DOI: 10.5061/dryad.5x69p8ddf
title: Dynamically induced spatial segregation in multispecies bacterial bioconvection

description: Active matter, from motile bacteria to animals, can exhibit striking
 collective and coherent behavior. Despite significant advances in
 understanding the behavior of homogeneous systems, little is known about
 the self-organization and dynamics of heterogeneous active matter, such as
 complex and diverse bacterial communities. Under oxygen gradients, many
 bacterial species swim towards air-liquid interfaces in auto-organized,
 directional bioconvective flows, whose spatial scales exceed the cell size
 by orders of magnitude. Here we show that multispecies bacterial
 suspensions undergoing oxytactic-driven bioconvection exhibit dynamically
 driven spatial segregation, despite the enhanced mixing of bioconvective
 flows, and the fact that these species coexist in their natural habitat.
 Segregation is observed as patterns of spatially interlocked domains, with
 local dominance of one of the constituent species in the suspension. Our
 findings suggest that segregation mechanisms involve minimization of
 collisions under conditions of hydrodynamic flow rather than biological
 repulsion. Thus, species with different motile characteristics in the same
 ecological context can enhance their access to limiting resources. This
 work provides novel insights on the role of heterogeneity in active
 matter, as well as on the dynamics of complex microbial communities, their
 spatial organization and their collective behavior.
description: # Dynamically induced spatial segregation in multispecies bacterial
 bioconvection
 [https://doi.org/10.5061/dryad.5x69p8ddf](https://doi.org/10.5061/dryad.5x69p8ddf) ## Description of the data and file structure Deposited data includes the following data files used to generate different figures in the main text, with their respective description. Files of Word document type .docx and Excel files .xlsx. ### Files and variables #### File: Data_Fig_4a_Characterization_of_interspecies_interactions_during_bioconvection.docx **Description:** Each table corresponds to the indicated binary bacterial suspension. Replicates correspond to plated replicates for CFUs counting, and experiments are independent. The upper table contains the colony forming units (CFU) counted on agar plates for a diluted binary suspension at time 0 and 1 hours, relative to the time when species were mixed. The concentration of mixtures at time 0 hours was calculated from the single species cultures that were used for mixing. Bacteria concentration (CFUs∙mL-1) was calculated from the CFUs data according to the dilution factor. The bacterial concentration was used to calculate the relative fraction of each constituent species in the binary mixture shown in Fig. 4a. #### File: Data_Fig._5b_Persistence_length_as_a_function_of_bacterial_concentration_updated.xlsx **Description:** Each sheet corresponds to an independent experiment in which the persistence length of individual trajectories were measured for each species. The grouped columns in each sheet correspond to different bacterial concentrations measured by optical density (OD). Within each grouped column, each individual column correspond to a different movie, and the numbers correspond to the median persistence length calculated for a single trajectory. #### File: Data_Fig._5c_Tracks_used_in_aligment.xlsx **Description:** Each sheet displays the (x, y) components of trajectories of individual cells as a function of time (frame number), corresponding to the indicated bacterial species. Trajectories were transformed so that all started at the origin (0, 0), and their first segments were parallel. #### File: Data_Fig._5d_Velocitiy_histograms.xlsx **Description:** Each sheet corresponds to the mean speed  (micrometers/sec) of cells of the indicated bacterial species. Each column corresponds to an independent experiment, and each value, to the mean speed of a single trajectory. ## Code/software File “Code_persistence_length_and_speed.m” expects a folder with one or more “.csv” files containing bacterial trajectory data, which are outputs of the Trackmate plugin (Fiji distribution of ImageJ). An example file is deposited as well to run the code. Input: Variable folder_name shall contain folder name and path. Output: The MATLAB-file’s output is the median of the persistence length of all trajectories in the folder and the median velocity. The persistence length is computed according to “Ott, A. and Magnasco, M. and Simon, A. and Libchaber, A. (1993), Measurement of the persistence length of polymerized actin using fluorescence microscopy, Phys. Rev. E, 48 (3), R1642-R1645.” File "Segregation.m" is a Matlab file of simulations of a toy model of two particle types.  For details see README_code in Zenodo