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Back to the future of soil metagenomics

Journal Article · · Frontiers in Microbiology
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  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)
+ Show Author Affiliations
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 of horizontal gene transfer in the stability of microbial communities? Do highly diverse microbial communities confer resistance and resilience in soils?
Research Organization:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC05-76RL01830
OSTI ID:
1337254
Report Number(s):
PNNL-SA--116061
Journal Information:
Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Vol. 7; ISSN 1664-302X
Publisher:
Frontiers Research FoundationCopyright Statement
Country of Publication:
United States
Language:
English

References (26)

Brazilian Microbiome Project: Revealing the Unexplored Microbial Diversity—Challenges and Prospects journal October 2013
Isolation of bacterial DNA from soil journal January 1980
Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products journal October 1998
Soil eukaryotic functional diversity, a metatranscriptomic approach journal September 2007
Structure, fluctuation and magnitude of a natural grassland soil metagenome journal February 2012
Archaea predominate among ammonia-oxidizing prokaryotes in soils journal August 2006
Insights into the phylogeny and coding potential of microbial dark matter journal July 2013
Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes journal March 2015
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes journal May 2013
Ecology and exploration of the rare biosphere journal March 2015
Tackling soil diversity with the assembly of large, complex metagenomes journal March 2014
Detection of micro-organisms in soil after in situ hybridization with rRNA-targeted, fluorescently labelled oligonucleotides journal May 1992
Comparative Metagenomics of Microbial Communities journal April 2005
Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States journal October 2013
Characterization of Denitrification Gene Clusters of Soil Bacteria via a Metagenomic Approach journal November 2008
High diversity in DNA of soil bacteria. journal January 1990
The Earth Microbiome project: successes and aspirations journal August 2014
Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics journal April 2015
Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project journal January 2010
Mastering methodological pitfalls for surviving the metagenomic jungle: Prospects & Overviews journal June 2013
Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products journal October 1998
TerraGenome: a consortium for the sequencing of a soil metagenome journal April 2009
Characterization of Denitrification Gene Clusters of Soil Bacteria via a Metagenomic Approach journal November 2008
High diversity in DNA of soil bacteria. journal January 1990
Reconstructing Rare Soil Microbial Genomes using in situ Enrichments and Metagenomics dataset January 2015
Reconstructing Rare Soil Microbial Genomes using in situ Enrichments and Metagenomics dataset January 2015

Cited By (15)

Biophysical processes supporting the diversity of microbial life in soil journal August 2017
Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes journal June 2016
Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil journal April 2020
Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination journal March 2018
Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain) journal March 2018
Antibiotics and Antibiotics Resistance Genes Dissemination in Soils book January 2017
Advancements in Microbial Genome Sequencing and Microbial Community Characterization book January 2019
Phylogenetic diversity and metabolic potential of microbiome of natural healing clay from Chamliyal (J&K) journal July 2018
Microbial indicators for soil quality journal October 2017
Analysis of soil eDNA functional genes: potential to increase profitability and sustainability of pastoral agriculture journal July 2016
Managing soil microbiology: realising opportunities for the productive land-based sectors journal February 2018
New approaches for metagenome assembly with short reads journal February 2019
Simple discovery of bacterial biocatalysts from environmental samples through functional metaproteomics journal March 2017
Muddy Waters: Unintentional Consequences of Blue Carbon Research Obscure Our Understanding of Organic Carbon Dynamics in Seagrass Ecosystems journal May 2017
Biophysical processes supporting the diversity of microbial life in soil text January 2017

Figures / Tables (1)

TABLE 1(p. 3)table TABLE 1

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Related Subjects

58 GEOSCIENCES
59 BASIC BIOLOGICAL SCIENCES
metagenomic
microbial ecology
soil ecology
soil microbiology
terrestrial microbiology