Kuzyakov Y, Razavi BS. Rhizosphere size and shape: Temporal dynamics and spatial stationarity. Soil Biol Biochem. 2019;135:343–60.
Google Scholar
Teixeira PJ, Colaianni NR, Fitzpatrick CR, Dangl JL. Beyond pathogens: Microbiota interactions with the plant immune system. Curr Opin Microbiol. 2019;49:7–17.
Google Scholar
Alirezaeizanjani Z, Großmann R, Pfeifer V, Hintsche M, Beta C. Chemotaxis strategies of bacteria with multiple run modes. Sci Adv. 2020;6:eaaz6153.
Google Scholar
Gao S, Wu H, Yu X, Qian L, Gao X. Swarming motility plays the major role in migration during tomato root colonization by Bacillus subtilis SWR01. Biol Control. 2016;98:11–17.
Google Scholar
Mitchell JG, Kogure K. Bacterial Motility: Links to the environment and a driving force for microbial physics. FEMS Microbiol Ecol. 2006;55:3–16.
Google Scholar
Kalamara M, Spacapan M, Mandic-Mulec I, Stanley-Wall NR. Social behaviours by Bacillus subtilis: Quorum sensing, kin discrimination and beyond. Mol Microbiol. 2018;110:863–78.
Google Scholar
Posada LF, Álvarez JC, Romero-Tabarez M, de-Bashan L, Villegas-Escobar V. Enhanced molecular visualization of root colonization and growth promotion by Bacillus subtilis EA-CB0575 in different growth systems. Microbiol Res. 2018;217:69–80.
Google Scholar
Beauregard PB, Yunrong C, Vlamakis H, Losick R, Kolter R. Bacillus subtilis Biofilm induction by plant polysaccharides. Proc Natl Acad Sci USA. 2013;110:1621–30.
Google Scholar
Allard-Massicotte R, Tessier L, Lécuyer F, Lakshmanan V, Lucier J. Bacillus subtilis early colonization of Arabidopsis thaliana roots involves multiple chemotaxis receptors. mBio 2016;7:1–10.
Google Scholar
Massalha H, Korenblum E, Malitsky S, Shapiro OH, Aharoni A. Live imaging of root-bacteria interactions in a microfluidics setup. Proc Natl Acad Sci USA. 2017;114:4549–54.
Google Scholar
Koch DL, Subramanian G. Collective hydrodynamics of swimming microorganisms: Living fluids. Annu Rev Fluid Mech. 2011;43:637–59.
Google Scholar
Wioland H, Lushi E, Goldstein RE. Directed collective motion of bacteria under channel confinement. New J Phys. 2016;18:eaaz6153.
Google Scholar
Petroff A, Libchaber A. Erratum: Hydrodynamics and collective behavior of the tethered bacterium Thiovulum majus. Proc Natl Acad Sci USA. 2016;111:5. E537-E545
Kearns DB. A field guide to bacterial swarming motility. Nat Rev Microbiol. 2010;8:634–44.
Google Scholar
Bais HP, Fall R, Vivanco JM. Biocontrol of Bacillus subtilis against infection of arabidopsis roots by Pseudomonas syringae is facilitated by biofilm formation and surfactin production. Plant Physiol. 2004;134:307–19.
Google Scholar
De Souza R, Ambrosini A, Passaglia LMP. Plant growth-promoting bacteria as inoculants in agricultural soils. Genet Mol Biol. 2015;38:401–19.
Google Scholar
Roy K, Ghosh D, DeBruyn JM, Dasgupta T, Wommack KE, Liang X, et al. Temporal dynamics of soil virus and bacterial populations in agricultural and early plant successional soils. Front Microbiol. 2020;11:1–13.
Google Scholar
Liu Y, Patko D, Engelhardt IC, George TS, Stanley-Wall NP, Ladmiral V. et al. Whole plant-environment microscopy reveals how Bacillus subtilis utilises the soil pore space to colonise plant roots. Proc Natl Acad Sci USA. 2021;118:e2109176118.
Google Scholar
Einstein A. On the motion of small particles suspended in liquids at rest required by the molecular-kinetic theory of heat. Ann Phys. 1905;17:549–60.
Google Scholar
Shellard A, Mayor R. Rules of Collective Migration: From the wildebeest to the neural crest: Rules of neural crest migration. Philos Trans R Soc B Biol Sci. 2020;375:1–9.
Google Scholar
Torney CJ, Lamont M, Debell L, Angohiatok RJ, Leclerc LM, Berdahl AM. Inferring the rules of social interaction in migrating caribou. Philos Trans R Soc B Biol Sci. 2018;373:20170385.
Google Scholar
Ballerini MN, Cabibbo R, Candelier A, Cavagna E, Cisbani I, Giardina V, et al. Interaction ruling animal collective behavior depends on topological rather than metric distance: Evidence from a field study. Proc Natl Acad Sci USA. 2008;105:1232–37.
Google Scholar
Cavagna A, Cimarelli A, Giardina I, Parisi G, Santagati R, Stefanini F, et al. Scale-free correlations in starling flocks. Proc Natl Acad Sci USA. 2010;107:11865–70.
Google Scholar
Katz Y, Tunstrøm C, Ioannou CC, Huepe C, Couzin ID. Inferring the structure and dynamics of interactions in schooling fish. Proc Natl Acad Sci USA. 2011;108:18720–25.
Google Scholar
Buhl JD, Sumpter JT, Couzin ID, Hale JJ, Despland E, Miller ER, et al. From disorder to order in marching locusts. Science 2006;312:1402–6.
Google Scholar
Seeley TD, Visscher PK. Quorum Sensing during nest-site selection by honeybee swarms. Behav Ecol Sociobiol. 2004;56:594–601.
Google Scholar
Zhang HP, Be’er A, Florin EL, Swinney HL. Collective motion and density fluctuations in bacterial colonies. Proc Natl Acad Sci USA. 2010;107:13626–30.
Google Scholar
Hughey LF, Hein AM, Strandburg-Peshkin A, Jensen FH. Challenges and solutions for studying collective animal behaviour in the wild. Philos Trans R Soc B Biol Sci. 2018;373:1–13.
Google Scholar
Nadell CD, Xavier JB, Foster KR. The sociobiology of biofilms. FEMS Microbiol Rev. 2009;33:206–24.
Google Scholar
Velicer GJ, Vos M. Sociobiology of the myxobacteria. Ann Rev Microbiol. 2009;63:599–623.
Google Scholar
Branda SS, González-Pastor JE, Ben-Yehuda S, Losick R, Kolter R. Fruiting body formation by Bacillus subtilis. Proc Natl Acad Sci USA. 2001;98:11621–26.
Google Scholar
Cordero OX, Wildschutte H, Kirkup B, Proehl S, Ngo L, Hussain F, et al. Antibiotic production and resistance. Sci Rep. 2012;337:1228–31.
Google Scholar
Muñoz-Dorado J, Marcos-Torres FJ, García-Bravo E, Moraleda-Muñoz A, Pérez J. Myxobacteria: Moving, killing, feeding, and surviving together. Front Microbiol. 2016;7:1–18.
Google Scholar
Li C, Hurley A, Hu W, Warrick JW, Lozano GL, Ayuso JM, et al. Social motility of biofilm-like microcolonies in a gliding bacterium. Nat Commun. 2021;12:1–12.
Google Scholar
Sokolov A, Aranson IS, Kessler JO, Goldstein RE. Concentration dependence of the collective dynamics of swimming bacteria. Phys Rev Lett. 2007;98:158102.
Google Scholar
Cisneros LH, Cortez R, Dombrowski C, Goldstein RE, Kessler JO. Fluid dynamics of self-propelled microorganisms, from individuals to concentrated populations. Exp Fluids. 2007;43:737–53.
Google Scholar
Tuval I, Cisneros L, Dombrowski C, Wolgemuth CW, Kessler JO, Goldstein RE. Bacterial swimming and oxygen transport near contact lines. Proc Natl Acad Sci USA. 2005;102:2277–82.
Google Scholar
Li G, Tam L, Tang JX. Amplified effect of brownian motion in bacterial near-surface swimming. Proc Natl Acad Sci USA. 2008;105:18355–59.
Google Scholar
Lushi E, Wioland H, Goldstein RE. Fluid flows created by swimming bacteria drive self-organization in confined suspensions. Proc Natl Acad Sci USA. 2014;111:9733–38.
Google Scholar
Ryan SD, Sokolov A, Berlyand L, Aranson IS. Correlation properties of collective motion in bacterial suspensions. New J Phys. 2013;15:105021.
Google Scholar
Damton NC, Turner L, Rojevsky S, Berg HC. Dynamics of bacterial swarming. Biophys J. 2010;98:2082–90.
Google Scholar
Ingham CJ, Jacob EB. Swarming and complex pattern formation in Paenibacillus vortex studied by imaging and tracking cells. BMC Microbiol. 2008;8:1–16.
Google Scholar
Ariel G, Rabani A, Benisty S, Partridge JD, Harshey RM, Be’Er A. Swarming bacteria migrate by lévy walk. Nat Commun. 2015;6:8396.
Google Scholar
Hamze K, Autret S, Hinc K, Laalami S, Julkowska D, Briandet R, et al. Single-cell analysis in situ in a Bacillus subtilis swarming community identifies distinct spatially separated subpopulations differentially expressing Hag (Flagellin), including specialized swarmers. Microbiol. 2011;157:2456–69.
Google Scholar
Ghelardi E, Salvetti S, Ceragioli M, Gueye SA, Celandroni F, Senesi S. Contribution of surfactin and swrA to flagellin expression, swimming, and surface motility in Bacillus subtilis. Appl Environ Microbiol. 2012;78:6540–44.
Google Scholar
Wilde A, Mullineaux CW. Light-controlled motility in prokaryotes and the problem of directional light perception. FEMS Microbiol Rev. 2017;41:900–22.
Google Scholar
Zhang J, Luo Y, Poh CL. Blue light-directed cell migration, aggregation, and patterning. J Mol Biol. 2020;432:3137–48.
Google Scholar
Tian T, Sun B, Shi H, Gao T, He Y, Li Y, et al. Sucrose triggers a novel signalling cascade promoting Bacillus subtilis rhizosphere colonization. ISME J 2021;15:2723–37.
Google Scholar
Harshey RM, Partridge JD. Shelter in a swarm. J Mol Biol. 2015;427:3683–94.
Google Scholar
Burdett IDJ, Kirkwood TBL, Whalley JB. Growth kinetics of individual Bacillus subtilis cells and correlation with nucleoid extension. J Bacteriol. 1986;167:219–30.
Google Scholar
Sharpe ME, Hauser PM, Sharpe RG, Errington J. Bacillus subtilis cell cycle as studied by fluorescence microscopy: Constancy of cell length at initiation of DNA replication and evidence for active nucleoid partitioning. J Bacteriol. 1998;180:547–55.
Google Scholar
Rousk J, Bååth E. Growth of saprotrophic fungi and bacteria in soil. FEMS Microbiol Ecol. 2011;78:17–30.
Google Scholar
Bennett RA, Lynch JM. Bacterial growth and development in the rhizosphere of gnotobiotic cereal plants. Microbiol. 1981;125:95–102.
Google Scholar
Felici C, Vettori L, Giraldi E, Forino LMC, Toffanin A, Tagliasacchi AM, et al. Single and co-inoculation of Bacillus subtilis and Azospirillum brasilense on Lycopersicon Esculentum: Effects on plant growth and rhizosphere microbial community. Appl Soil Ecol. 2008;40:260–70.
Google Scholar
Arkhipova TN, Galimsyanova NF, Kuzmina LY, Vysotskaya LB, Sidorova LV, Gabbasova IM, et al. Effect of seed bacterization with plant growth-promoting bacteria on wheat productivity and phosphorus mobility in the rhizosphere. Plant Soil Environ. 2019;65:313–19.
Google Scholar
Marschner P, Crowley D, Rengel Z. Rhizosphere interactions between microorganisms and plants govern iron and phosphorus acquisition along the root axis – model and research methods. Soil Biol Biochem. 2011;43:883–94.
Google Scholar
Lagos ML, Maruyama F, Nannipieri P, Mora ML, Jorquera MA. Current Overview on the study of bacteria in the rhizosphere by modern molecular techniques: A Mini-Review. J Soil Sci Plant Nutr. 2015;15:504–23.
Gerwig J, Kiley TB, Gunka K, Stanley-Wall N, Stülke J. The protein tyrosine kinases epsB and ptkA differentially affect biofilm formation in Bacillus Subtilis. Microbiol. 2014;160:682–91.
Google Scholar
Shoesmith JG. The measurement of bacterial motility. J Gen Microbiol. 1960;22:528–35.
Google Scholar
Schneider WR, Doetsch RN. Effect of viscosity on bacterial motility. J Bacteriol. 1974;117:696–701.
Google Scholar
Kaiser GE, Doetsch RN. Enhanced translational motion of Leptospira in viscous environments. Nature 1975;255:656–57.
Google Scholar
Ryan SD, Haines BM, Berlyand L, Ziebert F, Aranson IS. Viscosity of bacterial suspensions: Hydrodynamic interactions and self-induced noise. Phys Rev E Stat Nonlin Soft Matter Phys. 2011;E83:050904.
Google Scholar
López HM, Gachelin J, Douarche C, Auradou H, Clément E. Turning bacteria suspensions into superfluids. Phys Rev Lett. 2015;115:028301.
Google Scholar
Butler MT, Wang Q, Harshey RM. Cell density and mobility protect swarming bacteria against antibiotics. Proc Natl Acad Sci USA. 2010;107:3776–81.
Google Scholar
Erktan A, Or D, Scheu S. The physical structure of soil: Determinant and consequence of trophic interactions. Soil Biol Biochem. 2020;148:107876.
Google Scholar
Rønn R, Thomsen IK, Jensen B. Naked amoebae, flagellates and nematodes in soil of different texture. Eur J Soil Biol. 1995;31:135–41.
Downie H, Holden N, Otten W, Spiers AJ, Valentine TA, Dupuy LX. Transparent soil for imaging the rhizosphere. PLoS ONE. 2012;7:1–6.
Google Scholar
Mills AL. Keeping in Touch: Microbial life on soil particle surfaces. Adv Agron. 2003;78:1–43.
Google Scholar
Downie HF, Valentine TA, Otten W, Spiers AJ, Dupuy LX. Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo. Plant Signal Behav. 2014;9:e970421.
Google Scholar
O’Callaghan FE, Braga RA, Neilson R, MacFarlane SA, Dupuy LX. New live screening of plant-nematode interactions in the rhizosphere. Sci Rep. 2018;8:1–17.
Google Scholar
Sharma K, Palatinszky M, Nikolov G, Berry D, Shank EA. Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms. ELife 2020;9:1–28.
Bickel S, Or D. Soil bacterial diversity mediated by microscale aqueous-phase processes across biomes. Nat Commun. 2020;11:1–9.
Google Scholar
Farré M, Sanchís J, Barceló D. Analysis and assessment of the occurrence, the fate and the behavior of nanomaterials in the environment. Trends Anal Chem. 2011;30:517–27.
Google Scholar
Verhamme DT, Kiley TB, Stanley-Wall NR. DegU co-ordinates multicellular behaviour exhibited by Bacillus subtilis. Mol Microbiol. 2007;65:554–68.
Google Scholar
Konkol MA, Blair KM, Kearns DB. Plasmid-encoded comi inhibits competence in the ancestral 3610 strain of Bacillus subtilis. J Bacteriol. 2013;195:4085–93.
Google Scholar
Stanley NR, Lazazzera BA. Defining the genetic differences between wild and domestic strains of Bacillus subtilis that affect poly-γ-DL-glutamic acid production and biofilm formation. Mol Microbiol. 2005;57:1143–58.
Google Scholar
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2020. URL https://www.R-project.org/.
Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, et al. (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9:676–82.
Google Scholar
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