skip to main content


Title: Back to the future of soil metagenomics

Here, 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 ofmore » horizontal gene transfer in the stability of microbial communities? Do highly diverse microbial communities confer resistance and resilience in soils?« less
 [1] ;  [2] ;  [3] ;  [4] ;  [5] ;  [6] ;  [7] ;  [8] ;  [9] ;  [10] ;  [11] ;  [12] ;  [13] ;  [14] ;  [15] ;  [16] ;  [17] ;  [18] ;  [19] ;  [20] more »;  [21] ;  [22] ;  [23] ;  [24] ;  [25] ;  [26] ;  [27] ;  [28] ;  [29] ;  [30] ;  [25] ;  [31] ;  [32] ;  [33] ;  [34] ;  [35] ;  [36] ;  [37] ;  [38] ;  [14] ;  [39] ;  [30] ;  [40] ;  [41] ;  [41] ;  [42] ;  [43] ;  [14] « less
  1. Univ. de Lyon, Ecully (France); Helmholtz Zentrum Munchen Deutsches Forschungszentrum fur Gesundheit und Umwelt (GmbH), Neuherberg (Germany)
  2. Aix-Marseille Univ., Saint-Paul-lez Durance (France)
  3. Catholic Univ. of Louvain, Louvain-la-Neuve (Belgium); Yachay Tech Univ., Urcuqui (Ecuador)
  4. Centre for Ecology and Hydrology, Oxford (United Kingdom)
  5. Institute of Microbiology of the Czech Academy of Sciences, Praha (Czech Republic)
  6. Centre National de Genotypage, Evry (France)
  7. Norwegian Univ. of Life Sciences, Aas (Norway)
  8. Aix-Marseille Univ., Saint-Paul-lez-Durance (France)
  9. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  10. The Hebrew Univ. of Jerusalem, Rehovot (Israel)
  11. Technical Research Centre of Finland, Espoo (Finland)
  12. Utrecht Univ., Utrecht (Netherlands)
  13. Univ. Nacional de La Plata, La Plata (Argentina)
  14. Swansea Univ., Swansea (United Kingdom)
  15. Univ. de Bourgogne, Dijon (France)
  16. Univ. d'Evry Val d'Essonne, Evry (France)
  17. Univ. of Ljubljana, Ljubljana (Slovenia)
  18. Univ. of East Anglia, Norwich (United Kingdom)
  19. Oregon State Univ., Corvallis, OR (United States)
  20. NALINOV, Dremil Lafage (France)
  21. Univ. of Florence, Florence (Italy)
  22. Univ. of Waterloo, Waterloo, ON (Canada)
  23. National Univ. of Ireland, Cork (Ireland); Curtin Univ., Perth, WA (Australia)
  24. National Ecological Observatory Network, Boulder, CO (United States)
  25. Bielefeld Univ., Bielefeld (Germany)
  26. Rene Rachou Research Centre - CPqRR/FIOCRUZ, Belo Horizonte (Brazil)
  27. Consejo Superior de Investigaciones Cientificas, Granada (Spain)
  28. Federal Univ. of Pampa, Sao Gabriel (Brazil)
  29. Helmholtz Zentrum Munchen Deutsches Forschungszentrum fur Gesundheit und Umwelt (GmbH), Neuherberg (Germany)
  30. Univ. of Vienna, Vienna (Austria)
  31. AIT Austrian Institute of Technology GmbH, Tulln (Austria)
  32. Sodertorn Univ., Huddinge (Sweden)
  33. Univ. of Copenhagen, Frederiksberg (Denmark)
  34. Univ. of Copenhagen, Copenhagen (Denmark)
  35. Thunen-Institute of Biodiversity, Braunschweig (Germany)
  36. Univ. of Western Ontario, London, ON (Canada)
  37. Univ. of Patras, Agrinio (Greece)
  38. Univ. of Groningen, Groningen (Netherlands)
  39. Institute of Sustainability Sciences, Zurich (Switzerland)
  40. The Univ. of Hong Kong, Hong Kong (China)
  41. Shanghai Jiao Tong Univ., Shanghai (China)
  42. Chinese Academy of Sciences (CAS), Xiamen (China)
  43. Univ. de Lyon, Ecully (France)
Publication Date:
Report Number(s):
Journal ID: ISSN 1664-302X
Grant/Contract Number:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 1664-302X
Frontiers Research Foundation
Research Org:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org:
Country of Publication:
United States
58 GEOSCIENCES; 59 BASIC BIOLOGICAL SCIENCES; metagenomic; soil microbiology; terrestrial microbiology; soil ecology; microbial ecology
OSTI Identifier: