Bacteria Can “Learn” New Skills, Even Without Inheriting Them

Sam Westreich, PhD

What this means for antibiotic resistance and the rise of superbugs
Just consider this guy to be a bacterium, with knowledge raining down on him. Use your imagination!Photo by Dmitry Ratushny on Unsplash

By most modern measures, bacteria are not considered to be very smart. They can’t even hold a pencil, much less pass a standardized test. They don’t respond to themselves in a mirror, they tend to be in a state of constant war, and they can never remember where they put their car keys.

But bacteria are, in a word, adaptable. There’s a reason why we find bacteria on nearly every surface of our homes and our bodies, inside and out, including even on the products we use to clean the aforementioned surfaces.

Sanitize a surface, and bacteria will be moving back on board the instant that the disinfectant dries. Throw bacteria in with most commonly used antibiotics, and even though mass destruction occurs, a few of them will occasionally adapt to handle the lethal, toxic compounds that we specifically chose to destroy them.

Seriously, some bacteria even have a partial resistance to bleach (although it usually isn’t enough to help them at the concentrations we use for sanitizing). For pretty much any harsh environment, there’s at least one bacterium that’s found a way to survive there.

And what’s even crazier? Bacteria can teach their survival tricks to others. They don’t even need to breed to pass on their knowledge; they can literally just hand it off.

(Well, not literally. Bacteria don’t have hands. They can’t even form pseudopods, the tendril-like extensions used by amoebas and our own immune cells.)

This means that, for bacteria, they don’t need to be descended from an incredibly lucky ancestor who figured out bleach resistance. They can learn the skill just from being in the local area.

The process is called horizontal gene transfer, and it’s more than an interesting ability. It’s a real danger to us, especially when it comes to one specific type of genetic information: antibiotic resistance.

Let’s talk about how bacteria acquire and store newfound abilities, and then how they transfer these abilities to their friends, family, acquaintances, and total strangers.

It’s all a numbers game

We humans tend to care whether an individual lives or dies. It’s pretty much the entire plot of The Martian, a great book by Andy Weir with an excellent movie adaptation starring Matt Damon; an international group of astronauts and scientific agencies around the world all pitch in to help rescue a single man.

Bacteria would not give five stars to this movie. Bacteria live in very accelerated timescales, and they spend practically all of that time focused on breeding. You couldn’t build Tinder for bacteria, even if they had the ability to swipe; they’d be swiping right on everyone, so hard that they’d break their tiny, tiny little phones.

Bacteria breed fast. Escherichia coli, for example, is able to sprout a new generation every 30 minutes. They have many adaptations to help breed as fast as possible; for example, their DNA (which is all stored in a single large loop) is constantly being copied. Even as their main DNA is being copied, their machinery are already at work making even more copies of those still-being-formed copies!

Analogy time: it’s like if you were copying someone’s essay in grade school, right before the bell rang and it was due. But there were classmates looking over your shoulder, copying down your (copied) essay in turn. You better write fast, to keep ahead of them as they plagiarize what you’re already plagiarizing!

Of course, when you’re rushing to grow and copy DNA as fast as you can, you’re going to make mistakes. And bacterial DNA replication is a pretty error-prone process, as fas as these things go. The average bacterial mutation rate is about 1 in every 10 million DNA bases copied, although this can be up to 100x higher or lower in certain species.

1 in 10 million sounds low, but the average bacterial genome is about 5 million bases. This means that a new mutation is introduced on every other replication (on average).

In comparison, humans have a mutation rate of more like 1 in every 100 million bases, about 10x lower than bacteria — and we breed much less often.

Now, most of these mutations don’t do anything; they have no effect on the bacterium’s survival chances or abilities. Of those mutations that do have an effect, the majority of effects are negative: they break an important protein, or make the bacterium less efficient.

But a small fraction of those mutations may enhance a bacterium’s ability, or even unlock a new ability. It’s a vanishingly small fraction — but that’s why bacterial survival is all a numbers game. When there are billions or trillions of you, only a few need to survive.

As Lord Farquaad would put it, “Some of you may die, but it’s a sacrifice I’m willing to make.”

And once a bacterium figures out a new survival trick, it hands off that skill to every other bacterium in the area — even to members of entirely different species.

It does so through horizontal gene transfer.

