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Antibiotic resistant bacteria inside a biofilm, 3D illustration. Biofilm is a community of bacteria where they aquire antibiotic resistance and communicate with each other by quorum sensing molecules
Antibiotic resistant bacteria inside a biofilm, 3D illustration. Biofilm is a community of bacteria where they aquire antibiotic resistance and communicate with each other by quorum sensing molecules

In What Ways Are Bacteria Intelligent?

As antibiotic resistance grows, researchers are discovering that these microbes are not just single, simple cells

Recently, Princeton University physicist Robert Austin challenged his graduate student Trung Phan to design a maze that he (Austin) couldn’t solve:

Austin, Phan discovered, tended to retrace his steps when he encountered a dead end. So Tran decided on a maze without dead ends. The true purpose of the experiment, as Sophia Chen recounts at Wired, was to design a maze that bacteria can solve with remarkable skill based on their colony organization which, if you like, stands in for a brain:

Curiously, bacteria—single-celled organisms that are among the simplest living things—are well known for working together, creating problem-solving units that are more than the sum of their parts. For example, to protect themselves from your immune system, the bacteria in your mouth will unionize to form a film on your teeth known as dental plaque. Myxococcus, a type of bacteria that lives in soil, forms thread-like networks between microbes so that they can hunt prey in a pack. Many bacteria, including E.coli, are also capable of communicating among themselves to determine if microbes nearby are their own species or an enemy, by exchanging certain chemicals in a process known as “quorum sensing.”

Sophia Chen, “These Bacteria Ate Their Way Through a Really Tricky Maze” at Wired (June 9, 2020)

Quorum sensing is the ability of bacteria to communicate with one another, which allows them to coordinate the gene expression, and thus the behavior, of the entire community in response to changes in the density of the cell population.

Phan and his team placed 10 E.coli bacteria (pictured) in the middle of a silicon chip laced with broth and watched them exit the chip maze through a microscope.

As they cleared paths of food, the E.coli tended to move toward unexplored, broth-rich areas, which ultimately helped them evacuate the maze. It took about 10 hours for about 1 percent of the multiple generations of bacteria to collectively solve the puzzle. That may not sound fast, but it’s five times faster than if the organisms had just been swimming around randomly, says Phan.

Sophia Chen, “These Bacteria Ate Their Way Through a Really Tricky Maze” at Wired (June 9, 2020)

By the time the experiment ended, the original 10 bacteria numbered over a million. The paper is open access.

E coli bacteria also navigated a fractal-like maze with no exits (a dead end). Trapped in the fractal’s smallest branches, they built themselves up in clumps and launched themselves out of the dead ends in waves. They seemed to respond to chemicals emitted by other bacteria when co-ordinating their behavior.

As microbiologist James Berleman of Saint Mary’s College told Chen, bacteria must navigate many complex situations in nature, for example, our small intestine. Austin and Trung’s larger goal is to use their findings to develop better antibiotics. We can’t fight what we don’t really understand.

No one is, of course, claiming that the bacteria are individually intelligent. Rather, like a massive termite colony, they can communicate in surprisingly complex ways to achieve collective goals. At Quanta, John Rennie notes,

Intelligence is not a quality to attribute lightly to microbes. There is no reason to think that bacteria, slime molds and similar single-cell forms of life have awareness, understanding or other capacities implicit in real intellect. But particularly when these cells commune in great numbers, their startling collective talents for solving problems and controlling their environment emerge.

John Rennie, “Seeing the Beautiful Intelligence of Microbes” at Quanta (November 13, 2017)

What can microorganisms do besides solve mazes?

They can map their terrain: At Quanta, Rennie introduced detailed time-lapse photography from Life at the Edge of Sight: A Photographic Exploration of the Microbial World (Harvard University Press, 2017) that showed the many remarkable adaptations of life forms that many of us might think of as “crude patches of goo”:

The slime mold Physarum polycephalum sometimes barely qualifies as a microorganism at all: When it oozes across the leaf litter of a forest floor during the active, amoeboid stage of its life cycle, it can look like a puddle of yellowish goo between an inch and a meter across. Yet despite its size, Physarum is a huge single cell, with tens of thousands of nuclei floating in an uninterrupted mass of cytoplasm. In this form, Physarum is a superbly efficient hunter. When sensors on its cell membrane detect good sources of nutrients, contractile networks of proteins (closely related to the ones found in human muscle) start pumping streams of cytoplasm in that direction, advancing the slime mold toward what it needs.

