Back to the Future of Soil Metagenomics

Joseph Nesme¹, Wafa Achouak², Spiros N Agathos³, Mark Bailey⁴, Petr Baldrian⁵, Dominique Brunel⁶, Åsa Frostegård⁷, Thierry Heulin², Janet K Jansson⁸, Edouard Jurkevitch⁹, Kristiina L Kruus¹⁰, George A Kowalchuk¹¹, Antonio Lagares¹², Hilary M Lappin-Scott¹³, Philippe Lemanceau¹⁴, Denis Le Paslier¹⁵, Ines Mandic-Mulec¹⁶, J Colin Murrell¹⁷, David D Myrold¹⁸, Renaud Nalin¹⁹, Paolo Nannipieri²⁰, Josh D Neufeld²¹, Fergal O'Gara²², John J Parnell²³, Alfred Pühler²⁴, Victor Pylro²⁵, Juan L Ramos²⁶, Luiz F W Roesch²⁷, Michael Schloter²⁸, Christa Schleper²⁹, Alexander Sczyrba³⁰, Angela Sessitsch³¹, Sara Sjöling³², Jan Sørensen³³, Søren J Sørensen³⁴, Christoph C Tebbe³⁵, Edward Topp³⁶, George Tsiamis³⁷, Jan Dirk van Elsas³⁸, Geertje van Keulen³⁹, Franco Widmer⁴⁰, Michael Wagner⁴¹, Tong Zhang⁴², Xiaojun Zhang⁴³, Liping Zhao⁴³, Yong-Guan Zhu⁴⁴, Timothy M Vogel⁴⁵, Pascal Simonet³⁹

Affiliations

¹ Environmental Microbial Genomics Group, Laboratoire Ampère, Centre National de la Recherche Scientifique, UMR5005, Institut National de la Recherche Agronomique, USC1407, Ecole Centrale de Lyon, Université de LyonEcully, France; Research Unit for Environmental Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)Neuherberg, Germany.
² Aix-Marseille Université, CEA, Centre National de la Recherche Scientifique, Laboratoire d'Écologie Microbienne de la Rhizosphère et Environnements Extrêmes, UMR 7265, Biologie Végétale et de Microbiologie Environnementales Saint-Paul-lez-Durance, France.
³ Earth and Life Institute, Catholic University of LouvainLouvain-la-Neuve, Belgium; School of Life Sciences and Biotechnology, Yachay Tech UniversityUrcuquí, Ecuador.
⁴ Natural Environment Research Council, Centre for Ecology and Hydrology Oxford, UK.
⁵ Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences Praha, Czech Republic.
⁶ Institut National de la Recherche Agronomique, US1279, Etude du Polymorphisme des Génomes Végétaux, CEA, Institut de Génomique, Centre National de Génotypage Evry, France.
⁷ NMBU Nitrogen Group, Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences Aas, Norway.
⁸ Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory Richland, WA, USA.
⁹ Department of Plant Pathology and Microbiology, The Faculty of Agriculture, Food and Environment, The Otto Warburg-Minerva Center in Agricultural Biotechnology, The Hebrew University of Jerusalem Rehovot, Israel.
¹⁰ Enzymology of Renewable Biomass, VTT, Technical Research Centre of Finland Espoo, Finland.
¹¹ Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University Utrecht, Netherlands.
¹² Departamento de Ciencia Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Centro Científico Tecnológico-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de La Plata La Plata, Argentina.
¹³ Department of Biosciences, Swansea University Swansea, UK.
¹⁴ Institut National de la Recherche Agronomique, UMR 1347, Agroécologie, Université de Bourgogne Dijon, France.
