Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Topological defects promote layer formation in Myxococcus xanthus colonies


The soil bacterium Myxococcus xanthus lives in densely packed groups that form dynamic three-dimensional patterns in response to environmental changes, such as droplet-like fruiting bodies during starvation1. The development of these multicellular structures begins with the sequential formation of cell layers in a process that is poorly understood2. Here, using confocal three-dimensional imaging, we find that motile, rod-shaped M. xanthus cells are densely packed and aligned in each layer, forming an active nematic liquid crystal. Cell alignment is nearly perfect throughout the population except at point defects that carry half-integer topological charge. We observe that new cell layers preferentially form at the position of +1/2 defects, whereas holes preferentially open at −1/2 defects. To explain these findings, we model the bacterial colony as an extensile active nematic fluid with anisotropic friction. In agreement with our experimental measurements, this model predicts an influx of cells towards the +1/2 defects and an outflux of cells from the −1/2 defects. Our results suggest that cell motility and mechanical cell–cell interactions are sufficient to promote the formation of cell layers at topological defects, thereby seeding fruiting bodies in colonies of M. xanthus.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Dense colonies of M. xanthus form layered active nematic liquid crystals.
Fig. 2: Nematic alignment and topological defects in M. xanthus colonies.
Fig. 3: New layers and new holes preferentially form at +1/2 and −1/2 topological defects, respectively.
Fig. 4: Asymmetric cell flows around topological defects explain the formation of new layers and holes.

Data availability

Source data are provided with this paper. All other data that support the plots and findings of this study are available from the authors upon request.

Code availability

All codes are available from the authors upon request.


  1. 1.

    Kaiser, D. Coupling cell movement to multicellular development in myxobacteria. Nat. Rev. Microbiol. 1, 45–54 (2003).

    MathSciNet  Google Scholar 

  2. 2.

    Curtis, P. D., Taylor, R. G., Welch, R. D. & Shimkets, L. J. Spatial organization of Myxococcus xanthus during fruiting body formation. J. Bacteriol. 189, 9126–9130 (2007).

    Google Scholar 

  3. 3.

    Zhang, Y., Ducret, A., Shaevitz, J. & Mignot, T. From individual cell motility to collective behaviors: insights from a prokaryote, Myxococcus xanthus. FEMS Microbiol. Rev. 36, 149–164 (2012).

    Google Scholar 

  4. 4.

    Kim, S. K. & Kaiser, D. Cell alignment required in differentiation of Myxococcus xanthus. Science 249, 926–928 (1990).

    ADS  Google Scholar 

  5. 5.

    Jelsbak, L. & Søgaard-Andersen, L. Pattern formation by a cell surface-associated morphogen in Myxococcus xanthus. Proc. Natl Acad. Sci. USA 99, 2032–2037 (2002).

    ADS  Google Scholar 

  6. 6.

    Liu, G. et al. Self-driven phase transitions drive Myxococcus xanthus fruiting body formation. Phys. Rev. Lett. 122, 248102 (2019).

    ADS  Google Scholar 

  7. 7.

    Kaiser, D. & Warrick, H. Transmission of a signal that synchronizes cell movements in swarms of Myxococcus xanthus. Proc. Natl Acad. Sci. USA 111, 13105–13110 (2014).

    ADS  Google Scholar 

  8. 8.

    Doostmohammadi, A., Ignés-Mullol, J., Yeomans, J. M. & Sagués, F. Active nematics. Nat. Commun. 9, 3246 (2018).

    ADS  Google Scholar 

  9. 9.

    Marchetti, M. C. et al. Hydrodynamics of soft active matter. Rev. Mod. Phys. 85, 1143–1189 (2013).

    ADS  Google Scholar 

  10. 10.

    Aranson, I. S. Topological defects in active liquid crystals. Phys. Usp. 62, 892–909 (2019).

    ADS  Google Scholar 

  11. 11.

    Bär, M., Großmann, R., Heidenreich, S. & Peruani, F. Self-propelled rods: insights and perspectives for active matter. Annu. Rev. Condens. Matter Phys. 11, 441–466 (2020).

    Google Scholar 

  12. 12.

    Sengupta, A. Microbial active matter: a topological framework. Front. Phys. 8, 184 (2020).

    Google Scholar 

  13. 13.

    de Gennes, P.-G. & Prost, J. The Physics of Liquid Crystals 2nd edn (Oxford Univ. Press, 1993).

  14. 14.

