Intra-colony channel morphology in Escherichia coli biofilms is governed by nutrient availability and substrate stiffness

Biofilm - Tập 4 - Trang 100084 - 2022
Beatrice Bottura1, Liam M. Rooney2, Paul A. Hoskisson2, Gail McConnell1
1Department of Physics, SUPA, University of Strathclyde, G4 0NG, Glasgow, UK
2Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, G4 0RE, Glasgow, UK

Tài liệu tham khảo

Donlan, 2002, Biofilms: microbial life on surfaces, Emerg Infect Dis, 8, 881, 10.3201/eid0809.020063 Yin, 2019, Biofilms: the microbial “protective clothing” in extreme environments, Int J Mol Sci, 20, 3423, 10.3390/ijms20143423 Cont, 2020, Biofilms deform soft surfaces and disrupt epithelia, Elife, 9, 10.7554/eLife.56533 Mimura, 2000, Reaction–diffusion modelling of bacterial colony patterns, Phys Stat Mech Appl, 282, 283, 10.1016/S0378-4371(00)00085-6 Tokita, 2009, Pattern formation of bacterial colonies by escherichia coli, J Phys Soc Jpn, 78, 10.1143/JPSJ.78.074005 Fei, 2020, Nonuniform growth and surface friction determine bacterial biofilm morphology on soft substrates, Proc Natl Acad Sci USA, 117, 7622, 10.1073/pnas.1919607117 Bryers, 2008, Medical biofilms, Biotechnol Bioeng, 100, 1, 10.1002/bit.21838 Song, 2014, Stiffness of cross-linked poly (dimethylsiloxane) affects bacterial adhesion and antibiotic susceptibility of attached cells, Langmuir, 30, 10354, 10.1021/la502029f Kolewe, 2015, Fewer bacteria adhere to softer hydrogels, ACS Appl Mater Interfaces, 7, 19562, 10.1021/acsami.5b04269 Song, 2017, How bacteria respond to material stiffness during attachment: a role of escherichia coli flagellar motility, ACS Appl Mater Interfaces, 9, 22176, 10.1021/acsami.7b04757 Saha, 2013, Influence of polyelectrolyte film stiffness on bacterial growth, Biomacromolecules, 14, 520, 10.1021/bm301774a Grant, 2014, The role of mechanical forces in the planar-to-bulk transition in growing escherichia coli microcolonies, J R Soc Interface, 11, 10.1098/rsif.2014.0400 Paliy, 2007, Growth of e. coli bl21 in minimal media with different gluconeogenic carbon sources and salt contents, Appl Microbiol Biotechnol, 73, 1169, 10.1007/s00253-006-0554-8 Shehata, 1971, Effect of nutrient concentration on the growth of escherichia coli, J Bacteriol, 107, 210, 10.1128/jb.107.1.210-216.1971 Bauchop, 1960, The growth of micro-organisms in relation to their energy supply, Microbiology, 23, 457, 10.1099/00221287-23-3-457 Kandemir, 2018, Mechanical interactions between bacteria and hydrogels, Sci Rep, 8, 1, 10.1038/s41598-018-29269-x Witten, 1983, Diffusion-limited aggregation, Phys Rev B, 27, 5686, 10.1103/PhysRevB.27.5686 Fujikawa, 1991, Bacterial fractal growth in the concentration field of nutrient, J Phys Soc Jpn, 60, 88, 10.1143/JPSJ.60.88 Beyenal, 2000, Combined effect of substrate concentration and flow velocity on effective diffusivity in biofilms, Water Res, 34, 528, 10.1016/S0043-1354(99)00147-5 Díaz-Pascual, 2021, Spatial alanine metabolism determines local growth dynamics of escherichia coli colonies, Elife, 10, 10.7554/eLife.70794 Wolfsberg, 2018, Metabolism in dense microbial colonies: 13c metabolic flux analysis of e. coli grown on agar identifies two distinct cell populations with acetate cross-feeding, Metab Eng, 49, 242, 10.1016/j.ymben.2018.08.013 Benomar, 2015, Nutritional stress induces exchange of cell material and energetic coupling between bacterial species, Nat Commun, 6, 1, 10.1038/ncomms7283 Massol-Deyá, 1995, Channel structures in aerobic biofilms of fixed-film reactors treating contaminated groundwater, Appl Environ Microbiol, 61, 769, 10.1128/aem.61.2.769-777.1995 Tolker-Nielsen, 2000, Spatial organization of microbial biofilm communities, Microb Ecol, 40, 75, 10.1007/s002480000057 Birjiniuk, 2014, Single particle tracking reveals spatial and dynamic organization of the escherichia coli biofilm matrix, New J Phys, 16, 10.1088/1367-2630/16/8/085014 Rooney, 2020, Intra-colony channels in