Microbial Warfare: Bacterial machinery for competition, killing and defense

Bacteria can infect us. We know that. But, we typically think that bacteria and other microorganisms only target humans and animals. Well, I hate to break the news, but for bacteria it’s not all about us humans.

In fact, it’s almost more important for bacteria to protect themselves against other bacteria and viruses. And, man, do they have an arsenal of tools and weapons to attack, compete with and defend themselves against their competitors!

Bacterial Dueling and Type 6 Secretion

One such tool is the type 6 secretion system (T6SS). This is a sort of piston-like structure that both punches holes in neighboring cells and secretes killing compounds into those cells to destroy them.

Yup - I made this. And I have never been more proud of a graphic in my life!!!!!

Yup - I made this. And I have never been more proud of a graphic in my life!!!!!

This system is thought to be important for what has been called “bacterial dueling.” The flashes of fluorescent light originally used to study this phenomenon (seen here) indicate the expression of these systems, as if the bacteria are having a Star Wars lightsaber duel. However, in this case, it’s not a battle between good and evil Jedi. These microscopic wars are occurring between bacterial species.

The process is “tit for tat”, meaning that for the bacteria to attack, it must first be attacked. It’s as if the bacteria act as either “aggressors” or “pacifists.” Those that have a T6SS (i.e. lightsaber) are “aggressors” and those that do not are “pacifists.” If one aggressor attacks another aggressor, they will fight until one aggressor wins (i.e. kills the other bacteria). Think Luke Skywalker and Darth Vader in the Empire Strikes Back. However, if an aggressor encounters pacifist bacteria, there will be no dueling and neither will be killed. In this case, the aggressor and pacifist bacteria will learn to live together peacefully, forming a community made of multiple bacterial species that coexist together.

What happens if bacteria encounter another bacteria of the same species? Sibling warfare. But, this warfare is not lethal. In fact, the sister bacteria of the same species often have proteins, called immunity proteins, that protect themselves from being killed by their own species. Who knew that bacterial siblings quarrel like human siblings do?

This is a particularly interesting offensive strategy that bacteria have to kill off competitors in their environment. But, it’s certainly not the only one.

Bacterially-produced antibiotics

Did you know that bacterial also make antibiotics?

It’s true! Many bacteria produce compounds, called bacteriocins, that function as, essentially, a natural antibiotic which they can use against competing bacteria. In fact, almost all bacteria on the planet produce different versions of these killing substances!

Typically, bacteria produce these compounds when they begin to run out of nutrients in their environment. As a result, they secrete these killing compounds into the environment to kill off their competitors. They kill the neighboring bacteria by forming holes in the cell surface or by degrading the neighboring cells DNA or RNA. As a result, the bacteria is able to reduce the number of competitive bacteria in their environment, allowing the bacteria to have access to more food and space.

But, if these are secreted outside the cell, can’t they just come back and kill the bacteria? Yes! They definitely can and they can kill nearby sister bacteria. But, just like the last example, the bacteria protect themselves against the killing compounds that they produce with immunity proteins. This allows them to thrive while their competitors are killed off. Makes you think bacteria aren’t very good at sharing, huh?

Between these naturally-produced bacteriocins and the “dueling” T6SS machinery, it turns out that bacterial are quite ruthless! But, not all bacterial mechanisms are so offensive. 

CRISPR – The key to bacterial memory and immunity

Our immune system is able to recognize and eliminate invading bacteria and viruses. This ability to “remember” a given threat is the basis for vaccines. But, did you know that bacteria have a similar system?

This system is called CRISPR (never mind what it stands for). In the diagram to the right, there is a structure in the upper-left corner that looks like a lunar lander. This is a bacteriophage—a virus that only infects bacteria. If everything goes well for that virus, it will hijack the bacteria. It’s like viral mind control! As a result, the bacteria will begin making copies of the virus until the bacterial cell explodes. Basically, the virus causes the bacteria to commit suicide while it produces clones of the virus. However, this is not always the fate of the virus.


Alternatively, a bacterial system called CAS may recognize the virus as foreign (A in the picture above). When it does, it takes a piece of viral DNA and stores it in a special place within the bacteria’s DNA (B). This piece of viral DNA serves as sort of barcode that corresponds specifically to that virus (C). If the bacteria or its offspring ever encounters this virus again, the CAS system will attempt to match the new virus DNA to these stored barcodes (D). If there is a match, the CAS system will destroy the virus before it ever has a chance to harm the bacterial cell (E).

This crafty system is one of the more recent discoveries in bacteria’s offensive arsenal. Perhaps bacteria are much craftier than we might think! But bacterial strategies can get even more defensive than this.

Biofilms – a bacterial bunker

“The best defense is a good offense.” We use this quote in sports and the military. But, it turns out that it can be easily applied to bacteria, too.

Biofilms are communities of bacteria that adhere to both manmade and natural surfaces. The plaque on your teeth that your dentist harrangues you about? That’s a biofilm. That disgusting, slimy scum that covers the rocks in the pond by your house? Biofilm.

But, bacteria are supposed to be selfish, right? So, why do they form these communities? Well, the short answer is protection. I’ll resist continuing the Star Wars analogy, but these biofilms are sort of like bunkers or bases, shielding the bacteria from threats. These might be human threats, like our immune system or antibiotics, but they can also be threats from the environment, like drying out, UV rays, or limitations in nutrients. Biofilms also protect bacteria from other bacterial competitors.

Lastly, biofilms put many different types of bacteria in close proximity. This enables bacteria to not only share nutrients with each other, but to share traits that give these bacteria an advantage. These traits could include antibiotic resistance traits, metabolic traits, etc. Acquiring these new traits, though not an offensive measure, gives these bacteria a competitive advantage over their neighbors.


No matter where you look, microbial warfare is a messy game. Whether it’s two bacteria duking it out in a deadly duel, sibling rivalry with bacterially-produced antibiotics, bacterial immunity or bacterial bunkers, these tiny organism are much craftier than we give them credit for. They’ll pull out all of the stops to survive, and not just against us, but against each other.