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      Distinct types of multicellular aggregates in Pseudomonas aeruginosa liquid cultures

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          Abstract

          Pseudomonas aeruginosa forms suspended multicellular aggregates when cultured in liquid media. These aggregates may be important in disease, and/or as a pathway to biofilm formation. The polysaccharide Psl and extracellular DNA (eDNA) have both been implicated in aggregation, but previous results depend strongly on the experimental conditions. Here we develop a quantitative microscopy-based method for assessing changes in the size distribution of suspended aggregates over time in growing cultures. For exponentially growing cultures of P. aeruginosa PAO1, we find that aggregation is mediated by cell-associated Psl, rather than by either eDNA or secreted Psl. These aggregates arise de novo within the culture via a growth process that involves both collisions and clonal growth, and Psl non-producing cells do not aggregate with producers. In contrast, we find that stationary phase (overnight) cultures contain a different type of multicellular aggregate, in which both eDNA and Psl mediate cohesion. Our findings suggest that the physical and biological properties of multicellular aggregates may be very different in early-stage vs late-stage bacterial cultures.

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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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            The biofilm matrix.

            The microorganisms in biofilms live in a self-produced matrix of hydrated extracellular polymeric substances (EPS) that form their immediate environment. EPS are mainly polysaccharides, proteins, nucleic acids and lipids; they provide the mechanical stability of biofilms, mediate their adhesion to surfaces and form a cohesive, three-dimensional polymer network that interconnects and transiently immobilizes biofilm cells. In addition, the biofilm matrix acts as an external digestive system by keeping extracellular enzymes close to the cells, enabling them to metabolize dissolved, colloidal and solid biopolymers. Here we describe the functions, properties and constituents of the EPS matrix that make biofilms the most successful forms of life on earth.
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              Microbial biofilms.

              Direct observations have clearly shown that biofilm bacteria predominate, numerically and metabolically, in virtually all nutrient-sufficient ecosystems. Therefore, these sessile organisms predominate in most of the environmental, industrial, and medical problems and processes of interest to microbiologists. If biofilm bacteria were simply planktonic cells that had adhered to a surface, this revelation would be unimportant, but they are demonstrably and profoundly different. We first noted that biofilm cells are at least 500 times more resistant to antibacterial agents. Now we have discovered that adhesion triggers the expression of a sigma factor that derepresses a large number of genes so that biofilm cells are clearly phenotypically distinct from their planktonic counterparts. Each biofilm bacterium lives in a customized microniche in a complex microbial community that has primitive homeostasis, a primitive circulatory system, and metabolic cooperativity, and each of these sessile cells reacts to its special environment so that it differs fundamentally from a planktonic cell of the same species.
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                Author and article information

                Contributors
                g.melaugh@ed.ac.uk
                Journal
                NPJ Biofilms Microbiomes
                NPJ Biofilms Microbiomes
                NPJ Biofilms and Microbiomes
                Nature Publishing Group UK (London )
                2055-5008
                28 July 2023
                28 July 2023
                2023
                : 9
                : 52
                Affiliations
                [1 ]GRID grid.4305.2, ISNI 0000 0004 1936 7988, SUPA, School of Physics and Astronomy, , University of Edinburgh, ; Edinburgh, EH9 3FD UK
                [2 ]GRID grid.4305.2, ISNI 0000 0004 1936 7988, School of Engineering, , University of Edinburgh, ; Edinburgh, EH9 3JL UK
                [3 ]GRID grid.42327.30, ISNI 0000 0004 0473 9646, Program in Molecular Medicine, , The Hospital for Sick Children, ; Toronto, M5G 0A4 ON Canada
                [4 ]GRID grid.261331.4, ISNI 0000 0001 2285 7943, Departments of Microbial Infection and Immunity, Microbiology, Infectious Diseases Institute, , Ohio State University, ; Columbus, OH 43210 USA
                [5 ]GRID grid.17063.33, ISNI 0000 0001 2157 2938, Department of Biochemistry, , University of Toronto, ; Toronto, M5S 1A8 ON Canada
                [6 ]GRID grid.9613.d, ISNI 0000 0001 1939 2794, Theoretical Microbial Ecology, Institute of Microbiology, Faculty of Biological Sciences, , Friedrich Schiller University, ; Jena, 07745 Germany
                Author information
                http://orcid.org/0000-0002-5431-4844
                http://orcid.org/0000-0002-2776-062X
                http://orcid.org/0000-0003-4110-2962
                Article
                412
                10.1038/s41522-023-00412-5
                10382557
                36596826
                2be19a12-1f75-4cfa-99c2-cadf005fdedc
                © The Author(s) 2023

                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
                : 24 June 2022
                : 15 June 2023
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100000266, RCUK | Engineering and Physical Sciences Research Council (EPSRC);
                Award ID: EP/J007404
                Award ID: EP/J007404
                Award ID: EP/J007404
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100000854, Human Frontier Science Program (HFSP);
                Award ID: RGY0081/2012
                Award ID: RGY0081/2012
                Award Recipient :
                Funded by: European Research Council 682237 "EVOSTRUC" NBIC/BBSRC/UKRI BB/496 R012415/1
                Funded by: Canadian Institute for Health Research Banting Fellowship Cystic Fibrosis Canada postdoctoral fellowship
                Funded by: National Institute of Health R01AI077628, R01AI134895, R01AI143916
                Funded by: Canadian institute for Health Research 43998 Canadian Institute for Health Research FDN154327 P. Lynne Howell was the recipient of a Tier I Canada Research Chair
                Funded by: European Research Council 682237 "EVOSTRUC" NBIC/BBSRC/UKRI BB/496 R012415/1 Deutsche Forschungsgemeinschaft (DFG) Project ID 390713860 "Balance of the Microverse"
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                © Springer Nature Limited 2023

                biofilms,applied microbiology
                biofilms, applied microbiology

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