Soil-specific limitations for access and analysis of soil microbial communities by metagenomics
2011
Lombard, Nathalie | Prestat, Emmanuel | van Elsas, Jan, Dirk | Simonet, Pascal | Ampère (AMPERE) ; École Centrale de Lyon (ECL) ; Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL) ; Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon) ; Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | Department of Microbial Ecology ; University of Groningen [Groningen] | Office of Naval Research N000140610090-P00005 National Institutes of Environmental Health Sciences SRP R01ES016197-01 | ANR-07-POGM-0002,SEPTANTE,SEcond volet des études d'impact de Plantes TrANnsgéniques sur les bacTéries de l'Environnement(2007)
International audience
Показать больше [+] Меньше [-]Английский. Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. Its physicochemical properties affect microbial distributions inside the soil matrix, metagenome extraction and its subsequent analyses. To better understand the bias inherent to soil metagenome 'processing', we focus on soil physicochemical properties and their effects on the perceived bacterial distribution. In the light of this information, each step of soil metagenome processing is then discussed, with an emphasis on strategies for optimal soil sampling. Then, the interaction of cells and DNA with the soil matrix and the consequences for microbial DNA extraction are examined. Soil DNA extraction methods are compared and the veracity of the microbial profiles obtained is discussed. Finally, soil metagenomic sequence analysis and exploitation methods are reviewed.
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