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Through the Microscope, Bacterial Colonies Look Like Bustling Cities

They come and go from diverse neighborhoods, build towers, and cooperate.

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Paula Watnick and Roberto Kolter were the first to compare biofilms to cities. I found this metaphor—from their 2000 paper, “Biofilm, City of Microbes”—to be a perfect description of what one would see at the microscale when descending into the microbial world.

Biofilms are intricate communities of microorganisms that form on various surfaces, from rocks to medical devices. If you pay attention, you can find biofilms everywhere. Much like our human cities, biofilms in nature are complex, highly differentiated, and multicultural. Multiple different species of bacteria fill distinct niches in the microbial community and stay and leave in strategic and deliberate ways.

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LET’S HANG ON: Biofilms profoundly impact the environment, playing crucial roles in nutrient cycling, wastewater treatment, and even pathogen persistence.

In human cities, “chefs and grocers may settle together in the restaurant district, while musicians may settle near concert halls,” write Watnick and Kolter. The same is true for biofilms. Bacteria select their place in the biofilm based on which microenvironments suit them best and which neighboring bacteria offer the most rewarding symbiotic relationships.

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GET IT TOGETHER: The ability of bacterial colonies to self-organize is not only fascinating from a scientific standpoint, but it also has practical applications in fields such as medicine and biotechnology.

When humans settle in a city, they first select a neighborhood, then choose a home that suits their needs, and, ideally, form cooperative relationships with their new neighbors. When a bacterium joins a biofilm, it follows a similar pattern. First, the bacterium approaches a natural surface, such as a rock, then it forms “a transient association” with the surface or with other microbes previously attached to the surface, or both—the neighborhood. This perch allows the bacterium to search for a perfect place to settle down.

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TURING TEST: During my exploration of biofilm formation, I observed a surprising pattern formation. While growing a biofilm on a filter, a pattern emerged that resembled Turing patterns. A Turing pattern is a type of pattern that emerges in a system when there is a balance between two opposing forces, such as diffusion and chemical reaction. It was first described by mathematician Alan Turing and is characterized by a repetitive pattern of spots or stripes. Turing patterns can be seen in various natural phenomena, such as the skin of some animals and the patterns on seashells, and also in artificial systems such as chemical reactions and bacterial growth on surfaces.

When the bacterium joins a microcolony, its attachment becomes longer lasting—it has chosen its new home. But if environmental conditions become unfavorable, the biofilm-associated bacterium may detach and swim away to find new living quarters. Some bacteria stay put, while others migrate—much like a bustling city. As the biofilm matures, it grows into a complex three-dimensional structure—with skyscraper-like structures.

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I took these photographs of biofilms through a microscope during my study of the microbiome. The bacteria were modified to carry either green or blue fluorescent protein, which allow us to track different bacterial species and study their patterns at the colony level.  

Adapted with permission from David Ciccarese’s Instagram account, @microscaleworld.

Lead image: Tasnuva Elahi; with images by Sensvector and Kudryashka / Shutterstock

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