    Giomi, L., Bowick, M. J., Ma, X. & Marchetti, M. C. Defect annihilation and proliferation in active nematics. Phys. Rev. Lett. 110, 228101 (2013).

    ADS  Google Scholar 

  15. 15.

    Shi, X.-Q. & Ma, Y.-Q. Topological structure dynamics revealing collective evolution in active nematics. Nat. Commun. 4, 3013 (2013).

    ADS  Google Scholar 

  16. 16.

    Narayan, V., Ramaswamy, S. & Menon, N. Long-lived giant number fluctuations in a swarming granular nematic. Science 317, 105–108 (2007).

    ADS  Google Scholar 

  17. 17.

    Sanchez, T., Chen, D. T. N., DeCamp, S. J., Heymann, M. & Dogic, Z. Spontaneous motion in hierarchically assembled active matter. Nature 491, 431–434 (2012).

    ADS  Google Scholar 

  18. 18.

    Kumar, N., Zhang, R., de Pablo, J. J. & Gardel, M. L. Tunable structure and dynamics of active liquid crystals. Sci. Adv. 4, eaat7779 (2018).

    ADS  Google Scholar 

  19. 19.

    Duclos, G., Erlenkämper, C., Joanny, J.-F. & Silberzan, P. Topological defects in confined populations of spindle-shaped cells. Nat. Phys. 13, 58–62 (2017).

    Google Scholar 

  20. 20.

    Kawaguchi, K., Kageyama, R. & Sano, M. Topological defects control collective dynamics in neural progenitor cell cultures. Nature 545, 327–331 (2017).

    ADS  Google Scholar 

  21. 21.

    Saw, T. B. et al. Topological defects in epithelia govern cell death and extrusion. Nature 544, 212–216 (2017).

    ADS  Google Scholar 

  22. 22.

    Blanch-Mercader, C. et al. Turbulent dynamics of epithelial cell cultures. Phys. Rev. Lett. 120, 208101 (2018).

    ADS  Google Scholar 

  23. 23.

    Doostmohammadi, A., Thampi, S. P. & Yeomans, J. M. Defect-mediated morphologies in growing cell colonies. Phys. Rev. Lett. 117, 048102 (2016).

    ADS  Google Scholar 

  24. 24.

    Dell’Arciprete, D. et al. A growing bacterial colony in two dimensions as an active nematic. Nat. Commun. 9, 4190 (2018).

    ADS  Google Scholar 

  25. 25.

    Yaman, Y. I., Demir, E., Vetter, R. & Kocabas, A. Emergence of active nematics in chaining bacterial biofilms. Nat. Commun. 10, 2285 (2019).

    ADS  Google Scholar 

  26. 26.

    van Holthe tot Echten, D., Nordemann, G., Wehrens, M., Tans, S., & Idema, T. Defect dynamics in growing bacterial colonies. Preprint at (2020).

  27. 27.

    Li, H. et al. Data-driven quantitative modeling of bacterial active nematics. Proc. Natl Acad. Sci. USA 116, 777–785 (2019).

    ADS  Google Scholar 

  28. 28.

    Saw, T. B., Xi, W., Ladoux, B. & Lim, C. T. Biological tissues as active nematic liquid crystals. Adv. Mater. 30, 1802579 (2018).

    Google Scholar 

  29. 29.

    Peng, C., Turiv, T., Guo, Y., Wei, Q.-H. & Lavrentovich, O. D. Command of active matter by topological defects and patterns. Science 354, 882–885 (2016).

    ADS  Google Scholar 

  30. 30.

    Genkin, M. M., Sokolov, A., Lavrentovich, O. D. & Aranson, I. S. Topological defects in a living nematic ensnare swimming bacteria. Phys. Rev. X 7, 011029 (2017).

    Google Scholar 

  31. 31.

    Endresen, K. D., Kim, M. & Serra, F. Topological defects of integer charge in cell monolayers. Preprint at (2019).

  32. 32.

    Turiv, T. et al. Topology control of human fibroblast cells monolayer by liquid crystal elastomer. Sci. Adv. 6, eaaz6485 (2020).

    ADS  Google Scholar 

  33. 33.

    Guillamat, P., Blanch-Mercader, C., Kruse, K. & Roux, A. Integer topological defects organize stresses driving tissue morphogenesis. Preprint at (2020).

  34. 34.

    Maroudas-Sacks, Y. et al. Topological defects in the nematic order of actin fibers as organization centers of Hydra morphogenesis. Preprint at (2020).

  35. 35.

    Su, P.-T. et al. Bacterial colony from two-dimensional division to three-dimensional development. PLoS ONE 7, e48098 (2012).