Horizontal gene transfer, the sex-free way of passing on your genes

When most of us consider passing on genes to others, we think of sexual reproduction. When I have kids, they inherit a decently sized chunk of my genetics. If I evolve a sixth finger on each hand, or the ability to eat Cheez Curlz without getting fat, there’s a decent chance that my children may inherit that ability as well.

But for bacteria, there are three additional methods for sharing genetic material:

  1. Transformation
  2. Transduction
  3. Conjugation

Here’s how they each work.

Transformation — picking up random bits and bobs of DNA

When bacterial cells stumble upon a piece of DNA floating around in their environment, they sometimes pick it up and bring it into their cell. In the right circumstances, they’ll actually slot this foreign DNA into their own chromosome, making it a part of themselves.

Why? Well, maybe it’s got some useful genes on it! When there are billions of you all floating around, it makes sense to take risks. That new piece of DNA could contain protein-making instructions that are useful.

Bacteria need to enter a certain state and turn on certain proteins to become “competent,” ready to pick up foreign DNA bits, and they often switch to this state when they are limited in nutrients, or if there’s a high bacterial density (lots of family around, time to try something new!).

Transduction — new DNA from viruses

Bacteria aren’t immune to viruses. There are a whole class of viruses, called bacteriophages, that prey specifically on bacteria. These are the viruses that look like the crazy moon lander, with the spindly arms.
A digital rendering of a bacteriophage virus. The viral DNA is in the round bulb, while the tube and legs allow it to latch onto bacteria.Wikipedia

Normally, if a virus latches onto a bacterium, it’s bad news; that bacterium is about to be hijacked by the viral DNA inside the virus.

But sometimes, individual viruses aren’t assembled properly. Instead of containing a full set of viral-hijacking genes, they only have a small bit of viral DNA, or maybe even some DNA from the original bacterial victim. When this is injected into a new bacterium, it may be incorporated into their genome.

Conjugation — let’s trade DNA

Unlike the earlier two methods, transformation and transduction, this method requires at least 2 bacteria to be present. Some species of bacteria will reach out and touch each other, opening up a temporary channel, and trade bits of genetic material.

When conjugation occurs, bacteria don’t trade their full genome; instead, they’ll copy out a smaller part of their genome, which forms its own circle and is called a plasmid. These plasmids aren’t vital to the bacterium’s survival, since they’re copied out of the genome. Thus, it’s fine to trade them away.

Conjugation is not sex, since it’s not combining genes to create a new shared genome for offspring, but it is a method of information transfer that requires two bacteria to be present. It’s more like one kid happening onto the answer key for an upcoming test and making copies to share with all his friends.

What do these exchange methods mean for us?

The big takeaway here is that bacteria are incredibly adaptable, and they have a myriad of different mechanisms for doing so. If they’re in a stressful environment (like one with an antibiotic present, or a harsh environment where they’re not normally suited to thrive), they will accept any available aid. This can include:

  • Picking up random bits of DNA in the environment and trying them, seeing whether they offer an advantage
  • Incorporating bits of DNA that come from failed viral takeovers, seeing whether they’ve got a use
  • Accepting exchanges of random chunks of DNA from other bacteria, in hopes that something good is being passed on

As well as all these methods, they’re also constantly replicating, along with the errors that get picked up each time they copy their DNA, hoping to randomly stumble upon the mutation that lets them thrive.

Most of the time, these methods are failures. Most DNA in the environment, or from viruses, is junk. The copied plasmids from other bacteria usually don’t contain anything useful.

But when you reproduce every 30 minutes and you can number in the trillions, you’re fine to hunt for those long shots. Bacteria will do anything to survive, and that includes making use of the information in their environment.

All of this is just more reason to make sure that, if cleaning a surface or an area, we don’t skimp! It matters less for surfaces, but more for our own bodies. One of the most critical areas where this is important is when taking a course of antibiotics. Stop early, and you risk some bacteria getting out, maybe even with the secret to resisting that antibiotic.

And once one bacterium makes it out, it can go wide with that information. We all need to be vigilant!


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A microbiome scientist working at a tech startup in Silicon Valley, Sam Westreich provides insights into science and technology, exploring the strangest areas of biology, science, and biotechnology.

Mountain View, CA

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