Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

Nathalie Lombard (1) , Emmanuel Prestat (1) , Jan Dirk van Elsas (2) , Pascal Simonet (1)

1 AMPERE - Ampère
2 Department of Microbial Ecology

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.

Mots clés: SHORT READ DATA; BACTERIAL COMMUNITIES; PLASMID DNA; SPATIAL-DISTRIBUTION; ENVIRONMENTAL-SAMPLES; PROKARYOTIC DIVERSITY; soil DNA extraction; microbial distribution; soil sampling; metagenomics; microbial diversity; metagenome sequencing; MOLECULAR-WEIGHT DNA; 16S RIBOSOMAL-RNA; NATURAL GENETIC-TRANSFORMATION; POLYMERASE-CHAIN-REACTION

Domaines: Sciences de l'environnement; Ecologie, Environnement

Nathalie Lombard, Emmanuel Prestat, Jan Dirk van Elsas, Pascal Simonet. Soil-specific limitations for access and analysis of soil microbial communities by metagenomics. FEMS Microbiology Ecology, 2011, 78 (1), pp.31-49. ⟨10.1111/j.1574-6941.2011.01140.x⟩. ⟨hal-00630138⟩