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      Plant-associated Bacillus mobilizes its secondary metabolites upon perception of the siderophore pyochelin produced by a Pseudomonas competitor

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          Abstract

          Bacillus velezensis is considered as model species for plant-associated bacilli providing benefits to its host such as protection against phytopathogens. This is mainly due to the potential to secrete a wide range of secondary metabolites with specific and complementary bioactivities. This metabolite arsenal has been quite well defined genetically and chemically but much remains to be explored regarding how it is expressed under natural conditions and notably how it can be modulated upon interspecies interactions in the competitive rhizosphere niche. Here, we show that B. velezensis can mobilize a substantial part of its metabolome upon the perception of Pseudomonas, as a soil-dwelling competitor. This metabolite response reflects a multimodal defensive strategy as it includes polyketides and the bacteriocin amylocyclicin, with broad antibiotic activity, as well as surfactin lipopeptides, contributing to biofilm formation and enhanced motility. Furthermore, we identified the secondary Pseudomonas siderophore pyochelin as an info-chemical, which triggers this response via a mechanism independent of iron stress. We hypothesize that B. velezensis relies on such chelator sensing to accurately identify competitors, illustrating a new facet of siderophore-mediated interactions beyond the concept of competition for iron and siderophore piracy. This phenomenon may thus represent a new component of the microbial conversations driving the behavior of members of the rhizosphere community.

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          Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

          The Interactive Tree Of Life ( https://itol.embl.de ) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 5 introduces a completely new tree display engine, together with numerous new features. For example, a new dataset type has been added (MEME motifs), while annotation options have been expanded for several existing ones. Node metadata display options have been extended and now also support non-numerical categorical values, as well as multiple values per node. Direct manual annotation is now available, providing a set of basic drawing and labeling tools, allowing users to draw shapes, labels and other features by hand directly onto the trees. Support for tree and dataset scales has been extended, providing fine control over line and label styles. Unrooted tree displays can now use the equal-daylight algorithm, proving a much greater display clarity. The user account system has been streamlined and expanded with new navigation options and currently handles >1 million trees from >70 000 individual users. Graphical Abstract iTOL: an online tool for the tree display and annotation.
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            Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.

            In 2001 and 2002, we published two papers (Bioinformatics, 17, 282-283, Bioinformatics, 18, 77-82) describing an ultrafast protein sequence clustering program called cd-hit. This program can efficiently cluster a huge protein database with millions of sequences. However, the applications of the underlying algorithm are not limited to only protein sequences clustering, here we present several new programs using the same algorithm including cd-hit-2d, cd-hit-est and cd-hit-est-2d. Cd-hit-2d compares two protein datasets and reports similar matches between them; cd-hit-est clusters a DNA/RNA sequence database and cd-hit-est-2d compares two nucleotide datasets. All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST.
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              APE: Analyses of Phylogenetics and Evolution in R language.

              Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.
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                Author and article information

                Contributors
                sofijaandric@yahoo.com
                thibault.meyer@univ-lyon1.fr
                marc.ongena@uliege.be
                Journal
                ISME J
                ISME J
                The ISME Journal
                Nature Publishing Group UK (London )
                1751-7362
                1751-7370
                10 November 2022
                10 November 2022
                February 2023
                : 17
                : 2
                : 263-275
                Affiliations
                [1 ]GRID grid.410510.1, ISNI 0000 0001 2297 9043, Microbial Processes and Interactions Laboratory, , Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, ; Gembloux, Belgium
                [2 ]GRID grid.4861.b, ISNI 0000 0001 0805 7253, Laboratory of Gene Expression and Cancer, , GIGA-MBD, University of Liège, ; Liège, Belgium
                [3 ]GRID grid.5342.0, ISNI 0000 0001 2069 7798, Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, , Ghent University, ; Ghent, Belgium
                [4 ]GRID grid.5477.1, ISNI 0000000120346234, Present Address: Ecology and Biodiversity, Department of Biology, , Utrecht University, ; Padualaan 8, 3584 CH Utrecht, The Netherlands
                [5 ]GRID grid.7849.2, ISNI 0000 0001 2150 7757, Present Address: UMR Ecologie Microbienne, F-69622, , University of Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, ; Villeurbanne, France
                Author information
                http://orcid.org/0000-0001-7015-8354
                http://orcid.org/0000-0003-4359-733X
                http://orcid.org/0000-0002-2184-4822
                http://orcid.org/0000-0002-6804-5059
                http://orcid.org/0000-0002-7847-2441
                http://orcid.org/0000-0002-0850-3249
                http://orcid.org/0000-0002-8526-9804
                http://orcid.org/0000-0002-7418-4354
                Article
                1337
                10.1038/s41396-022-01337-1
                9860033
                36357782
                0286d13c-0329-40f1-b60f-f1ce13b5163b
                © The Author(s) 2022

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 18 March 2022
                : 12 October 2022
                : 13 October 2022
                Funding
                Funded by: National Funds for Scientific Research (FRS-FNRS)
                Funded by: F.R.I.A. fellowship (Formation à la Recherche dans l’Industrie et l’Agriculture)
                Funded by: EOS project ID 30650620
                Funded by: Institutional fundings (University of Liege)
                Funded by: University Liege PhD grant
                Categories
                Article
                Custom metadata
                © International Society for Microbial Ecology 2023

                Microbiology & Virology
                microbial ecology,soil microbiology
                Microbiology & Virology
                microbial ecology, soil microbiology

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