Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure |
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Authors: | Sébastien Terrat Richard Christen Samuel Dequiedt Mélanie Lelièvre Virginie Nowak Tiffanie Regnier Dipankar Bachar Pierre Plassart Patrick Wincker Claudy Jolivet Antonio Bispo Philippe Lemanceau Pierre‐Alain Maron Christophe Mougel Lionel Ranjard |
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Affiliation: | 1. INRA‐Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, 17, rue Sully, B.V. 86510, 21065 Dijon Cedex, France.;2. INRA‐Université de Bourgogne, Plateforme GenoSol, CMSE, 17, rue Sully, B.V. 86510, 21065 Dijon Cedex, France.;3. CNRS UMR 6543, Laboratoire de Biologie Virtuelle, Centre de Biochimie, Parc Valose. F 06108 Nice, France;4. Université de Nice, UMR 6543, Laboratoire de Biologie Virtuelle, Centre de Biochimie, Parc Valose. F 06108 Nice, France.;5. Commissariat à l'Energie Antomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France;6. INRA Orléans – US 1106, Unité INFOSOL, Avenue de la Pomme de Pin – BP 20619 Ardon, 45166 Olivet cedex, France;7. ADEME, Service Agriculture et Forêt – 20, Avenue du Grésillé– BP 90406‐49004 Angers Cedex 01, France |
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Abstract: | Three soil DNA extraction procedures (homemade protocols and commercial kit) varying in their practicability were applied to contrasting soils to evaluate their efficiency in recovering: (i) soil DNA and (ii) bacterial diversity estimated by 16S rDNA pyrosequencing. Significant differences in DNA yield were systematically observed between tested procedures. For certain soils, 10 times more DNA was recovered with one protocol than with the others. About 15 000 sequences of 16S rDNA were obtained for each sample which were clustered to draw rarefaction curves. These curves, as well as the PCA ordination of community composition based on OTU clustering, did not reveal any significant difference between procedures. Nevertheless, significant differences between procedures were highlighted by the taxonomic identification of sequences obtained at the phylum to genus levels. Depending on the soil, differences in the number of genera detected ranged from 1% to 26% between the most and least efficient procedures, mainly due to a poorer capacity to recover populations belonging to Actinobacteria, Firmicutes or Crenarchaeota. This study enabled us to rank the relative efficiencies of protocols for their recovery of soil molecular microbial biomass and bacterial diversity and to help choosing an appropriate soil DNA extraction procedure adapted to novel sequencing technologies. |
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