 |
 |
|
|
| HAL : hal-00630138, version 1 |
| DOI : 10.1111/j.1574-6941.2011.01140.x |
| Fiche détaillée |  Récupérer au format |
 |
| FEMS Microbiology Ecology 78, 1 (2011) 31-49 |
|
|
|
|
| Soil-specific limitations for access and analysis of soil microbial communities by metagenomics |
|
|
| Nathalie Lombard 1Emmanuel Prestat 1 |
|
|
| (10/2011) |
|
|
|
| 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. |
|
|
|
|
|
|
|
|
|
|
|
| 1 : | Ampère |
|
|
|
CNRS : UMR5005 – Université Claude Bernard - Lyon I – Institut National des Sciences Appliquées (INSA) - Lyon – Ecole Centrale de Lyon |
|
|
| 2 : | Department of Microbial Ecology |
|
|
|
University of Groningen |
|
|
|
|
|
|
|
|
|
| Domaine | : | Sciences de l'environnement Sciences du Vivant/Ecologie, Environnement |
|
|
| soil DNA extraction – microbial distribution – soil sampling – metagenomics – microbial diversity – metagenome sequencing – MOLECULAR-WEIGHT DNA – 16S RIBOSOMAL-RNA – NATURAL GENETIC-TRANSFORMATION – POLYMERASE-CHAIN-REACTION – SHORT READ DATA – BACTERIAL COMMUNITIES – PLASMID DNA – SPATIAL-DISTRIBUTION – ENVIRONMENTAL-SAMPLES – PROKARYOTIC DIVERSITY |
|
| hal-00630138, version 1 | |
| http://hal.archives-ouvertes.fr/hal-00630138 | |
| oai:hal.archives-ouvertes.fr:hal-00630138 | |
| Contributeur : Publications Ampère | |
| Soumis le : Vendredi 7 Octobre 2011, 14:12:58 | |
| Dernière modification le : Vendredi 7 Octobre 2011, 14:23:00 | |