e. coli function as a nutrient uptake system, ISME J, 14, 2461, 10.1038/s41396-020-0700-9 McConnell, 2016, A novel optical microscope for imaging large embryos and tissue volumes with sub-cellular resolution throughout, Elife, 5, 10.7554/eLife.18659 Chen, 2003, Impact of carbon and nitrogen conditions on e. coli surface thermodynamics, Colloids Surf B Biointerfaces, 28, 135, 10.1016/S0927-7765(02)00143-1 Warren, 2019, Spatiotemporal establishment of dense bacterial colonies growing on hard agar, Elife, 8, 10.7554/eLife.41093 Wimpenny, 1979, The growth and form of bacterial colonies, Microbiology, 114, 483 Gingichashvili, 2021, Topography and expansion patterns at the biofilm-agar interface in bacillus subtilis biofilms, Microorganisms, 9, 84, 10.3390/microorganisms9010084 Yan, 2019, Mechanical instability and interfacial energy drive biofilm morphogenesis, Elife, 8, 10.7554/eLife.43920 Nijjer, 2021, Mechanical forces drive a reorientation cascade leading to biofilm self-patterning, Nat Commun, 12, 1, 10.1038/s41467-021-26869-6 Qin, 2020, Cell position fates and collective fountain flow in bacterial biofilms revealed by light-sheet microscopy, Science, 369, 71, 10.1126/science.abb8501 Serra, 2021, Bacterial multicellularity: the biology of escherichia coli building large-scale biofilm communities, Annu Rev Microbiol, 75, 269, 10.1146/annurev-micro-031921-055801 Yao, 2012, Regulation of cell size in response to nutrient availability by fatty acid biosynthesis in escherichia coli, Proc Natl Acad Sci USA, 109, E2561, 10.1073/pnas.1209742109 Chanson, 2004 Batchelor, 2000 Waldrop, 2014, Biofilm growth has a threshold response to glucose in vitro, Clin Orthop Relat Res, 472, 3305, 10.1007/s11999-014-3538-5 Pirt, 1967, A kinetic study of the mode of growth of surface colonies of bacteria and fungi, Microbiology, 47, 181 Chen, 2014, Two-dimensionality of yeast colony expansion accompanied by pattern formation, PLoS Comput Biol, 10, 10.1371/journal.pcbi.1003979 Chacón, 2018, The spatial and metabolic basis of colony size variation, ISME J, 12, 669, 10.1038/s41396-017-0038-0 Yang, 2017, Influence of physical effects on the swarming motility of pseudomonas aeruginosa, Biophys J, 112, 1462, 10.1016/j.bpj.2017.02.019 Reshes, 2008, Timing the start of division in e. coli: a single-cell study, Phys Biol, 5, 10.1088/1478-3975/5/4/046001 Ju, 2001, Individual-based modelling of biofilms, Microbiology, 147, 2897, 10.1099/00221287-147-11-2897 Alpkvist, 2006, Three-dimensional biofilm model with individual cells and continuum eps matrix, Biotechnol Bioeng, 94, 961, 10.1002/bit.20917 Lardon, 2011, idynomics: next-generation individual-based modelling of biofilms, Environ Microbiol, 13, 2416, 10.1111/j.1462-2920.2011.02414.x Xavier, 2005, A framework for multidimensional modelling of activity and structure of multispecies biofilms, Environ Microbiol, 7, 1085, 10.1111/j.1462-2920.2005.00787.x Yan, 2016, Vibrio cholerae biofilm growth program and architecture revealed by single-cell live imaging, Proc Natl Acad Sci USA, 113, E5337, 10.1073/pnas.1611494113 Hartmann, 2019, Emergence of threedimensional order and structure in growing biofilms, Nat Phys, 15, 251, 10.1038/s41567-018-0356-9 Drescher, 2016, Architectural transitions in vibrio cholerae biofilms at single-cell resolution, Proc Natl Acad Sci USA, 113, E2066, 10.1073/pnas.1601702113 Lambertsen, 2004, Mini-tn7 transposons for site-specific tagging of bacteria with fluorescent proteins, Environ Microbiol, 6, 726, 10.1111/j.1462-2920.2004.00605.x Elbing, 2019, Recipes and tools for culture of escherichia coli, Curr Protoc Mol Biol, 125, e83, 10.1002/cpmb.83 Schniete, 2018, Fast optical sectioning for widefield fluorescence mesoscopy with the mesolens based on hilo microscopy, Sci Rep, 8, 1, 10.1038/s41598-018-34516-2 Schindelin, 2012, Fiji: an open-source platform for biological-image analysis, Nat Methods, 9, 676, 10.1038/nmeth.2019 Donnelly Iglewicz, 1993, vol. 16