    ADS  Google Scholar 

  36. 36.

    Grant, M. A. A., Wacław, B., Allen, R. J. & Cicuta, P. The role of mechanical forces in the planar-to-bulk transition in growing Escherichia coli microcolonies. J. R. Soc. Interface 11, 20140400 (2014).

    Google Scholar 

  37. 37.

    Duvernoy, M.-C. et al. Asymmetric adhesion of rod-shaped bacteria controls microcolony morphogenesis. Nat. Commun. 9, 1120 (2018).

    ADS  Google Scholar 

  38. 38.

    Beroz, F. et al. Verticalization of bacterial biofilms. Nat. Phys. 14, 954–960 (2018).

    Google Scholar 

  39. 39.

    Warren, M. R. et al. Spatiotemporal establishment of dense bacterial colonies growing on hard agar. Elife 8, e41093 (2019).

    Google Scholar 

  40. 40.

    You, Z., Pearce, D. J. G., Sengupta, A. & Giomi, L. Mono- to multilayer transition in growing bacterial colonies. Phys. Rev. Lett. 123, 178001 (2019).

    ADS  Google Scholar 

  41. 41.

    Balagam, R. et al. Myxococcus xanthus gliding motors are elastically coupled to the substrate as predicted by the focal adhesion model of gliding motility. PLoS Comput. Biol. 10, e1003619 (2014).

    Google Scholar 

  42. 42.

    Giomi, L., Bowick, M. J., Mishra, P., Sknepnek, R. & Marchetti, M. C. Defect dynamics in active nematics. Phil. Trans. A 372, 20130365 (2014).

    ADS  Google Scholar 

  43. 43.

    Pismen, L. M. Dynamics of defects in an active nematic layer. Phys. Rev. E 88, 050502 (2013).

    ADS  Google Scholar 

  44. 44.

    Shankar, S., Ramaswamy, S., Marchetti, M. C. & Bowick, M. J. Defect unbinding in active nematics. Phys. Rev. Lett. 121, 108002 (2018).

    ADS  Google Scholar 

  45. 45.

    Shrivastava, A. et al. Cargo transport shapes the spatial organization of a microbial community. Proc. Natl Acad. Sci. USA 115, 8633–8638 (2018).

    Google Scholar 

  46. 46.

    Takatori, S. C. & Mandadapu, K. K. Motility-induced buckling and glassy dynamics regulate three-dimensional transitions of bacterial monolayers. Preprint at (2020).

  47. 47.

    Miroshnikova, Y. A. et al. Adhesion forces and cortical tension couple cell proliferation and differentiation to drive epidermal stratification. Nat. Cell Biol. 20, 69–80 (2018).

    Google Scholar 

  48. 48.

    Janssen, G. R., Wireman, J. W. & Dworkin, M. Effect of temperature on the growth of Myxococcus xanthus. J. Bacteriol. 130, 561–562 (1977).

    Google Scholar 

  49. 49.

    Vromans, A. J. & Giomi, L. Orientational properties of nematic disclinations. Soft Matter 12, 6490–6495 (2016).

    ADS  Google Scholar 

  50. 50.

    Lucas, B. D. & Kanade, T. An iterative image registration technique with an application to stereo vision (DARPA). In Proc. DARPA Image Understanding Workshop 121–130 (1981).

Download references


We thank F. Beroz, M. Black, C. Fei, E. Han, M. C. Marchetti, J. McEnany and C. Yang for discussions. This work was supported in part by the National Science Foundation, through award PHY-1806501 (J.W.S.); the Center for the Physics of Biological Function (PHY-1734030); and by the National Institutes of Health award R01GM082938 (N.S.W.). R.A. acknowledges support from the Human Frontiers of Science Program (LT000475/2018-C). We acknowledge the use of Princeton’s Imaging and Analysis Center, which is partially supported by the Princeton Center for Complex Materials, a National Science Foundation (NSF)-MRSEC program (DMR-1420541).

Author information




K.C. performed the experiments and analysed the data. R.A. developed the theory and fitted the predictions to the experimental data. All authors interpreted the results and designed the experiments. N.S.W. and J.W.S. supervised the study. K.C. and R.A. wrote the manuscript with input from all the authors.

Corresponding author

Correspondence to Ricard Alert.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature Physics thanks Daniel Beller, Anupam Sengupta and Yilin Wu for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Statistics of M. xanthus motility.

Histograms of the cell speed (a) and time between velocity reversals (b) of cells migrating in a low-cell-density environment.

