I am an engineer entering the field of microbiology. I was watching bacterial colonies (lab strain E. coli to be specific) being grown on agar plates. I was surprised that the bacterial colony was not a monolayer (i.e. a single layer of cells), but a mound with bacteria piled on top of each other (except may be at the edge of the colony). Why doesn't bacteria spread out in a monolayer over the entire agar surface? And, how do bacteria in the pile which are not in direct contact with the agar survive? Is it that nutrients are passed upwards by those cells which are in direct contact with the agar surface?

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    $\begingroup$ I like your question. :) You can start by learning about the bacterial extracellular matrix. If you still have a question, or don't understand something you read, edit your question or ask a new one with link and quote. On this site, people need to to show evidence of trying to answer the question when they post. Not doing so is both a down vote reason and a close vote reason (not my rules, just informing you.) We actually like to help people who are willing to learn on their own as well. Good luck in your new endeavors! $\endgroup$ Feb 1 at 12:27
  • $\begingroup$ @anongoodnurse Thanks for the reference. After reading it I believe that the answer to my question is that only bacteria in direct contact with the agar surface are metabolically active, while those away are inactive (though not dead). This arrangement is necessary to protect the colony from external insults. So, may be under the right conditions you can coax the colony to spread out in a monolayer. $\endgroup$
    – Deep
    Feb 8 at 6:36
  • $\begingroup$ Close! All bacteria produce an extracellular matrix through which nutrients pass. the nutrients in the agar diffuse both passively and actively through the matrix feeding all the cells (within limits, meaning that a colony does not grow indefinitely. The bacteria also share between each other. Some bacteria become specialized, if you will, and unable to form a colony on their own. Having read the paper once (which was not an "easy" paper, nor too technical), try it once more and see if you can get more out of it. $\endgroup$ Feb 8 at 12:53

1 Answer 1


As suggested by your conversation in the comments with anon, the bacterial colony is the outcome of a mechanistic growth model in which nutrient diffusion occurs from below to above.

For an explicit mathematical model of this process (which also incorporates mechanical forces), you can see this paper (Warren et al. 2019). Notably, this mounding occurs even in the absence of an extracellular matrix, and is proposed to be related to cell orientations within the colony. I reproduce Figure 4 which shows some of the relevant results:

figure 4 from warren et al. 2019 showing some features of colony morphology

The cross-sectional anatomy of a simulated colony. (A) Snapshot of cross-sectional view of the colony at t=20h . Cyan represents horizontally oriented cells (≥45o with z-axis); Yellow represents vertically oriented cells (≤45o with z-axis). (B) Fraction of vertically oriented cells averaged over z vs radius. (C) A side view of the azimuthally averaged director field, indicating the orientation of the rod-like cells. (D) A side view of the azimuthally averaged velocity field. (E) Vertical component of velocity, Vz , at various values of z along the center of the colony. Increase in vertical speed is seen only for the bottom 10 µm (F) A cross-sectional view of the colony, color representing the time since last division. Purple and blue represent cells that have not divided for the past 10 h, and red represents the actively dividing cells. (G) A cross-sectional view of the local growth rate in the colony, with the color bar showing the values of local growth rate. A disc-shaped 'growth zone' is revealed by the red color at the bottom of the colony.

Other similar models describe "verticalization" of bacterial colonies as an explicitly mechanical process (Beroz et al 2018), without regard for nutrient flow. However, differences in these models lead to qualitatively different results for how tall colonies get.


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