A graphic depiction of cells during the clock-and–wavefront process. This is a complex patterning mechanism that occurs in multicellular organisms. These complex patterns were believed to be absent in unicellular communities. Credit: Nicholas Wilson.
Over the past several years, research from University of California San Diego biologist Gurol Suel’s laboratory 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 one another, while another proved biofilms have a robust capacity for memory.
Suel, together with researchers from Stanford University and the Universitat Fabra in Spain have now discovered a feature of biofilms which makes these communities far more advanced than previously thought. Biological Sciences graduate student Kwang-Tao Chou, former Biological Sciences graduate student Daisy Lee, Suel and their colleagues discovered that biofilm cells are organized in elaborate patterns, a feature that previously only had been associated with higher-level organisms such as plants and animals. The findings, which describe the culmination of eight years of research, are published Jan. 6 in the journal Cell.
” We are finding that biofilms can be much more complex than we thought,” Suel, a UC San Diego Professor in the Division of Biological Sciences Section of Molecular Biology with affiliations to the San Diego Center for Systems Biology and BioCircuits institute, and Center for Microbiome Innovation. Our biological results show that cell patterning in development is much more common than we thought. The ability of cells to divide themselves in time and space is not something that evolved only with vertebrates and plants, but could have been present for billions of years. “
Researchers at UC San Diego discovered that Bacillus subtilis (a bacterium found in soil) creates concentric rings similar to developmental “stripes”, which are created by a segmentation timer. Researchers discovered that bacteria biofilms employ a clock and wavefront process to pattern cells in a manner similar to animals and plants. Credit: Kwang-Tao Chou.
Biofilm communities contain cells from different types. Scientists had never thought of the possibility that cells from different types could be organized in regulated complex patterns. For the new study, the 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 fruit flies to humans. The biofilm expands and eats nutrients. A “wave” of nutrient loss moves through cells in the bacterial community. This freezes a cell’s molecular clock at a particular time and place, creating a complex pattern of segments from different cell types.
The breakthrough achieved by the researchers was the identification of the genetic circuit that underlies the biofilm’s ability generate concentric rings of gene expression patterns. They were then able make predictions that showed biofilms could naturally generate many segments.
“Our discovery demonstrates that bacterial biofilms employ a developmental patterning mechanism hitherto believed to be exclusive to vertebrates and plant systems,” the authors note in the Cell paper.
The study’s findings offer implications for a multitude of research areas. Biofilms are ubiquitous in our daily lives and are therefore of great interest to many research areas, including medicine, the food industry, and the military. Biofilms as systems with the capability to test how simple cell systems can organize themselves into complex patterns could be useful in developmental biology to investigate specific aspects of the clock and waveform mechanism that functions in vertebrates, as one example.
“We can see that bacterial communities are not just globs of cells,” said Suel, who envisions research collaborations offering bacteria as new paradigms for studying developmental patterns. “Having a bacterial community allows us to give some answers that are not possible in the vertebrate or plant systems. Bacteria offer more experimentally accessible systems that could lead to new insights in the field of developmental patterns. “
Image shows a B. subtilis biofilm undergoing a transition between stressed cells (green), and cells that differentiate into dormantspores (magenta). Credit: Kwang-Tao Chou.
Coauthors of the paper include: Kwang-Tao Chou (UC San Diego graduate student), Dong-yeon Lee (former UC San Diego graduate student, now a postdoctoral scholar at Stanford University), Jian-geng Chiou (UC San Diego postdoctoral scholar), Leticia Galera-Laporta (UC San Diego postdoctoral scholar), San Ly (former UC San Diego researcher), Jordi Garcia-Ojalvo (Universitat Pompeu Fabra Professor) and Gurol Suel (UC San Diego Professor).
Gurol M. Suel, A segmentation clock patterns cellular differentiation in a bacterial biofilm, Cell (2022). DOI: 10.1016/j.cell.2021.12.001. www.cell.com/cell/fulltext/S0092-8674(21)01404-5
‘Simple’ bacteria found to organize in elaborate patterns (2022, January 6)
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