocruz Minas - René Rachou Research Center / Instituto René Rachou [Belo Horizonte, Brésil]
26 GMRV - Grupo de Modelado y Realidad Virtual [Madrid]
27 Department for Terrestrial Ecogenetics
28 Archaea Biology and Ecogenomics Group
29 CeBiTec - Center for Biotechnology
30 AIT - Austrian Institute of Technology [Vienna]
31 School of Natural Sciences and Environmental Studies
32 Section of Microbiology [Copenhagen]
33 Thünen Institute of Biodiversity
34 AAFC - Agriculture and Agri-Food
35 Department of Environmental and Natural Resources Management
36 GELIFES, Department of Microbial Ecology
37 Institute for Sustainability Sciences
38 University of Kassel
39 RPI - Rensselaer Polytechnic Institute
40 Laboratory of Molecular Microbial Ecology and Ecogenomics, Department of Biological Sciences, School of Life Sciences and Biotechnology
41 Key Lab of Urban Environment and Health, Institute of Urban Environment
Wafa Achouak
- Fonction : Auteur
- PersonId : 750629
- IdHAL : wafa-achouak
- ORCID : 0000-0003-4297-6661
- IdRef : 077246810
Denis Le Paslier
- Fonction : Auteur
- PersonId : 742161
- IdHAL : denis-le-paslier
- ORCID : 0000-0003-4335-9956
- IdRef : 080524486
Alfred Pühler
- Fonction : Auteur
- PersonId : 929159
Christa Schleper
- Fonction : Auteur
- PersonId : 761568
- ORCID : 0000-0002-1918-2735
Alexander Sczyrba
- Fonction : Auteur
- PersonId : 784780
- ORCID : 0000-0002-4405-3847
Pascal Simonet
- Fonction : Auteur
- PersonId : 786
- IdHAL : pascal-simonet
- IdRef : 066970911
Résumé
Direct extraction and characterization of microbial community DNA through PCR amplicon surveys and metagenomics has revolutionized the study of environmental microbiology and microbial ecology. In particular, metagenomic analysis of nucleic acids provides direct access to the genomes of the “uncultivated majority.” Accelerated by advances in sequencing technology, microbiologists have discovered more novel phyla, classes, genera, and genes from microorganisms in the first decade and a half of the twenty-first century than since these “many very little living animalcules” were first discovered by van Leeuwenhoek (Table 1). The unsurpassed diversity of soils promises continued exploration of a range of industrial, agricultural, and environmental functions. The ability to explore soil microbial communities with increasing capacity offers the highest promise for answering many outstanding who, what, where, when, why, and with whom questions such as: Which microorganisms are linked to which soil habitats? How do microbial abundances change with changing edaphic conditions? How do microbial assemblages interact and influence one another synergistically or antagonistically? What is the full extent of soil microbial diversity, both functionally and phylogenetically? What are the dynamics of microbial communities in space and time? How sensitive are microbial communities to a changing climate? What is the role of horizontal gene transfer in the stability of microbial communities? Do highly diverse microbial communities confer resistance and resilience in soils?
| Origine | Publication financée par une institution |
|---|
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