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      The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization

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          Abstract

          Bacteria of the genera Pseudomonas and Bacillus can promote plant growth and protect plants from pathogens. However, the interactions between these plant-beneficial bacteria are understudied. Here, we explore the interaction between Bacillus subtilis 3610 and Pseudomonas chlororaphis PCL1606. We show that the extracellular matrix protects B. subtilis colonies from infiltration by P. chlororaphis. The absence of extracellular matrix results in increased fluidity and loss of structure of the B. subtilis colony. The P. chlororaphis type VI secretion system (T6SS) is activated upon contact with B. subtilis cells, and stimulates B. subtilis sporulation. Furthermore, we find that B. subtilis sporulation observed prior to direct contact with P. chlororaphis is mediated by histidine kinases KinA and KinB. Finally, we demonstrate the importance of the extracellular matrix and the T6SS in modulating the coexistence of the two species on melon plant leaves and seeds.

          Abstract

          Pseudomonas and Bacillus can promote plant growth but their mutual interactions are unclear. Here, the authors show that the extracellular matrix protects Bacillus colonies from infiltration by Pseudomonas cells, while the Pseudomonas type VI secretion system stimulates Bacillus sporulation.

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            Fiji: an open-source platform for biological-image analysis.

            Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
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              Cytoscape: a software environment for integrated models of biomolecular interaction networks.

              Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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                Author and article information

                Contributors
                diego_romero@uma.es
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                23 April 2019
                23 April 2019
                2019
                : 10
                : 1919
                Affiliations
                [1 ]ISNI 0000 0001 2298 7828, GRID grid.10215.37, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, , Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), ; 29071 Málaga, Spain
                [2 ]Nano-imaging Unit, Andalusian Centre for Nanomedicine and Biotechnology, BIONAND, 29071 Málaga, Spain
                [3 ]ISNI 0000 0001 2107 4242, GRID grid.266100.3, University of California San Diego, Collaborative Mass Spectrometry Innovation Center, ; La Jolla, CA 92093 USA
                [4 ]ISNI 0000 0004 0386 2845, GRID grid.503246.6, Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), , CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, ; 33600 Pessac, France
                Author information
                http://orcid.org/0000-0002-1131-8917
                http://orcid.org/0000-0002-2267-0844
                http://orcid.org/0000-0002-2994-9688
                http://orcid.org/0000-0001-5499-2728
                http://orcid.org/0000-0002-6561-3022
                http://orcid.org/0000-0002-2257-7682
                http://orcid.org/0000-0003-3723-9552
                http://orcid.org/0000-0003-0798-0964
                http://orcid.org/0000-0003-2716-9861
                http://orcid.org/0000-0001-7176-7813
                http://orcid.org/0000-0002-3003-1030
                http://orcid.org/0000-0002-2052-6515
                Article
                9944
                10.1038/s41467-019-09944-x
                6478825
                31015472
                9bc256b0-924a-4296-8554-97d72b1c2c29
                © The Author(s) 2019

                Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 13 September 2018
                : 5 April 2019
                Funding
                Funded by: FundRef https://doi.org/10.13039/100010663, EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council);
                Award ID: BacBio 637971
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100003329, Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness);
                Award ID: AGL2016-78662-R
                Award Recipient :
                Categories
                Article
                Custom metadata
                © The Author(s) 2019

                Uncategorized
                microbiology,biofilms,environmental microbiology,microbial communities
                Uncategorized
                microbiology, biofilms, environmental microbiology, microbial communities

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