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Bacterial community structures in rhizosphere microsites of ryegrass (Lolium perenne var. Nui) as revealed by pyrosequencing

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Abstract

Management of soils to facilitate plant beneficial microbial interactions requires basic knowledge of the species composition and microbial community structures in the plant rhizosphere. Here, we examined composition of bacterial communities associated with rhizosphere microsites located at the root tips and mature root zones of Lolium perenne when grown in Chilean ash-derived volcanic soils (Andisols: Freire and Piedras Negras soil series). Community structures were analyzed by pyrosequencing of 16S ribosomal RNA (rRNA) genes followed by in silico analysis for phylogenetic assignments (MOTHUR and Visualization tool for Taxonomic Compositions of Microbial Community (VITCOMIC)). Analysis of the community structure revealed significant differences in community structures in relation to the soil series, which differed particularly in the relative abundance of Cyanobacteria and Firmicutes. However, no significant differences were observed with respect to root microsite location in the same Andisol series. Predominant taxa included members of the Proteobacteria, Actinobacteria, and Acidobacteria. Analysis by VITCOMIC showed that dominant bacterial groups comprised only 5 to 10 % of the total bacterial community and the remaining majority of bacteria included low-abundant taxa (Fusobacteria, Thermotogae, Lentisphaerae, Tenericutes, Deferribacteres Spirochaetes, Planctomycetes, Thermotogae, and Deinococcus-Thermus), most of which have not been previously reported or associated with the plant rhizosphere according to GenBank database. The results indicate that most of bacteria in the Chilean Andisols have not been described to the rhizosphere plants and their functional traits are still largely unknown.

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Acknowledgments

This study was supported by FONDECYT Project no.1120505 and 1141247. This research was partially supported by the supercomputing infrastructure of the NLHPC (ECM-02) (Responsible Dr. Andres Avila) at Centro de Modelación y Computación Científica at Universidad de La Frontera (CMCC-UFRO). L. Lagos thanks the CONICYT PhD Scholarships no. 21120698.

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Authors and Affiliations

  1. Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile

    Lorena M. Lagos & Fernanda P. Cid

  2. Programa de Magister en Ciencias de la Ingeniería mención Biotecnología, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile

    Oscar U. Navarrete

  3. Microbial Genomics and Ecology, Graduate School of Medical and Dental Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan

    Fumito Maruyama

  4. 318 Science Laboratories I, Department of Environmental Sciences, University of California Riverside, 900 University Ave., Riverside, CA, 92521, USA

    David E. Crowley

  5. Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile

    María L. Mora & Milko A. Jorquera

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  1. Lorena M. Lagos
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  2. Oscar U. Navarrete
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Correspondence to Milko A. Jorquera.

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Lagos, L.M., Navarrete, O.U., Maruyama, F. et al. Bacterial community structures in rhizosphere microsites of ryegrass (Lolium perenne var. Nui) as revealed by pyrosequencing. Biol Fertil Soils 50, 1253–1266 (2014). https://doi.org/10.1007/s00374-014-0939-2

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  • DOI: https://doi.org/10.1007/s00374-014-0939-2

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