¹⁵ CEA/Direction des sciences du vivant/Institut de Génomique. Genoscope, Centre National de la Recherche Scientifiue UMR 8030, Université d'Evry Val d'Essonne Evry, France.
¹⁶ Department of Food Science and Technology, Biotechnical Faculty- University of Ljubljana Ljubljana, Slovenia.
¹⁷ School of Environmental Sciences, University of East Anglia Norwich, UK.
¹⁸ Department of Crop and Soil Science, Oregon State University Corvallis, OR, USA.
¹⁹ NALINOV Dremil Lafage, France.
²⁰ Department of Agrifood and Environmental Science, University of Florence Florence, Italy.
²¹ Department of Biology, University of Waterloo Waterloo, ON, Canada.
²² BIOMERIT Research Centre, School of Microbiology, National University of IrelandCork, Ireland; School of Biomedical Science, Curtin UniversityPerth, WA, Australia.
²³ National Ecological Observatory Network Boulder, CO, USA.
²⁴ Center for Biotechnology, Institute for Genome Research and Systems Biology, Genome Research of Industrial Microorganisms, Bielefeld University Bielefeld, Germany.
²⁵ Genomics and Computational Biology Group, René Rachou Research Centre - CPqRR/FIOCRUZ Belo Horizonte, Brazil.
²⁶ Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain.
²⁷ Federal University of Pampa São Gabriel, Brazil.
²⁸ Research Unit for Environmental Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) Neuherberg, Germany.
²⁹ Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna Vienna, Austria.
³⁰ Center for Biotechnology and Faculty of Technology, Computational Metagenomics, Bielefeld University Bielefeld, Germany.
³¹ Health and Environment Department, Bioresources, AIT Austrian Institute of Technology GmbH Tulln, Austria.
³² School of Natural Sciences and Environmental Studies, Södertörn University Huddinge, Sweden.
³³ Section of Genetics and Microbiology, Department of Plant and Environmental Microbiology, University of Copenhagen Frederiksberg, Denmark.
³⁴ Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark.
³⁵ Thünen-Institute of Biodiversity Braunschweig, Germany.
³⁶ Agriculture and Agri-Food Canada, Department of Biology, University of Western Ontario London, ON, Canada.
³⁷ Department of Environmental and Natural Resources Management, University of Patras Agrinio, Greece.
³⁸ Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen Groningen, Netherlands.
³⁹ Institute of Life Science, Medical School, Swansea University Swansea, UK.
⁴⁰ Molecular Ecology, Institute for Sustainability Sciences, Agroscope Zürich, Switzerland.
⁴¹ Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna Vienna, Austria.
⁴² Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong Hong Kong, China.
⁴³ Group of Microbial Ecology and Ecogenomics, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China.
⁴⁴ Institute of Urban Environment, Chinese Academy of Sciences Xiamen, China.
⁴⁵ Environmental Microbial Genomics Group, Laboratoire Ampère, Centre National de la Recherche Scientifique, UMR5005, Institut National de la Recherche Agronomique, USC1407, Ecole Centrale de Lyon, Université de Lyon Ecully, France.

