‘Simple’ bacteria found to organize themselves in surprisingly elaborate patterns

Researchers at UC San Diego have found that Bacillus subtilis, a bacterium found in soil, creates concentric rings reminiscent of developmental “bands” created by a segmentation clock. The researchers found that bacterial biofilms use a clock and wavefront process for cell patterning similar to plants and animals. 1 credit

Discovered genetic mechanism that allows bacterial cell communities to organize themselves into surprisingly sophisticated segments, revealing similarity to how plants and animals develop.

In recent years, research from the lab of biologist Gürol Süel at the University of California, San Diego has uncovered a series of remarkable features exhibited by clusters of bacteria that live together in communities known as biofilms.

Biofilms are prevalent in the living world, inhabiting sewer pipes, kitchen counters, and even the surface of our teeth. A previous research study demonstrated that these biofilms employ sophisticated systems to communicate with each other, while another proved that biofilms have a robust memory capacity.

Süel’s lab, along with researchers from Stanford University and Universitat Pompeu Fabra in Spain, have now found a feature of biofilms that reveals these communities are far more advanced than previously thought. Biological sciences graduate student Kwang-Tao Chou, former biological sciences graduate student Daisy Lee, Süel and their colleagues found that biofilm cells are organized in elaborate patterns, a feature previously only associated with ‘to higher-level organisms such as plants and animals. The results, which describe the culmination of eight years of research, are published on January 6, 2022 in the journal Cell.

Clock and wave front

An artistic depiction of cells in the clock and wavefront process, a sophisticated developmental patterning mechanism associated with multicellular organisms. Communities of single-celled organisms were thought to lack these sophisticated patterns. 1 credit

“We find that biofilms are much more sophisticated than we thought,” said Süel, a UC San Diego professor in the Molecular Biology Section of the Division of Biological Sciences, with affiliations at the San Diego Center for Systems. Biology, Bio Circuits Institute and Center. for Microbiome Innovation. “From a biological perspective, our results suggest that the concept of cell patterning during development is much older than previously thought. Apparently, the ability of cells to segment themselves in space and time didn’t just appear with plants and vertebrates, but can date back over a billion years.


Bacterial biofilms form segments (green) during growth, similar to vertebrates during development. Accelerated film (left) and maximum projection (right) of a Bacillus subtilis biofilm. Green color indicates nitrogen stress response as reported by PnasA-yfp. The fluorescence images were superimposed on the corresponding brightfield images. Scale bar, 1 mm. 1 credit

Biofilm communities are made up of cells of different types. Previously, scientists had not thought that these disparate cells could be organized into complex regulated patterns. For the new study, scientists developed experiments and a mathematical model that revealed the genetic basis for a “clock and wavefront” mechanism, previously only seen in highly evolved organisms ranging from plants to flies. from fruits to humans. As the biofilm expands and consumes nutrients, a “wave” of nutrient depletion travels through the cells of the bacterial community and freezes a molecular clock inside each cell at a time and at a specific position, creating a complex composite pattern of repeating segments of distinct cell types.

The breakthrough for researchers was the ability to identify the genetic circuitry underlying biofilm’s ability to generate concentric rings of biofilm community-wide gene expression patterns. The researchers were then able to model predictions showing that biofilms could inherently generate many segments.

“Our finding demonstrates that bacterial biofilms utilize a developmental patterning mechanism hitherto thought to be exclusive to vertebrate and plant systems,” the authors note in the Cell paper.

Transition Biofilm

The image depicts a B. subtilis biofilm in transition between stressed cells (green) and cells differentiating into dormant spores (magenta). 1 credit

The study findings offer implications for a multitude of research areas. Because biofilms are ubiquitous in our lives, they are of interest for applications ranging from medicine to the food industry and even the military. Biofilms as systems capable of testing how simple cellular systems can organize themselves into complex patterns could be useful in developmental biology to study specific aspects of the clock and waveform mechanism that operates in vertebrates, for example.

“We can see that bacterial communities are not just blood cells,” said Süel, who envisions research collaborations offering bacteria as new paradigms to study developmental patterns. “Having a bacterial system allows us to provide answers that are difficult to obtain in vertebrate and plant systems, because bacteria offer more experimentally accessible systems that could provide new insights for the field of development.”

Reference: “A segmentation clock patterns cellular differentiation in a bacterial biofilm” by Kwang-Tao Chou, Dong-yeon D. Lee, Jian-geng Chiou, Leticia Galera-Laporta, San Ly, Jordi Garcia-Ojalvo and Gürol M. Süel, January 6, 2022, Cell.
DOI: 10.1016/j.cell.2021.12.001

The co-authors of the article are: Kwang-Tao Chou (graduate student at UC San Diego), Dong-yeon Lee (former graduate student at UC San Diego, now postdoctoral researcher at Stanford University), Jian -geng Chiou (UC San Diego postdoctoral fellow), Leticia Galera-Laporta (UC San Diego postdoctoral fellow), San Ly (former UC San Diego researcher), Jordi Garcia-Ojalvo (professor Universitat Pompeu Fabra) and Gürol Süel ( professor at UC San Diego).

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