John Rennie, “Seeing the Beautiful Intelligence of Microbes” at Quanta (November 13, 2017)

If Physarum cytoplasm finds that an explored area lacks nutrients, it will leave a chemical trail to tell the rest of the slime mold not to go back there.

They can work together in a complex community. Most bacteria, Rennie tells us, are not solitary. They live in biofilms like the plaque on our teeth, the better to resist antibacterial agents, though a few move off to colonize new spots. The biofilms are “elaborate functional structures” with, for example, deep wrinkles to absorb oxygen:

Within the biofilm, the bacteria divide the labor of maintaining the colony and differentiate into forms specialized for their function. In this biofilm of the common soil bacterium Bacillus subtilis, for example, some cells secrete extracellular matrix and anchor in place, while some stay motile; cells at the edges of the biofilm may divide for growth, while others in the middle release spores for surviving tough conditions and colonizing new locations.

John Rennie, “Seeing the Beautiful Intelligence of Microbes” at Quanta (November 13, 2017)

In nature, life is much more complex than in a dedicated lab. A biofilm in the wild must contend, for example, with other types of bacteria “freeloading” the surfactant, extracellular matrix, etc., provided for its own members. And the biofilm protects its own:

Biofilms rebuff such freeloaders in different ways. For example, the B. subtilis colonies in this image adopt a strategy of “kin discrimination,” in which they secrete antibiotic compounds that are toxic to other species but not to their own. Proteus mirabilis bacteria defend their interests in a different way based on “self-recognition”: The P. mirabilis biofilms examine encroaching cells, stab any from a different species with a spearlike structure and inject them with poisons that will kill almost all but closely related species.

John Rennie, “Seeing the Beautiful Intelligence of Microbes” at Quanta (November 13, 2017)

Biofilms remember things. There are remarkable parallels between biofilms of bacteria and the neurons that process human memories:

“Even just a few years ago people didn’t think bacterial cells and neurons were anything alike because they are such different cells,” said [University of California – San Diego Professor Gürol] Süel. “This finding in bacteria provides clues and a chance to understand some key features of the brain in a simpler system. If we understand how something as sophisticated as a neuron came to be—its ancient roots—we have a better chance of understanding how and why it works a certain way.”

University of California – San Diego, “They remember: Communities of microbes found to have working memory” at (April 27, 2020)

Süel’s lab found that bacteria use ion channels to communicate with each other. The researchers were able to encode complex memory patterns, which lasted for hours, in biofilms of a bacterium called Bacillus subtilis. They could see memory depicted down to a single cell: “When we perturbed these bacteria with light they remembered and responded differently from that point on,” said Süel. “So for the first time we can directly visualize which cells have the memory. That’s something we can’t visualize in the human brain.” Paper. (paywall)

Those little lumps of protoplasm we wash off our hands are a complex microscopic ecology, full of communities of life forms and their many strategies, similar to the animal and plant ecologies we can actually see.

But wait. If bacteria use ion channels to remember, could we turn them into living computers?

That’s the plan, according to Süel and colleagues:

If we can imprint memories in biofilms, can we also encode more complex spatial memory patterns? The researchers think this is possible, and that it makes way for biological computation. It might even go as far as imprinting “synthetic circuits in bacterial biofilms, by activating different kinds of computations in separate areas of the biofilm,” according to the study.

Alison Escalate, “Scientists Just Brought Us One Step Closer To A Living Computer” at Forbes (April 29, 2020)

Of course, even if biofilm computers are theoretically possible, they are likely to prove more fragile than silicon and metal ones. Our data could be eaten by a predatory microbe…

As we struggle with the growing problem of antibiotic resistance, it is worth considering that we may have underestimated bacteria in the past. Knowing our enemy better may help us even the odds. They may be smarter than we thought they were. But at least we are now better informed than we were.

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Denyse O'Leary

Denyse O'Leary is a freelance journalist based in Ottawa, Canada. Specializing in faith and science issues, she has published two books on the topic: Faith@Science and By Design or by Chance? She has written for publications such as The Toronto Star, The Globe & Mail, and Canadian Living. She is co-author, with neuroscientist Mario Beauregard, of The Spiritual Brain: A Neuroscientist'€™s Case for the Existence of the Soul. She received her degree in honors English language and literature.

In What Ways Are Bacteria Intelligent?