PMID: 26903960
PMCID: PMC4748112
DOI: 10.3389/fmicb.2016.00073

Back to the Future of Soil Metagenomics

Joseph Nesme et al. Front Microbiol. 2016.

. 2016 Feb 10:7:73.

doi: 10.3389/fmicb.2016.00073. eCollection 2016.

Authors

Affiliations

¹ Environmental Microbial Genomics Group, Laboratoire Ampère, Centre National de la Recherche Scientifique, UMR5005, Institut National de la Recherche Agronomique, USC1407, Ecole Centrale de Lyon, Université de LyonEcully, France; Research Unit for Environmental Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)Neuherberg, Germany.
² Aix-Marseille Université, CEA, Centre National de la Recherche Scientifique, Laboratoire d'Écologie Microbienne de la Rhizosphère et Environnements Extrêmes, UMR 7265, Biologie Végétale et de Microbiologie Environnementales Saint-Paul-lez-Durance, France.
³ Earth and Life Institute, Catholic University of LouvainLouvain-la-Neuve, Belgium; School of Life Sciences and Biotechnology, Yachay Tech UniversityUrcuquí, Ecuador.
⁴ Natural Environment Research Council, Centre for Ecology and Hydrology Oxford, UK.
⁵ Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences Praha, Czech Republic.
⁶ Institut National de la Recherche Agronomique, US1279, Etude du Polymorphisme des Génomes Végétaux, CEA, Institut de Génomique, Centre National de Génotypage Evry, France.
⁷ NMBU Nitrogen Group, Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences Aas, Norway.
⁸ Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory Richland, WA, USA.
⁹ Department of Plant Pathology and Microbiology, The Faculty of Agriculture, Food and Environment, The Otto Warburg-Minerva Center in Agricultural Biotechnology, The Hebrew University of Jerusalem Rehovot, Israel.
¹⁰ Enzymology of Renewable Biomass, VTT, Technical Research Centre of Finland Espoo, Finland.
¹¹ Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University Utrecht, Netherlands.
¹² Departamento de Ciencia Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Centro Científico Tecnológico-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de La Plata La Plata, Argentina.
¹³ Department of Biosciences, Swansea University Swansea, UK.
¹⁴ Institut National de la Recherche Agronomique, UMR 1347, Agroécologie, Université de Bourgogne Dijon, France.
¹⁵ CEA/Direction des sciences du vivant/Institut de Génomique. Genoscope, Centre National de la Recherche Scientifiue UMR 8030, Université d'Evry Val d'Essonne Evry, France.
¹⁶ Department of Food Science and Technology, Biotechnical Faculty- University of Ljubljana Ljubljana, Slovenia.
¹⁷ School of Environmental Sciences, University of East Anglia Norwich, UK.
¹⁸ Department of Crop and Soil Science, Oregon State University Corvallis, OR, USA.
¹⁹ NALINOV Dremil Lafage, France.
²⁰ Department of Agrifood and Environmental Science, University of Florence Florence, Italy.
²¹ Department of Biology, University of Waterloo Waterloo, ON, Canada.
²² BIOMERIT Research Centre, School of Microbiology, National University of IrelandCork, Ireland; School of Biomedical Science, Curtin UniversityPerth, WA, Australia.
²³ National Ecological Observatory Network Boulder, CO, USA.
²⁴ Center for Biotechnology, Institute for Genome Research and Systems Biology, Genome Research of Industrial Microorganisms, Bielefeld University Bielefeld, Germany.
²⁵ Genomics and Computational Biology Group, René Rachou Research Centre - CPqRR/FIOCRUZ Belo Horizonte, Brazil.
²⁶ Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain.
²⁷ Federal University of Pampa São Gabriel, Brazil.
²⁸ Research Unit for Environmental Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) Neuherberg, Germany.
²⁹ Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna Vienna, Austria.
³⁰ Center for Biotechnology and Faculty of Technology, Computational Metagenomics, Bielefeld University Bielefeld, Germany.
³¹ Health and Environment Department, Bioresources, AIT Austrian Institute of Technology GmbH Tulln, Austria.
³² School of Natural Sciences and Environmental Studies, Södertörn University Huddinge, Sweden.
³³ Section of Genetics and Microbiology, Department of Plant and Environmental Microbiology, University of Copenhagen Frederiksberg, Denmark.
³⁴ Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark.
³⁵ Thünen-Institute of Biodiversity Braunschweig, Germany.
³⁶ Agriculture and Agri-Food Canada, Department of Biology, University of Western Ontario London, ON, Canada.
³⁷ Department of Environmental and Natural Resources Management, University of Patras Agrinio, Greece.
³⁸ Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen Groningen, Netherlands.
³⁹ Institute of Life Science, Medical School, Swansea University Swansea, UK.
⁴⁰ Molecular Ecology, Institute for Sustainability Sciences, Agroscope Zürich, Switzerland.
⁴¹ Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna Vienna, Austria.
⁴² Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong Hong Kong, China.
⁴³ Group of Microbial Ecology and Ecogenomics, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China.
⁴⁴ Institute of Urban Environment, Chinese Academy of Sciences Xiamen, China.
⁴⁵ Environmental Microbial Genomics Group, Laboratoire Ampère, Centre National de la Recherche Scientifique, UMR5005, Institut National de la Recherche Agronomique, USC1407, Ecole Centrale de Lyon, Université de Lyon Ecully, France.

PMID: 26903960
PMCID: PMC4748112
DOI: 10.3389/fmicb.2016.00073

No abstract available

Keywords: metagenomic; microbial ecology; soil ecology; soil microbiology; terrestrial microbiology.

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References

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1. Delmont T. O., Simonet P., Vogel T. M. (2013). Mastering methodological pitfalls for surviving the metagenomic jungle. Bioessays 35, 744–754. 10.1002/bies.201200155 - DOI - PubMed

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Back to the Future of Soil Metagenomics

Affiliations

Back to the Future of Soil Metagenomics

Authors

Affiliations

References

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