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Diversity of Bacterial Communities in a Profile of a Winter Wheat Field: Known and Unknown Members

  • Soil Microbiology
  • Published:
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Abstract

In soils, bacteria are very abundant and diverse. They are involved in various agro-ecosystem processes such as the nitrogen cycle, organic matter degradation, and soil formation. Yet, little is known about the distribution and composition of bacterial communities through the soil profile, particularly in agricultural soils, as most studies have focused only on topsoils or forest and grassland soils. In the present work, we have used bar-coded pyrosequencing analysis of the V3 region of the 16S rRNA gene to analyze bacterial diversity in a profile (depths 10, 25, and 45 cm) of a well-characterized field of winter wheat. Taxonomic assignment was carried out with the Ribosomal Database Project (RDP) Classifier program with three bootstrap scores: a main run at 0.80, a confirmation run at 0.99, and a run at 0 to gain information on the unknown bacteria. Our results show that biomass and bacterial quantity and diversity decreased greatly with depth. Depth also had an impact, in terms of relative sequence abundance, on 81 % of the most represented taxonomic ranks, notably the ranks Proteobacteria, Bacteroidetes, Actinobacteridae, and Acidobacteria. Bacterial community composition differed more strongly between the topsoil (10 and 25 cm) and subsoil (45 cm) than between levels in the topsoil, mainly because of shifts in the carbon, nitrogen, and potassium contents. The subsoil also contained more unknown bacteria, 53.96 % on the average, than did the topsoil, with 42.06 % at 10 cm and 45.59 % at 25 cm. Most of these unknown bacteria seem to belong to Deltaproteobacteria, Actinobacteria, Rhizobiales, and Acidobacteria.

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Acknowledgments

We would like to thank Gembloux Agro-Bio Tech - University of Liège for financially supporting this study.

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Authors and Affiliations

  1. Unité de Microbiologie et Génomique, Université de Liège, Gembloux Agro-Bio Tech, Avenue Maréchal Juin 6, 5030, Gembloux, Belgium

    Aurore Stroobants, Florine Degrune, Daniel Portetelle & Micheline Vandenbol

  2. Unité Fertilité des sols et Protection des eaux (U9), Centre wallon de Recherches agronomiques, Rue du Bordia 4, 5030, Gembloux, Belgium

    Claire Olivier & Christian Roisin

  3. Bioinformatics, Progenus SA, Rue des Praules 2, 5030, Gembloux, Belgium

    Céline Muys

  4. Sciences et technologie de l’environnement, Gembloux Agro-Bio Tech, Université de Liège, Passage des Déportés 2, 5030, Gembloux, Belgium

    Gilles Colinet

  5. Unité de Phytotechnie des Régions tempérées, Université de Liège, Gembloux Agro-Bio Tech, Passage des Déportés 2, 5030, Gembloux, Belgium

    Bernard Bodson

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  1. Aurore Stroobants
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  2. Florine Degrune
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  9. Micheline Vandenbol
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Correspondence to Aurore Stroobants.

Electronic Supplementary Material

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Supplementary Table 1

Composition of bacterial communities present in the soil at three depths: 10, 25, and 45 cm. Relative abundances of the corresponding 16S rDNA sequences were calculated on the basis of an RDP Classifier run with the bootstrap scores of 0.80, 0.99, or 0 (XLS 36 kb)

Supplementary Table 2

Percentages of assignment. Percentages were calculated for each taxonomic rank by dividing the relative abundance of the relevant sequences obtained after the RDP Classifier run at 0.80 by that obtained after the run at score 0 (XLS 32 kb)

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Stroobants, A., Degrune, F., Olivier, C. et al. Diversity of Bacterial Communities in a Profile of a Winter Wheat Field: Known and Unknown Members. Microb Ecol 68, 822–833 (2014). https://doi.org/10.1007/s00248-014-0458-6

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  • DOI: https://doi.org/10.1007/s00248-014-0458-6

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