Extended Data Fig. 2 Correlation functions.

Spatial correlation functions of (a) the modified director field \({\hat{{\boldsymbol{n}}}}_{2\theta }=(\cos (2\theta ),\sin (2\theta ))\), and (b) of the velocity field v. Error bars are s.e.m. By fitting exponential decays, we obtain the nematic and the velocity correlation lengths: n = 16.0 ± 0.5 μm and v = 3.9 ± 0.1 μm, respectively.

Extended Data Fig. 3 Net inflow around topological defects.

Vnet, defined in Supplementary Eq. 15 in the Supplementary Note, is the average net inflow velocity through a circumference of radius R centered at a topological defect. Points are experimental data obtained from the average flow fields in Fig. 4c,d. Error bars (s.e.m) are barely visible because they are smaller than the point size. Solid curves are the theoretical predictions given in Supplementary Eq. 18 in the Supplementary Note, evaluated using the parameter values in Table I in the Supplementary Note. Vertical dashed lines indicate the radii at which the experimental net inflow magnitude is maximal. This maximal net inflow is presented in Fig. 4e.

Extended Data Fig. 4 Divergence of the flow field.

Theoretically predicted (a,b) and experimentally measured (c,d) divergence fields around topological defects. The defect schematics show the order parameter (color map) and a few director-field lines. The divergence of the two-dimensional flow field, v, shows pronounced cell accumulation (v < 0, purple) in front of +1/2 defects, and cell depletion (v < 0, green) in three lobes along the axes of symmetry of −1/2 defects. The parameter values used to plot panels a and b are listed in Table I in the Supplementary Note.

Extended Data Fig. 5 Simultaneous fits of the velocity profiles of +1/2 and −1/2 defects.

The black (grey) data points and the red (blue) curve are the experimentally measured and the fitted midline velocity profile of +1/2 (−1/2) defects, respectively. These simultaneous fits to +1/2 and −1/2 defects, with the common set of parameter values given in Table II in the Supplementary Note, are poorer than the separate fits to the +1/2 and −1/2 defects shown in Fig. 4f.

Extended Data Fig. 6 Predicted cell density profile along the midline of +1/2 defects.

The total cell density is ρ(x, 0) = ρ0 + δρ(x, 0), where δρ(x, 0) is given by Supplementary Eq. 31 in the Supplementary Note, with \({v}_{x}^{0}(x,0)\) obtained from the fits (parameter values in Table III in the Supplementary Note), and J=10−4 (μm·min)−1.

Extended Data Fig. 7 Probability distributions of the distance between defects and new layers (a), and between defects and new holes (b).

In Fig. 3f,g, we normalized these distributions with the distribution p0(r) of distances between defects and randomly selected points within the monolayer (excluding holes). Here, as commonly done for radial distribution functions g(r), we normalized the distributions by the area of an annulus of width dr (the histogram bin size), with A the area of the field of view. Both normalizations give similar results. Errors are s.d.

Extended Data Fig. 8 Average flow field around defects separately measured in each of the 8 replicate experiments.

Each of the separate averages includes a different number of defect frames. The total averages in Fig. 4c,d include all the defect frames across the 8 replicate experiments.

Supplementary information

Supplementary Information

Supplementary note including Tables 1–3 and Videos 1–6.

Reporting Summary

Supplementary Video 1

Reflectance field of a thin cell colony with new holes and cell layers appearing and disappearing.

Supplementary Video 2

Height field corresponding to Supplementary Video 1.

Supplementary Video 3

Reflectance field of a thin colony of ΔpilA mutant cells that lack pili. As for the wild-type cells, colonies of pili-lacking cells also produce new holes and new cell layers.

Supplementary Video 4

Colour map of the cell orientation angle, θ, overlaid on a magnified reflectance movie of the colony.

Supplementary Video 5

Nematic alignment field, S, of the colony.

Supplementary Video 6

Red and blue symbols track the positions and orientations of the +1/2 and −1/2 topological defects, respectively, as they spontaneously appear, move and annihilate within the cell colony. The colour map shows the number of layers overlaid on a laser-brightness movie of the colony. The colour code is the same as in Fig. 1d.

Source data

Source Data Fig. 3

Histogram data for Fig. 3f,g.

Source Data Fig. 4

Data for Fig. 4e.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Copenhagen, K., Alert, R., Wingreen, N.S. et al. Topological defects promote layer formation in Myxococcus xanthus colonies. Nat. Phys. 17, 211–215 (2021).

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing