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      Effect of the strain Bacillus amyloliquefaciens FZB42 on the microbial community in the rhizosphere of lettuce under field conditions analyzed by whole metagenome sequencing

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          Abstract

          Application of the plant associated bacterium Bacillus amyloliquefaciens FZB42 on lettuce ( Lactuca sativa) confirmed its capability to promote plant growth and health by reducing disease severity (DS) caused by the phytopathogenic fungus Rhizoctonia solani. Therefore this strain is commercially applied as an eco-friendly plant protective agent. It is able to produce cyclic lipopeptides (CLP) and polyketides featuring antifungal and antibacterial properties. Production of these secondary metabolites led to the question of a possible impact of strain FZB42 on the composition of microbial rhizosphere communities after its application. Rating of DS and lettuce growth during a field trial confirmed the positive impact of strain FZB42 on the health of the host plant. To verify B. amyloliquefaciens as an environmentally compatible plant protective agent, its effect on the indigenous rhizosphere community was analyzed by metagenome sequencing. Rhizosphere microbial communities of lettuce treated with B. amyloliquefaciens FZB42 and non-treated plants were profiled by high-throughput metagenome sequencing of whole community DNA. Fragment recruitments of metagenome sequence reads on the genome sequence of B. amyloliquefaciens FZB42 proved the presence of the strain in the rhizosphere over 5 weeks of the field trial. Comparison of taxonomic community profiles only revealed marginal changes after application of strain FZB42. The orders Burkholderiales, Actinomycetales and Rhizobiales were most abundant in all samples. Depending on plant age a general shift within the composition of the microbial communities that was independent of the application of strain FZB42 was observed. In addition to the taxonomic profiling, functional analysis of annotated sequences revealed no major differences between samples regarding application of the inoculant strain.

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          Plant-driven selection of microbes

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            GenBank

            GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 380 000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.
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              Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions

              Plant roots constantly secrete compounds into the soil to interact with neighboring organisms presumably to gain certain functional advantages at different stages of development. Accordingly, it has been hypothesized that the phytochemical composition present in the root exudates changes over the course of the lifespan of a plant. Here, root exudates of in vitro grown Arabidopsis plants were collected at different developmental stages and analyzed using GC-MS. Principle component analysis revealed that the composition of root exudates varied at each developmental stage. Cumulative secretion levels of sugars and sugar alcohols were higher in early time points and decreased through development. In contrast, the cumulative secretion levels of amino acids and phenolics increased over time. The expression in roots of genes involved in biosynthesis and transportation of compounds represented in the root exudates were consistent with patterns of root exudation. Correlation analyses were performed of the in vitro root exudation patterns with the functional capacity of the rhizosphere microbiome to metabolize these compounds at different developmental stages of Arabidopsis grown in natural soils. Pyrosequencing of rhizosphere mRNA revealed strong correlations (p<0.05) between microbial functional genes involved in the metabolism of carbohydrates, amino acids and secondary metabolites with the corresponding compounds released by the roots at particular stages of plant development. In summary, our results suggest that the root exudation process of phytochemicals follows a developmental pattern that is genetically programmed.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                27 May 2014
                2014
                : 5
                : 252
                Affiliations
                [1] 1Center for Biotechnology, Institute for Genome Research and Systems Biology, Bielefeld University Bielefeld, Germany
                [2] 2Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren, Germany
                [3] 3Research Unit Microbe-Plant Interactions, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH) Neuherberg, Germany
                Author notes

                Edited by: Michael Schloter, Helmholtz Zentrum München, Germany

                Reviewed by: Leo Van Overbeek, W-UR Plant Research International, Netherlands; David John Studholme, University of Exeter, UK; Anja Bettina Dohrmann, Johann Heinrich von Thünen Institute, Germany

                *Correspondence: Andreas Schlüter, Center for Biotechnology, Institute for Genome Research and Systems Biology, Universität Bielefeld, Universitätsstr. 27, 33615 Bielefeld, Germany e-mail: aschluet@ 123456cebitec.uni-bielefeld.de

                This article was submitted to Plant-Microbe Interaction, a section of the journal Frontiers in Microbiology.

                Article
                10.3389/fmicb.2014.00252
                4033844
                24904564
                08597fb2-c80e-443d-a116-9f071211e4b0
                Copyright © 2014 Kröber, Wibberg, Grosch, Eikmeyer, Verwaaijen, Chowdhury, Hartmann, Pühler and Schlüter.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 06 November 2013
                : 07 May 2014
                Page count
                Figures: 9, Tables: 11, Equations: 0, References: 42, Pages: 16, Words: 10048
                Categories
                Plant Science
                Original Research Article

                Microbiology & Virology
                metagenome sequencing,taxonomic profiling,b. amyloliquefaciens fzb42,lettuce,rhizosphere,fragment recruitment

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