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<title lang=en>Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure</title>
<creator>Terrat, Sebastien</creator>
<creator>Christen, Richard</creator>
<creator>Dequiedt, Samuel</creator>
<creator>Lelievre, Melanie</creator>
<creator>Nowak, Virginie</creator>
<creator>Regnier, Tiffanie</creator>
<creator>Bachar, Dipankar</creator>
<creator>Plassart, Pierre</creator>
<creator>Wincker, Patrick</creator>
<creator>Jolivet, Claudy</creator>
<creator>Bispo, Antonio</creator>
<creator>Lemanceau, Philippe</creator>
<creator>Maron, Pierre-Alain</creator>
<creator>Mougel, Christophe</creator>
<creator>Ranjard, Lionel</creator>
<contributor>Symbiose Marine (SM) ; Systématique, adaptation, évolution (SAE) ; Université Pierre et Marie Curie - Paris 6 (UPMC) - Centre National de la Recherche Scientifique (CNRS) - Université Pierre et Marie Curie - Paris 6 (UPMC) - Centre National de la Recherche Scientifique (CNRS) - Evolution Paris Seine ; Université Nice Sophia Antipolis (UNS) ; Université Côte d'Azur (UCA) - Université Côte d'Azur (UCA) - Centre National de la Recherche Scientifique (CNRS) - Université des Antilles et de la Guyane (UAG) - Université Pierre et Marie Curie - Paris 6 (UPMC) - Université Nice Sophia Antipolis (UNS) ; Université Côte d'Azur (UCA) - Université Côte d'Azur (UCA) - Université des Antilles et de la Guyane (UAG)</contributor>
<contributor>ADEME (French Environment and Energy Management Agency)</contributor>
<contributor> Regional Council of Burgundy</contributor>
<contributor> Genoscope (Evry, France)</contributor>
<contributor> French Scientific Group of Interest on soils</contributor>
<contributor> `GIS Sol', involving the French Ministry for Ecology and Sustainable Development (MEDAD)</contributor>
<contributor> French Ministry of Agriculture</contributor>
<contributor> French Institute for Environment (IFEN)</contributor>
<contributor> Environment and Energy Management Agency (ADEME)</contributor>
<contributor> French Institute for Research and Development (IRD)</contributor>
<contributor> National Institute for Agronomic Research (INRA)</contributor>
<description>International audience</description>
<source>ISSN: 1751-7915</source>
<source>Microbial Biotechnology</source>
<publisher>Wiley</publisher>
<identifier>hal-01546177</identifier>
<identifier>https://hal.archives-ouvertes.fr/hal-01546177</identifier>
<source>https://hal.archives-ouvertes.fr/hal-01546177</source>
<source>Microbial Biotechnology, Wiley, 2012, 5 (1), pp.135-141. 〈10.1111/j.1751-7915.2011.00307.x〉</source>
<identifier>DOI : 10.1111/j.1751-7915.2011.00307.x</identifier>
<relation>info:eu-repo/semantics/altIdentifier/doi/10.1111/j.1751-7915.2011.00307.x</relation>
<language>en</language>
<subject>[SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]</subject>
<type>info:eu-repo/semantics/article</type>
<type>Journal articles</type>
<description lang=en>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.</description>
<date>2012-01</date>
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