Link to originaL articLe Link to initiaL correspondence c1 Link to initiaL correspondence c2 We read with interest the comments on our Editorial (TerraGenome: a consortium for the sequencing of a whole-soil metagen- ome. Nature Rev. Microbiol. 7, 252 (2009)) 1 by Singh and colleagues (Soil genomics. Nature Rev. Microbiol. 7, 3 Aug 2009 (doi:10.1038/nrmicro2119-c1)) and Baveye (To sequence or not to sequence the whole- soil metagenome? Nature Rev. Microbiol. 7, 16 Sep 2009 (doi:10.1038.nrmicro2119-c2). Indeed, the soil metagenome is viewed increasingly as being crucial for biosphere function and human interdependence, and therefore the debate about methods for its exploration is warming up. The Terragenome international consor- tium initiative (http://www.terragenome. org/) will help coordinate efforts to fully explore and exploit the soil metagen- ome 1 . Although approaches vary, none is excluded even if global environmental DNA extraction techniques provide the highest (and most economically advanta- geous) genomic diversity. The tremendous quantity of genomic data extracted from the soil metagenome requires improved sequence analysis and better resources for function prediction. These resources are being supplied in part by initiatives to increase the number of individual micro- organisms that are sequenced and studied in terms of their ecosystem function and physiological characteristics (for example, the Genomic Encyclopedia of Bacteria and Archaea project (http://www.jgi.doe.gov/ programs/GEBA/)). This information is essential to provide a scaffold for metage- nomic studies, although the diversity of organisms studied in such initiatives is considerably less than that found in any one soil from which DNA has been extracted for metagenome analysis, for targeted sequencing or for the production of clone libraries. New technologies are necessary to understand the biological complexity of soil and the extensive diversity of the micro- biota present, especially the initial descrip- tive challenge from which functional and systems insights will be obtained. This is particularly relevant as the majority of the microorganisms in soil cannot yet be grown in the laboratory. A range of high- throughput and sophisticated molecular techniques have been developed to facilitate the analysis of soil biodiversity, including soil metagenomics for direct analysis and exploration of soil-extracted microbial- community DNA. This is the study and exploration of the collective genomes of all organisms present in a particular soil sample 2 and for the first time makes the prospect of completely sequencing a soil metagenome realistic. Owing to the enormity and complexity of the challenge of organizing this activity, so far only limited resources have been directed towards the sequencing of a soil metagenome, compared with those devoted to the human microbiome 3 or marine environments 4 . The deep metagenomic exploration of soil can provide information for the better manage- ment of this resource and for using informed approaches to ensure its functionality. To do this, the detail and range of microbial diver- sity should be described. We need to under- stand the extent of strain and species variation in soil and the fraction of the soil community that is active under a given condition. As well as determining the key functions of the community, we need to identify the dominant and rare community members (for example, bacteria, archaea, fungi, viruses and protists), determine their relative contributions to ecosystem functions and evaluate how the microbial community, as well as the physical and chemical composition of soils, varies at microscopic and macroscopic scales and over time. These data are useful for assessing and developing approaches to mitigate the effects of perturbations such as climate change, land-use change and anthropogenic inputs (including pollutants and fertilizers) on the composition, activity and function of the soil community. A coordinated approach for the study and assessment of soil biological diversity will push the boundaries of our knowledge. The lack of detailed knowledge of the world beneath our feet is alarming. This ignorance is a product of the small physical scale of the biota present, the magnitude of their diversity in space and time and, until recently, the lack of suitable analytical methods. Sequencing the soil metagenome is the first step to providing this informa- tion. Combined with other data, it will have considerable economic and environmental value, providing insights into the ecology of microorganisms that are beneficial to or threaten crop production, enhancing food security through the development of sus- tainable agricultural practices and ensuring the quality and provision of ecosystem services. The soil microbial community is also well known as a key resource for novel biocatalysts involved in either biosynthetic or biodegradation processes, including those that can be used for new drug dis- covery approaches 5–7 , the degradation of human-made polluting compounds 8–10 , the improvement of indispensable bioprocesses in the biotransformation industry, the pro- duction of biofuels 11 and the fundamentals of biodiversity and spatial complexity 12 . Soil metagenomics can only improve these activities, and the technological advances offered will provide fundamental data that will aid in sustaining the terrestrial environment. Timothy M. Vogel and Pascal Simonet are at the Environmental Microbial Genomics Group, Laboratoire AMPERE, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France. Penny R. Hirsch is at Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK. Janet K. Jansson is with the Lawrence Berkeley National Laboratory, Division of Earth Sciences, Berkeley, California 94720, USA. James M. Tiedje is at the Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA. Jan Dirk van Elsas is at the Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, PO BOX 14, 9750 AA Haren, The Netherlands. Renaud Nalin is at LibraGen, 3 rue des Satellites, 31400 Toulouse, France. Laurent Philippot is at the INRA, Université de Bourgogne, UMR Microbiologie du Sol et de l’Environnement, CMSE, BP 86510, 21065 Dijon cedex, France. Mark J. Bailey is at the Centre for Ecology & Hydrology, CEH-Wallingford, Maclean Building, Crowmarsh Gifford, Wallingford, Oxon OX10 8BB, UK. Correspondence to T.M.V., e-mail: timothy.vogel@ec-lyon.fr Advantages of the metagenomic approach for soil exploration: reply from Vogel et al . Timothy M. Vogel, Penny R. Hirsch, Pascal Simonet, Janet K. Jansson, James M. Tiedje, Jan Dirk van Elsas, Renaud Nalin, Laurent Philippot and Mark J. Bailey CorrespondenCe NATURE REVIEWS | Microbiology www.nature.com/reviews/micro © 2009 Macmillan Publishers Limited. All rights reserved